3MAH | pdb_00003mah

A putative c-terminal regulatory domain of aspartate kinase from porphyromonas gingivalis w83.

PDB DOI: https://doi.org/10.2210/pdb3MAH/pdb

Classification: TRANSFERASE
Organism(s): Porphyromonas gingivalis W83
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-03-23 Released: 2010-04-14
Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Moy, S., Joachimiak, A., Anderson, F.W., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free:
0.240 (Depositor), 0.235 (DCC)
R-Value Work:
0.211 (Depositor), 0.228 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3MAH

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

Literature

A Putative C-Terminal Regulatory Domain of Aspartate Kinase from Porphyromonas Gingivalis W83.

Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Moy, S., Joachimiak, A., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 17.72 kDa
Atom Count: 1,133
Modeled Residue Count: 139
Deposited Residue Count: 157
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartokinase	A	157	Porphyromonas gingivalis W83	Mutation(s): 0 Gene Names: lysC, PG2189, PG_2189 EC: 2.7.2.4
UniProt
Find proteins for Q7MT13 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MT13 Go to UniProtKB: Q7MT13
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7MT13
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.240 (Depositor), 0.235 (DCC)
R-Value Work: 0.211 (Depositor), 0.228 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.67	α = 90
b = 46.67	β = 90
c = 221.902	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
ARP	model building
Coot	model building
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing
RESOLVE	phasing
CCP4	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-04-14

Deposition Author(s):

Filippova, E.V.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-04-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.