4DZI | pdb_00004dzi

Crystal structure of amidohydrolase map2389c (target EFI-500390) from Mycobacterium avium subsp. paratuberculosis K-10

PDB DOI: https://doi.org/10.2210/pdb4DZI/pdb

Classification: HYDROLASE
Organism(s): Mycobacterium avium subsp. paratuberculosis S397
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-03-01 Released: 2012-03-21
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Raushel, F.M., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.203 (Depositor), 0.203 (DCC)
R-Value Work:
0.166 (Depositor), 0.167 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of amidohydrolase map2389c (target EFI-500390) from Mycobacterium avium

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Gerlt, J.A., Raushel, F.M., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 191.83 kDa
Atom Count: 14,003
Modeled Residue Count: 1,536
Deposited Residue Count: 1,692
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative TIM-barrel metal-dependent hydrolase	A, B, C, D	423	Mycobacterium avium subsp. paratuberculosis S397	Mutation(s): 0 Gene Names: MAP2389c, MAPs_35020

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] L [auth B] M [auth B] P [auth C] E [auth A], F [auth A], L [auth B], M [auth B], P [auth C], Q [auth C], S [auth D], T [auth D]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A]	J [auth A], O [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain O [auth B] Interactions & Density Focus chain J [auth A] Focus chain O [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	G [auth A] I [auth A] K [auth A] N [auth B] R [auth C] G [auth A], I [auth A], K [auth A], N [auth B], R [auth C], U [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.203 (Depositor), 0.203 (DCC)
R-Value Work: 0.166 (Depositor), 0.167 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.106	α = 90
b = 136.131	β = 113.09
c = 93.229	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-03-21

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-03-21
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations