Macromolecule Content

Total Structure Weight: 991.88 kDa
Atom Count: 70139
Modelled Residue Count: 8290
Deposited Residue Count: 8800
Unique protein chains: 1

6V9A

Agrobacterium tumefaciens ADP-Glucose pyrophosphorylase-S72D

PDB DOI: 10.2210/pdb6V9A/pdb

Classification: TRANSFERASE
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-12-13 Released: 2020-12-16
Deposition Author(s): Zheng, Y., Alghamdi, M.A., Ballicora, M.A., Liu, D.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.279
R-Value Work: 0.234
R-Value Observed: 0.236

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Site directed mutagenesis of Serine-72 reveals the location of the fructose 6-phosphate regulatory site of the Agrobacterium tumefaciens ADP-glucose pyrophosphorylase

Alghamdi, M.A., Hussien, R., Zheng, Y., Patel, H.P., Iglesias, A.A., Liu, D., Ballicora, M.A.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-1-phosphate adenylyltransferase	B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], A [auth H], I, J, K, L, M, N, O, P, Q, R, T, S [auth V]	440	Agrobacterium fabrum str. C58	Mutation(s): 1 Gene Names: glgC, Atu4076, AGR_L_1560 EC: 2.7.7.27
UniProt
Find proteins for Q8U8L5 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q8U8L5 Go to UniProtKB: Q8U8L5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8U8L5
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth P] SDF format, chain CA [auth D] SDF format, chain CB [auth Q] SDF format, chain EA [auth E] SDF format, chain EB [auth R] SDF format, chain GA [auth F] SDF format, chain GB [auth V] SDF format, chain IA [auth G] SDF format, chain IB [auth T] SDF format, chain KA [auth I] SDF format, chain MA [auth J] SDF format, chain PA [auth K] SDF format, chain SA [auth L] SDF format, chain U [auth H] SDF format, chain UA [auth M] SDF format, chain W [auth A] SDF format, chain WA [auth N] SDF format, chain YA [auth O] SDF format, chain Z [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth P] MOL2 format, chain CA [auth D] MOL2 format, chain CB [auth Q] MOL2 format, chain EA [auth E] MOL2 format, chain EB [auth R] MOL2 format, chain GA [auth F] MOL2 format, chain GB [auth V] MOL2 format, chain IA [auth G] MOL2 format, chain IB [auth T] MOL2 format, chain KA [auth I] MOL2 format, chain MA [auth J] MOL2 format, chain PA [auth K] MOL2 format, chain SA [auth L] MOL2 format, chain U [auth H] MOL2 format, chain UA [auth M] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth N] MOL2 format, chain YA [auth O] MOL2 format, chain Z [auth B]	AA [auth C], AB [auth P], CA [auth D], CB [auth Q], EA [auth E], AA [auth C], AB [auth P], CA [auth D], CB [auth Q], EA [auth E], EB [auth R], GA [auth F], GB [auth V], IA [auth G], IB [auth T], KA [auth I], MA [auth J], PA [auth K], SA [auth L], U [auth H], UA [auth M], W [auth A], WA [auth N], YA [auth O], Z [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain BB [auth P] SDF format, chain DA [auth D] SDF format, chain DB [auth Q] SDF format, chain FA [auth E] SDF format, chain FB [auth R] SDF format, chain HA [auth F] SDF format, chain HB [auth V] SDF format, chain JA [auth G] SDF format, chain JB [auth T] SDF format, chain LA [auth I] SDF format, chain NA [auth J] SDF format, chain OA [auth J] SDF format, chain QA [auth K] SDF format, chain RA [auth K] SDF format, chain TA [auth L] SDF format, chain V [auth H] SDF format, chain VA [auth M] SDF format, chain X [auth A] SDF format, chain XA [auth N] SDF format, chain Y [auth A] SDF format, chain ZA [auth O] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth P] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth Q] MOL2 format, chain FA [auth E] MOL2 format, chain FB [auth R] MOL2 format, chain HA [auth F] MOL2 format, chain HB [auth V] MOL2 format, chain JA [auth G] MOL2 format, chain JB [auth T] MOL2 format, chain LA [auth I] MOL2 format, chain NA [auth J] MOL2 format, chain OA [auth J] MOL2 format, chain QA [auth K] MOL2 format, chain RA [auth K] MOL2 format, chain TA [auth L] MOL2 format, chain V [auth H] MOL2 format, chain VA [auth M] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth N] MOL2 format, chain Y [auth A] MOL2 format, chain ZA [auth O]	BA [auth C], BB [auth P], DA [auth D], DB [auth Q], FA [auth E], BA [auth C], BB [auth P], DA [auth D], DB [auth Q], FA [auth E], FB [auth R], HA [auth F], HB [auth V], JA [auth G], JB [auth T], LA [auth I], NA [auth J], OA [auth J], QA [auth K], RA [auth K], TA [auth L], V [auth H], VA [auth M], X [auth A], XA [auth N], Y [auth A], ZA [auth O]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.279
R-Value Work: 0.234
R-Value Observed: 0.236
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.231	α = 107.998
b = 141.404	β = 101.626
c = 228.648	γ = 90.019

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2019-12-13
Released Date: 2020-12-16

Deposition Author(s):

Ballicora, M.A.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2020-12-16
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.