2C8H | pdb_00002c8h

Structure of the PN loop Q182A mutant C3bot1 Exoenzyme (NAD-bound state, crystal form I)

PDB DOI: https://doi.org/10.2210/pdb2C8H/pdb

Classification: TRANSFERASE
Organism(s): Clostridium botulinum
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2005-12-03 Released: 2007-02-27
Deposition Author(s): Stura, E.A., Menetrey, J., Flatau, G., Boquet, P., Menez, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 ?
R-Value Free:
0.259 (Depositor), 0.270 (DCC)
R-Value Work:
0.216 (Depositor), 0.220 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural Properties of Wild-Type and Two Artt Motif Mutants Clostridium Botulinum C3 Exoenzyme Isoform 1 in Different Substrate Complexed States and Crystal Forms.

Stura, E.A., Menetrey, J., Flatau, G., Boquet, P., Menez, A.

To be published.

Macromolecule Content

Total Structure Weight: 96.04 kDa
Atom Count: 7,257
Modelled Residue Count: 821
Deposited Residue Count: 844
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MONO-ADP-RIBOSYLTRANSFERASE C3	A, B, C, D	211	Clostridium botulinum	Mutation(s): 1 EC: 2.4.2
UniProt
Find proteins for Q7M0L1 (Clostridium botulinum) Explore Q7M0L1 Go to UniProtKB: Q7M0L1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7M0L1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D]	F [auth A] G [auth A] I [auth B] J [auth C] K [auth D] F [auth A], G [auth A], I [auth B], J [auth C], K [auth D], L [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 ?
R-Value Free: 0.259 (Depositor), 0.270 (DCC)
R-Value Work: 0.216 (Depositor), 0.220 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 105.388	α = 90
b = 75.611	β = 102.75
c = 120.783	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-02-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-02-27
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description

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Deposit Data

Help and Resources

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Structure of the PN loop Q182A mutant C3bot1 Exoenzyme (NAD-bound state, crystal form I)

Structural Properties of Wild-Type and Two Artt Motif Mutants Clostridium Botulinum C3 Exoenzyme Isoform 1 in Different Substrate Complexed States and Crystal Forms.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations