3BYW | pdb_00003byw

Crystal structure of an extracellular domain of arabinofuranosyltransferase from Corynebacterium diphtheriae

PDB DOI: https://doi.org/10.2210/pdb3BYW/pdb

Classification: TRANSFERASE
Organism(s): Corynebacterium diphtheriae NCTC 13129
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2008-01-16 Released: 2008-02-19
Deposition Author(s): Tan, K., Hatzos, C., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.263 (Depositor), 0.296 (DCC)
R-Value Work:
0.209 (Depositor), 0.256 (DCC)
R-Value Observed:
0.212 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The structure of an extracellular domain of arabinofuranosyltransferase from Corynebacterium diphtheriae.

Tan, K., Hatzos, C., Abdullah, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 152.57 kDa
Atom Count: 9,635
Modeled Residue Count: 1,269
Deposited Residue Count: 1,416
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative arabinofuranosyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H	177	Corynebacterium diphtheriae NCTC 13129	Mutation(s): 0 Gene Names: DIP0159
UniProt
Find proteins for Q6NK78 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NK78 Go to UniProtKB: Q6NK78
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NK78
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain IA [auth F] SDF format, chain JA [auth F] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain M [auth B] SDF format, chain LA [auth G] SDF format, chain KA [auth G] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain EA [auth E] SDF format, chain CA [auth E] SDF format, chain BA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain JA [auth F] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] MOL2 format, chain LA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain EA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain BA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain IA [auth F] mmCIF format, chain JA [auth F] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B] mmCIF format, chain LA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain EA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain BA [auth E]	BA [auth E] CA [auth E] DA [auth E] EA [auth E] I [auth A] BA [auth E], CA [auth E], DA [auth E], EA [auth E], I [auth A], IA [auth F], J [auth A], JA [auth F], KA [auth G], L [auth B], LA [auth G], M [auth B], N [auth B], R [auth C], S [auth C], U [auth D], V [auth D], W [auth D], X [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain KA [auth G] Focus chain L [auth B] Focus chain LA [auth G] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain KA [auth G] Focus chain L [auth B] Focus chain LA [auth G] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain HA [auth E] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain T [auth C] SDF format, chain P [auth B] SDF format, chain NA [auth H] SDF format, chain MA [auth G] SDF format, chain GA [auth E] SDF format, chain FA [auth E] SDF format, chain AA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain T [auth C] MOL2 format, chain P [auth B] MOL2 format, chain NA [auth H] MOL2 format, chain MA [auth G] MOL2 format, chain GA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain AA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain T [auth C] mmCIF format, chain P [auth B] mmCIF format, chain NA [auth H] mmCIF format, chain MA [auth G] mmCIF format, chain GA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain AA [auth D]	AA [auth D] FA [auth E] GA [auth E] HA [auth E] K [auth A] AA [auth D], FA [auth E], GA [auth E], HA [auth E], K [auth A], MA [auth G], NA [auth H], O [auth B], P [auth B], Q [auth B], T [auth C], Y [auth D], Z [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain K [auth A] Focus chain MA [auth G] Focus chain NA [auth H] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain K [auth A] Focus chain MA [auth G] Focus chain NA [auth H] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D]

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	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.263 (Depositor), 0.296 (DCC)
R-Value Work: 0.209 (Depositor), 0.256 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.885	α = 90
b = 80.619	β = 110.91
c = 115.826	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-02-19

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-02-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary