1S3T | pdb_00001s3t

BORATE INHIBITED BACILLUS PASTEURII UREASE CRYSTAL STRUCTURE

PDB DOI: https://doi.org/10.2210/pdb1S3T/pdb

Classification: HYDROLASE
Organism(s): Sporosarcina pasteurii
Mutation(s): Yes

Deposited: 2004-01-14 Released: 2004-04-06
Deposition Author(s): Benini, S., Rypniewski, W.R., Wilson, K.S., Ciurli, S., Mangani, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.205 (Depositor), 0.208 (DCC)
R-Value Work:
0.177 (Depositor), 0.188 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Molecular Details of Urease Inhibition by Boric Acid: Insights into the Catalytic Mechanism.

Benini, S., Rypniewski, W.R., Wilson, K.S., Mangani, S., Ciurli, S.

(2004) J Am Chem Soc 126: 3714-3715

PubMed: 15038715 Search on PubMed
DOI: https://doi.org/10.1021/ja049618p
Primary Citation Related Structures:
1S3T

PubMed Abstract:
The structure of the complex of urease, a Ni-containing metalloenzyme, with boric acid was determined at 2.10 A resolution. The complex shows the unprecedented binding mode of the competitive inhibitor to the dinuclear metal center, with the B(OH)3 molecule bridging the Ni ions and leaving in place the bridging hydroxide. Boric acid can be considered a substrate analogue of urea, and the structure supports the proposal that the Ni-bridging hydroxide acts as the nucleophile in the enzymatic process of urea hydrolysis.

Organizational Affiliation

York Structural Biology Laboratory, University of York, York, UK.

Macromolecule Content

Total Structure Weight: 87.1 kDa
Atom Count: 6,376
Modeled Residue Count: 792
Deposited Residue Count: 796
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urease gamma subunit	A	100	Sporosarcina pasteurii	Mutation(s): 1 EC: 3.5.1.5
UniProt
Find proteins for P41022 (Sporosarcina pasteurii) Explore P41022 Go to UniProtKB: P41022
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41022
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Urease beta subunit	B	126	Sporosarcina pasteurii	Mutation(s): 0 EC: 3.5.1.5
UniProt
Find proteins for P41021 (Sporosarcina pasteurii) Explore P41021 Go to UniProtKB: P41021
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41021
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Urease alpha subunit	C	570	Sporosarcina pasteurii	Mutation(s): 1 EC: 3.5.1.5
UniProt
Find proteins for P41020 (Sporosarcina pasteurii) Explore P41020 Go to UniProtKB: P41020
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41020
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C] mmCIF format, chain F [auth C]	F [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
BO3 Query on BO3 Download:Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C] mmCIF format, chain G [auth C]	G [auth C]	BORIC ACID B H₃ O₃ KGBXLFKZBHKPEV-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain D [auth C] MOL2 format, chain E [auth C] MOL2 format, chain D [auth C] mmCIF format, chain E [auth C] mmCIF format, chain D [auth C]	D [auth C], E [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain D [auth C] Focus chain E [auth C] Interactions & Density Focus chain D [auth C] Focus chain E [auth C]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CXM Query on CXM	A	L-PEPTIDE LINKING	C₆ H₁₁ N O₄ S		MET
KCX Query on KCX	C	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.205 (Depositor), 0.208 (DCC)
R-Value Work: 0.177 (Depositor), 0.188 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.906	α = 90
b = 130.906	β = 90
c = 189.366	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-04-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-04-06
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2015-07-08
Changes: Source and taxonomy
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2023-11-15
Changes: Data collection