5V0T

Crystal structure of an alpha,alpha-trehalose-phosphate synthase (UDP-forming) from Burkholderia xenovorans in complex with glucose-6-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.155 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of an alpha,alpha-trehalose-phosphate synthase (UDP-forming) from Burkholderia xenovorans in complex with glucose-6-phosphate

Mayclin, S.J.Dranow, D.M.Lorimer, D.Edwards, T.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha,alpha-trehalose-phosphate synthase (UDP-forming)
A, B, C, D, E
A, B, C, D, E, F, G, H
494Paraburkholderia xenovorans LB400Mutation(s): 0 
Gene Names: Bxe_A1242
EC: 2.4.1.15
UniProt
Find proteins for Q13W28 (Paraburkholderia xenovorans (strain LB400))
Explore Q13W28 
Go to UniProtKB:  Q13W28
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13W28
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

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CC [auth H]
EB [auth E]
I [auth A]
MA [auth C]
PB [auth F]
CC [auth H],
EB [auth E],
I [auth A],
MA [auth C],
PB [auth F],
UA [auth D],
V [auth B],
YB [auth G]
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
G6P
Query on G6P

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DC [auth H]
FB [auth E]
J [auth A]
NA [auth C]
QB [auth F]
DC [auth H],
FB [auth E],
J [auth A],
NA [auth C],
QB [auth F],
VA [auth D],
W [auth B],
ZB [auth G]
6-O-phosphono-alpha-D-glucopyranose
C6 H13 O9 P
NBSCHQHZLSJFNQ-DVKNGEFBSA-N
TAR
Query on TAR

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GB [auth E]D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
OXD
Query on OXD

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EA [auth B],
JB [auth E],
O [auth A],
RA [auth C],
UB [auth F]
OXALIC ACID
C2 H2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-N
EDO
Query on EDO

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AC [auth G]
EC [auth H]
FC [auth H]
HB [auth E]
K [auth A]
AC [auth G],
EC [auth H],
FC [auth H],
HB [auth E],
K [auth A],
L [auth A],
LA [auth B],
OA [auth C],
OB [auth E],
PA [auth C],
RB [auth F],
WA [auth D],
X [auth B],
XA [auth D],
Y [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

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AA [auth B]
BA [auth B]
BC [auth G]
CA [auth B]
DA [auth B]
AA [auth B],
BA [auth B],
BC [auth G],
CA [auth B],
DA [auth B],
GC [auth H],
IB [auth E],
M [auth A],
N [auth A],
QA [auth C],
SB [auth F],
TB [auth F],
YA [auth D],
Z [auth B],
ZA [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT
Query on FMT

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AB [auth D]
BB [auth D]
CB [auth D]
DB [auth D]
FA [auth B]
AB [auth D],
BB [auth D],
CB [auth D],
DB [auth D],
FA [auth B],
GA [auth B],
HA [auth B],
HC [auth H],
IA [auth B],
IC [auth H],
JA [auth B],
KA [auth B],
KB [auth E],
LB [auth E],
MB [auth E],
NB [auth E],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
SA [auth C],
T [auth A],
TA [auth C],
U [auth A],
VB [auth F],
WB [auth F],
XB [auth F]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.155 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.92α = 91.36
b = 105.95β = 90.37
c = 135.71γ = 89.97
Software Package:
Software NamePurpose
XSCALEdata scaling
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary