3OVG | pdb_00003ovg

The crystal structure of an amidohydrolase from Mycoplasma synoviae with Zn ion bound

PDB DOI: https://doi.org/10.2210/pdb3OVG/pdb

Classification: HYDROLASE
Organism(s): Mycoplasmopsis synoviae 53
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-09-16 Released: 2010-10-13
Deposition Author(s): Zhang, Z., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.210 (Depositor), 0.200 (DCC)
R-Value Work:
0.172 (Depositor), 0.170 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

The crystal structure of an amidohydrolase from Mycoplasma synoviae with Zn ion bound

Zhang, Z., Kumaran, D., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 248.2 kDa
Atom Count: 17,874
Modeled Residue Count: 2,106
Deposited Residue Count: 2,178
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
amidohydrolase	A, B, C, D, E A, B, C, D, E, F	363	Mycoplasmopsis synoviae 53	Mutation(s): 0 Gene Names: had, MS53_0025 EC: 3.1.1.104 (UniProt), 3.1.1.25 (UniProt)
UniProt
Find proteins for Q4A724 (Mycoplasmopsis synoviae (strain 53)) Explore Q4A724 Go to UniProtKB: Q4A724
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4A724
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain U [auth E] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] MOL2 format, chain X [auth F] MOL2 format, chain U [auth E] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] mmCIF format, chain X [auth F] mmCIF format, chain U [auth E] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A]	I [auth A] L [auth B] O [auth C] R [auth D] U [auth E] I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain W [auth F] SDF format, chain V [auth F] SDF format, chain T [auth E] SDF format, chain S [auth E] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain W [auth F] MOL2 format, chain V [auth F] MOL2 format, chain T [auth E] MOL2 format, chain S [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain W [auth F] mmCIF format, chain V [auth F] mmCIF format, chain T [auth E] mmCIF format, chain S [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] J [auth B] K [auth B] M [auth C] G [auth A], H [auth A], J [auth B], K [auth B], M [auth C], N [auth C], P [auth D], Q [auth D], S [auth E], T [auth E], V [auth F], W [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain V [auth F] Focus chain W [auth F]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS
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: 2.06 Å
R-Value Free: 0.210 (Depositor), 0.200 (DCC)
R-Value Work: 0.172 (Depositor), 0.170 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.256	α = 98.95
b = 89.186	β = 92.89
c = 96.059	γ = 119.86

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-10-13

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2010-10-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-02-22
Changes: Structure summary
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Refinement description
Version 1.5: 2023-12-06
Changes: Data collection