2ZSL | pdb_00002zsl

Crystal structure of glutamate-1-semialdehyde 2,1-aminomutase from Aeropyrum pernix

PDB DOI: https://doi.org/10.2210/pdb2ZSL/pdb

Classification: ISOMERASE
Organism(s): Aeropyrum pernix
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-17 Released: 2008-10-21
Deposition Author(s): Mizutani, H., Kunishima, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.188 (Depositor), 0.189 (DCC)
R-Value Work:
0.165 (Depositor), 0.166 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of glutamate-1-semialdehyde 2,1-aminomutase from Aeropyrum pernix

Mizutani, H., Kunishima, N.

To be published.

Macromolecule Content

Total Structure Weight: 46.78 kDa
Atom Count: 3,625
Modeled Residue Count: 420
Deposited Residue Count: 434
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate-1-semialdehyde 2,1-aminomutase	A	434	Aeropyrum pernix	Mutation(s): 0 EC: 5.4.3.8
UniProt
Find proteins for Q9Y9I9 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9Y9I9 Go to UniProtKB: Q9Y9I9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y9I9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PMP Query on PMP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C₈ H₁₃ N₂ O₅ P ZMJGSOSNSPKHNH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.188 (Depositor), 0.189 (DCC)
R-Value Work: 0.165 (Depositor), 0.166 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.006	α = 90
b = 101.842	β = 90
c = 148.346	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-10-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-10-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.