8HMO | pdb_00008hmo

Crystal Structure of metal-dependent hydrolase complexed with manganese from Bacillus smithii

PDB DOI: https://doi.org/10.2210/pdb8HMO/pdb

Classification: HYDROLASE
Organism(s): Bacillus smithii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-12-05 Released: 2023-12-06
Deposition Author(s): Yoneda, K., Sakuraba, H., Ohshima, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free:
0.299 (Depositor), 0.297 (DCC)
R-Value Work:
0.250 (Depositor), 0.255 (DCC)
R-Value Observed:
0.253 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of metal-dependent hydrolase complexed with manganese from Bacillus smithii

Yoneda, K., Sakuraba, H., Ohshima, T.

To be published.

Macromolecule Content

Total Structure Weight: 144.82 kDa
Atom Count: 9,914
Modeled Residue Count: 1,222
Deposited Residue Count: 1,278
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal-dependent hydrolase	A, B, C, D, E A, B, C, D, E, F	213	Bacillus smithii	Mutation(s): 0 Gene Names: BSM4216_2453 EC: 3.5.1.9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain Q [auth F] SDF format, chain P [auth E] SDF format, chain O [auth E] SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth F] MOL2 format, chain P [auth E] MOL2 format, chain O [auth E] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth F] mmCIF format, chain P [auth E] mmCIF format, chain O [auth E] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth B] J [auth B] K [auth C] G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D], O [auth E], P [auth E], Q [auth F], R [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.299 (Depositor), 0.297 (DCC)
R-Value Work: 0.250 (Depositor), 0.255 (DCC)
R-Value Observed: 0.253 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.21	α = 90
b = 70.198	β = 105.77
c = 104.839	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2023-12-06
Type: Initial release
Version 1.1: 2024-11-20
Changes: 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.