1NL7

Z. ramigera biosynthetic thiolase, acetylated enzyme complexed with CoA at pH 9.5

PDB DOI: https://doi.org/10.2210/pdb1NL7/pdb

Classification: TRANSFERASE
Organism(s): Zoogloea ramigera
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-01-06 Released: 2004-04-06
Deposition Author(s): Kursula, P., Wierenga, R.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.223
R-Value Work: 0.179
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structures of Z. ramigera biosynthetic thiolase

Kursula, P., Wierenga, R.K.

To be published.

Macromolecule Content

Total Structure Weight: 164.25 kDa
Atom Count: 12,691
Modelled Residue Count: 1,560
Deposited Residue Count: 1,568
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA acetyltransferase	A, B, C, D	392	Zoogloea ramigera	Mutation(s): 1 EC: 2.3.1.9
UniProt
Find proteins for P07097 (Shinella zoogloeoides) Explore P07097 Go to UniProtKB: P07097
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07097
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B]	G [auth A], J [auth B]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B]	E [auth A], F [auth A], H [auth B], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SCY Query on SCY	A, B, C, D	L-PEPTIDE LINKING	C₅ H₉ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.223
R-Value Work: 0.179
R-Value Observed: 0.181
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.374	α = 90
b = 79.059	β = 92.58
c = 148.881	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
REFMAC	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-04-06

Deposition Author(s):

Kursula, P.

Wierenga, R.K.

Revision History (Full details and data files)

Version 1.0: 2004-04-06
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2018-03-07
Changes: Data collection
Version 1.4: 2023-08-16
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

1NL7

Z. ramigera biosynthetic thiolase, acetylated enzyme complexed with CoA at pH 9.5

Crystal structures of Z. ramigera biosynthetic thiolase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)