4U13 | pdb_00004u13

Crystal structure of putative polyketide cyclase (protein SMa1630) from Sinorhizobium meliloti at 2.3 A resolution

PDB DOI: https://doi.org/10.2210/pdb4U13/pdb

Classification: TRANSFERASE
Organism(s): Sinorhizobium meliloti 1021
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-07-14 Released: 2014-09-10
Deposition Author(s): Shabalin, I.G., Bacal, P., Osinski, T., Cooper, D.R., Szlachta, K., Stead, M., Grabowski, M., Hammonds, J., Ahmed, M., Hillerich, B.S., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.224 (Depositor), 0.225 (DCC)
R-Value Work:
0.193 (Depositor), 0.200 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.8 of the entry. See complete history.

Literature

Crystal structure of a putative polyketide cyclase (protein SMa1630) from Sinorhizobium meliloti at 2.3 A resolution

Shabalin, I.G., Bacal, P., Osinski, T., Cooper, D.R., Szlachta, K., Stead, M., Grabowski, M., Hammonds, J., Ahmed, M., Hillerich, B.S., Bonanno, J., Seidel, R., Almo, S.C., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 24.06 kDa
Atom Count: 1,656
Modeled Residue Count: 218
Deposited Residue Count: 218
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative polyketide cyclase SMa1630	A, B	109	Sinorhizobium meliloti 1021	Mutation(s): 0 Gene Names: SMa1630
UniProt
Find proteins for Q92YJ1 (Rhizobium meliloti (strain 1021)) Explore Q92YJ1 Go to UniProtKB: Q92YJ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92YJ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.224 (Depositor), 0.225 (DCC)
R-Value Work: 0.193 (Depositor), 0.200 (DCC)
R-Value Observed: 0.194 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.764	α = 90
b = 42.295	β = 111.83
c = 62.287	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	phasing
HKL-3000	data scaling
PHENIX	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2014-09-10

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIH-5U54GM094662-04

Revision History (Full details and data files)

Version 1.0: 2014-09-10
Type: Initial release
Version 1.1: 2014-09-24
Changes: Refinement description, Structure summary
Version 1.2: 2015-08-26
Changes: Data collection
Version 1.3: 2017-09-20
Changes: Author supporting evidence, Derived calculations, Refinement description
Version 1.4: 2019-12-25
Changes: Author supporting evidence
Version 1.5: 2022-04-13
Changes: Database references, Structure summary
Version 1.6: 2023-09-27
Changes: Data collection, Refinement description
Version 1.7: 2023-11-15
Changes: Data collection
Version 1.8: 2024-10-30
Changes: Structure summary