4A1I

ykud from B.subtilis

PDB DOI: https://doi.org/10.2210/pdb4A1I/pdb

Classification: TRANSFERASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2011-09-15 Released: 2012-09-26
Deposition Author(s): Blaise, M., Fuglsang Midtgaard, S., Roi Midtgaard, S., Boesen, T., Thirup, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.218
R-Value Work: 0.173
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

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

Literature

Structures of Three New Crystal Forms of the Ykud L,D-Transpeptidase from B. Subtilis.

Blaise, M., Fuglsang Midtgaard, S., Roi Midtgaard, S., Boesen, T., Thirup, S.

To be published.

Macromolecule Content

Total Structure Weight: 144.13 kDa
Atom Count: 11,563
Modelled Residue Count: 1,316
Deposited Residue Count: 1,320
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE L, D-TRANSPEPTIDASE YKUD	A, B, C, D, E A, B, C, D, E, F, G, H	165	Bacillus subtilis	Mutation(s): 2 EC: 2
UniProt
Find proteins for O34816 (Bacillus subtilis (strain 168)) Explore O34816 Go to UniProtKB: O34816
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O34816
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain V [auth C] SDF format, chain Y [auth D] SDF format, chain DA [auth E] SDF format, chain IA [auth F] SDF format, chain M [auth A] SDF format, chain NA [auth G] SDF format, chain SA [auth H] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain SA [auth H]	DA [auth E] IA [auth F] M [auth A] NA [auth G] Q [auth B] DA [auth E], IA [auth F], M [auth A], NA [auth G], Q [auth B], SA [auth H], V [auth C], Y [auth D]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain IA [auth F] Focus chain M [auth A] Focus chain NA [auth G] Focus chain Q [auth B] Focus chain SA [auth H] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth E] Focus chain IA [auth F] Focus chain M [auth A] Focus chain NA [auth G] Focus chain Q [auth B] Focus chain SA [auth H] Focus chain V [auth C] Focus chain Y [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain KA [auth G] SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth G] SDF format, chain MA [auth G] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain PA [auth H] SDF format, chain QA [auth H] SDF format, chain RA [auth H] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain X [auth D] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth G] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth G] MOL2 format, chain MA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth H] MOL2 format, chain QA [auth H] MOL2 format, chain RA [auth H] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D]	AA [auth E] BA [auth E] CA [auth E] FA [auth F] GA [auth F] AA [auth E], BA [auth E], CA [auth E], FA [auth F], GA [auth F], HA [auth F], I [auth A], J [auth A], K [auth A], KA [auth G], L [auth A], LA [auth G], MA [auth G], O [auth B], P [auth B], PA [auth H], QA [auth H], RA [auth H], S [auth C], T [auth C], U [auth C], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth G] Focus chain L [auth A] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth H] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth G] Focus chain L [auth A] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth H] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain JA [auth F] SDF format, chain N [auth A] SDF format, chain OA [auth G] SDF format, chain W [auth C] SDF format, chain Z [auth D] SDF format, chain EA [auth E] SDF format, chain R [auth B] SDF format, chain TA [auth H] MOL2 format, chain JA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth G] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain TA [auth H]	EA [auth E] JA [auth F] N [auth A] OA [auth G] R [auth B] EA [auth E], JA [auth F], N [auth A], OA [auth G], R [auth B], TA [auth H], W [auth C], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth E] Focus chain JA [auth F] Focus chain N [auth A] Focus chain OA [auth G] Focus chain R [auth B] Focus chain TA [auth H] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain EA [auth E] Focus chain JA [auth F] Focus chain N [auth A] Focus chain OA [auth G] Focus chain R [auth B] Focus chain TA [auth H] Focus chain W [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.218
R-Value Work: 0.173
R-Value Observed: 0.174
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.45	α = 90
b = 91.85	β = 90.25
c = 123.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-09-26

Deposition Author(s):

Blaise, M.

Fuglsang Midtgaard, S.

Roi Midtgaard, S.

Boesen, T.

Thirup, S.

Revision History (Full details and data files)

Version 1.0: 2012-09-26
Type: Initial release
Version 1.1: 2012-10-03
Changes: Derived calculations
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description