2P10

CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHONOPYRUVATE HYDROLASE (MLL9387) FROM MESORHIZOBIUM LOTI MAFF303099 AT 2.15 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb2P10/pdb

Classification: HYDROLASE
Organism(s): Mesorhizobium japonicum MAFF 303099
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-03-01 Released: 2007-03-20
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.204
R-Value Work: 0.162
R-Value Observed: 0.165

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of hypothetical protein (NP_085906.1) from Mesorhizobium loti at 2.15 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 188.21 kDa
Atom Count: 12,944
Modelled Residue Count: 1,609
Deposited Residue Count: 1,716
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mll9387 protein	A, B, C, D, E A, B, C, D, E, F	286	Mesorhizobium japonicum MAFF 303099	Mutation(s): 11 Gene Names: NP_085906.1, mll9387
UniProt
Find proteins for Q981G2 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q981G2 Go to UniProtKB: Q981G2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q981G2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B]	L [auth A], M [auth A], Q [auth B], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth F] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain V [auth C] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain V [auth C]	BA [auth E] CA [auth F] G [auth A] H [auth A] I [auth A] BA [auth E], CA [auth F], G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], S [auth C], T [auth C], U [auth C], V [auth C], Y [auth D], Z [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BA [auth E] Focus chain CA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C]	AA [auth D] J [auth A] K [auth A] P [auth B] W [auth C] AA [auth D], J [auth A], K [auth A], P [auth B], W [auth C], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain W [auth C] Focus chain X [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.204
R-Value Work: 0.162
R-Value Observed: 0.165
Space Group: H 3
Diffraction Data: https://doi.org/10.18430/M32P10

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.269	α = 90
b = 180.269	β = 90
c = 185.514	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-03-20

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-03-20
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations