2GRE | pdb_00002gre

Crystal structure of Deblocking aminopeptidase from Bacillus cereus

PDB DOI: https://doi.org/10.2210/pdb2GRE/pdb

Classification: HYDROLASE
Organism(s): Bacillus cereus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-04-24 Released: 2006-05-23
Deposition Author(s): Chang, C., Wu, R., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.264 (Depositor), 0.195 (DCC)
R-Value Work:
0.194 (Depositor), 0.197 (DCC)
R-Value Observed:
0.198 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Deblocking aminopeptidase from Bacillus cereus

Chang, C., Wu, R., Abdullah, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 629.36 kDa
Atom Count: 39,559
Modeled Residue Count: 4,918
Deposited Residue Count: 5,584
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deblocking aminopeptidase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	349	Bacillus cereus	Mutation(s): 7 EC: 3.4.11
UniProt
Find proteins for Q81HB5 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q81HB5 Go to UniProtKB: Q81HB5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q81HB5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth K] SDF format, chain BA [auth L] SDF format, chain DA [auth N] SDF format, chain EA [auth O] SDF format, chain FA [auth P] SDF format, chain R [auth B] SDF format, chain S [auth C] SDF format, chain T [auth D] SDF format, chain U [auth E] SDF format, chain V [auth F] SDF format, chain W [auth G] SDF format, chain X [auth H] SDF format, chain Y [auth I] SDF format, chain Z [auth J] SDF format, chain Q [auth A] SDF format, chain CA [auth M] MOL2 format, chain AA [auth K] MOL2 format, chain BA [auth L] MOL2 format, chain DA [auth N] MOL2 format, chain EA [auth O] MOL2 format, chain FA [auth P] MOL2 format, chain R [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth E] MOL2 format, chain V [auth F] MOL2 format, chain W [auth G] MOL2 format, chain X [auth H] MOL2 format, chain Y [auth I] MOL2 format, chain Z [auth J] MOL2 format, chain Q [auth A] MOL2 format, chain CA [auth M] mmCIF format, chain AA [auth K] mmCIF format, chain BA [auth L] mmCIF format, chain DA [auth N] mmCIF format, chain EA [auth O] mmCIF format, chain FA [auth P] mmCIF format, chain R [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth E] mmCIF format, chain V [auth F] mmCIF format, chain W [auth G] mmCIF format, chain X [auth H] mmCIF format, chain Y [auth I] mmCIF format, chain Z [auth J] mmCIF format, chain Q [auth A] mmCIF format, chain CA [auth M]	AA [auth K] BA [auth L] CA [auth M] DA [auth N] EA [auth O] AA [auth K], BA [auth L], CA [auth M], DA [auth N], EA [auth O], FA [auth P], Q [auth A], R [auth B], S [auth C], T [auth D], U [auth E], V [auth F], W [auth G], X [auth H], Y [auth I], Z [auth J]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth M] Focus chain DA [auth N] Focus chain EA [auth O] Focus chain FA [auth P] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth M] Focus chain DA [auth N] Focus chain EA [auth O] Focus chain FA [auth P] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth D] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.264 (Depositor), 0.195 (DCC)
R-Value Work: 0.194 (Depositor), 0.197 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 240.918	α = 90
b = 240.918	β = 90
c = 294.824	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-05-23

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2006-05-23
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary