4CRY | pdb_00004cry

Direct visualisation of strain-induced protein post-translational modification

PDB DOI: https://doi.org/10.2210/pdb4CRY/pdb

Classification: LYASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2014-03-02 Released: 2015-03-25
Deposition Author(s): Monteiro, D.C.F., Patel, V., Bartlett, C.P., Grant, T.D., Nozaki, S., Gowdy, J.A., Snell, E.H., Niki, H., Pearson, A.R., Webb, M.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free:
0.150 (Depositor), 0.170 (DCC)
R-Value Work:
0.129 (Depositor), 0.150 (DCC)
R-Value Observed:
0.130 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Direct Visualisation of Strain-Induced Protein Post-Translational Modification

Monteiro, D.C.F., Patel, V., Bartlett, C.P., Grant, T.D., Nozaki, S., Gowdy, J.A., Snell, E.H., Niki, H., Pearson, A.R., Webb, M.E.

To be published.

Macromolecule Content

Total Structure Weight: 32.42 kDa
Atom Count: 2,271
Modelled Residue Count: 254
Deposited Residue Count: 280
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ASPARTATE 1-DECARBOXYLASE	A	41	Escherichia coli K-12	Mutation(s): 0 EC: 4.1.1.11
UniProt
Find proteins for P0A790 (Escherichia coli (strain K12)) Explore P0A790 Go to UniProtKB: P0A790
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A790
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PANZ	B	137	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P37613 (Escherichia coli (strain K12)) Explore P37613 Go to UniProtKB: P37613
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P37613
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ASPARTATE 1-DECARBOXYLASE	C [auth G]	102	Escherichia coli K-12	Mutation(s): 1 EC: 4.1.1.11
UniProt
Find proteins for P0A790 (Escherichia coli (strain K12)) Explore P0A790 Go to UniProtKB: P0A790
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A790
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO Query on ACO Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	C [auth G]	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.150 (Depositor), 0.170 (DCC)
R-Value Work: 0.129 (Depositor), 0.150 (DCC)
R-Value Observed: 0.130 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.4	α = 90
b = 86.4	β = 90
c = 81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-03-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-03-25
Type: Initial release
Version 1.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary