5F3M | pdb_00005f3m

Crystal structure of dihydroneopterin aldolase from Bacillus anthracis complexed with L-neopterin at 1.5 Angstroms resolution .

PDB DOI: https://doi.org/10.2210/pdb5F3M/pdb

Classification: ISOMERASE
Organism(s): Bacillus anthracis str. 'Ames Ancestor
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-12-03 Released: 2015-12-23
Deposition Author(s): Maltseva, N., Kim, Y., Shatsman, S., Anderson, W.F., Joachimiak, A., CSGID, Center for Structural Genomics of Infectious Diseases, Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 ?
R-Value Free:
0.161 (Depositor), 0.160 (DCC)
R-Value Work:
0.138 (Depositor), 0.140 (DCC)
R-Value Observed:
0.139 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of dihydroneopterin aldolase from Bacillus anthracis complexed with L-neopterin at 1.5 Angstroms resolution .

Maltseva, N., Kim, Y., Shatsman, S., Anderson, W.F., Joachimiak, A., CSGID, Center for Structural Genomics of Infectious Diseases

To be published.

Macromolecule Content

Total Structure Weight: 29.74 kDa
Atom Count: 2,440
Modeled Residue Count: 240
Deposited Residue Count: 246
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7,8-dihydroneopterin aldolase	A, B	123	Bacillus anthracis str. 'Ames Ancestor	Mutation(s): 0 Gene Names: folB EC: 4.1.2.25
UniProt
Find proteins for A0A6L7HSV1 (Bacillus anthracis) Explore A0A6L7HSV1 Go to UniProtKB: A0A6L7HSV1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6L7HSV1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NEU Query on NEU Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	L-NEOPTERIN C₉ H₁₁ N₅ O₄ BMQYVXCPAOLZOK-XINAWCOVSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth B]	E [auth A], F [auth A], G [auth A], J [auth B], M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth B]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 ?
R-Value Free: 0.161 (Depositor), 0.160 (DCC)
R-Value Work: 0.138 (Depositor), 0.140 (DCC)
R-Value Observed: 0.139 (Depositor)

Diffraction Data: https://doi.org/10.18430/m35f3m

Space Group: P 4 2₁ 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 87.974	α = 90
b = 87.974	β = 90
c = 104.549	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-12-23

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2015-12-23
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection
Version 1.3: 2024-10-09
Changes: Structure summary