4GY7 | pdb_00004gy7

Crystallographic structure analysis of urease from Jack bean (Canavalia ensiformis) at 1.49 A Resolution

PDB DOI: https://doi.org/10.2210/pdb4GY7/pdb

Classification: HYDROLASE
Organism(s): Canavalia ensiformis
Mutation(s): No

Deposited: 2012-09-05 Released: 2012-11-07
Deposition Author(s): Begum, A., Banumathi, S., Choudhary, M.I., Betzel, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.165 (Depositor), 0.182 (DCC)
R-Value Work:
0.151 (Depositor), 0.156 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystallographic structure analysis of urease from Jack bean (Canavalia ensiformis) at 1.49 A Resolution

Begum, A., Banumathi, S., Choudhary, M.I., Betzel, C.

To be published.

Macromolecule Content

Total Structure Weight: 93.01 kDa
Atom Count: 7,468
Modeled Residue Count: 836
Deposited Residue Count: 840
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urease	A	840	Canavalia ensiformis	Mutation(s): 0 EC: 3.5.1.5
UniProt
Find proteins for P07374 (Canavalia ensiformis) Explore P07374 Go to UniProtKB: P07374
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07374
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 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 A] SDF format, chain D [auth A] MOL2 format, chain X [auth A] MOL2 format, chain D [auth A] mmCIF format, chain X [auth A] mmCIF format, chain D [auth A]	D [auth A], X [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain X [auth A] Interactions & Density Focus chain D [auth A] Focus chain X [auth A]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain T [auth A] MOL2 format, chain T [auth A] mmCIF format, chain T [auth A]	T [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain T [auth A] Interactions & Density Focus chain T [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], U [auth A], V [auth A], W [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
ACN Query on ACN Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A]	O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	ACETONE C₃ H₆ O CSCPPACGZOOCGX-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A]	Y [auth A], Z [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain Y [auth A] Focus chain Z [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS
KCX Query on KCX	A	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.165 (Depositor), 0.182 (DCC)
R-Value Work: 0.151 (Depositor), 0.156 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.664	α = 90
b = 140.664	β = 90
c = 198.109	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-11-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-11-07
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection