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

Starting Model: experimental
View more details

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 DA [auth E] SDF format, chain IA [auth F] SDF format, chain M [auth A] SDF format, chain NA [auth G] SDF format, chain Q [auth B] SDF format, chain SA [auth H] SDF format, chain V [auth C] SDF 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 Q [auth B] MOL2 format, chain SA [auth H] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D]	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 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 I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth G] 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 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 I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth G] 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 EA [auth E] SDF format, chain JA [auth F] SDF format, chain N [auth A] SDF format, chain OA [auth G] SDF format, chain R [auth B] SDF format, chain TA [auth H] SDF format, chain W [auth C] SDF format, chain Z [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain JA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain TA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth D]	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