8VR5

crystal structure of the Pcryo_0618 aminotransferase from Psychrobacter cryohalolentis K5 in the presence of PMP and glutamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Biochemical Investigation of the Enzymes Required for the Production of 2,3,4-triacetoamido-2,3,4-trideoxy-l-arabinose in Psychrobacter cryohalolentis K5

Bockhaus, N.J.Dunsirn, M.M.Thoden, J.B.Holden, H.M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DegT/DnrJ/EryC1/StrS aminotransferase
A, B, C, D
380Psychrobacter cryohalolentis K5Mutation(s): 0 
Gene Names: Pcryo_0618
UniProt
Find proteins for Q1QD52 (Psychrobacter cryohalolentis (strain ATCC BAA-1226 / DSM 17306 / VKM B-2378 / K5))
Explore Q1QD52 
Go to UniProtKB:  Q1QD52
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1QD52
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PDG (Subject of Investigation/LOI)
Query on PDG

Download Ideal Coordinates CCD File 
M [auth B],
V [auth C],
Y [auth D]
N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC ACID
C13 H19 N2 O9 P
JMRKOGDJNHPMHS-SNVBAGLBSA-N
A1ADI
Query on A1ADI

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F [auth A],
N [auth B],
O [auth B]
2,2'-(1,4-diazepane-1,4-diyl)di(ethane-1-sulfonic acid)
C9 H20 N2 O6 S2
QZTMPPUJIVQNKS-UHFFFAOYSA-N
PMP (Subject of Investigation/LOI)
Query on PMP

Download Ideal Coordinates CCD File 
E [auth A]4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
Q [auth B]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
Q [auth B],
R [auth B],
S [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

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G [auth A],
P [auth B],
W [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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L [auth A],
T [auth B],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth D],
U [auth B],
X [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.493α = 90
b = 159.822β = 90
c = 115.864γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM134643

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release