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- PDB-7eqi: ChlB3 [Aceyltransferase] -

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Basic information

Entry
Database: PDB / ID: 7eqi
TitleChlB3 [Aceyltransferase]
ComponentsChlB3
KeywordsTRANSFERASE / Acyltransferase / ChlB3
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsSaeed, A.U. / Zheng, J.
CitationJournal: Molecules / Year: 2022
Title: Structural Insight of KSIII ( beta-Ketoacyl-ACP Synthase)-like Acyltransferase ChlB3 in the Biosynthesis of Chlorothricin.
Authors: Saeed, A.U. / Rahman, M.U. / Chen, H.F. / Zheng, J.
History
DepositionMay 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Experimental preparation
Category: citation / citation_author ...citation / citation_author / database_2 / exptl_crystal_grow
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal_grow.pdbx_details
Revision 1.2Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ChlB3
B: ChlB3
C: ChlB3
D: ChlB3
E: ChlB3
F: ChlB3
G: ChlB3
H: ChlB3


Theoretical massNumber of molelcules
Total (without water)296,1448
Polymers296,1448
Non-polymers00
Water1,53185
1
A: ChlB3
B: ChlB3


Theoretical massNumber of molelcules
Total (without water)74,0362
Polymers74,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-25 kcal/mol
Surface area23080 Å2
MethodPISA
2
C: ChlB3
D: ChlB3


Theoretical massNumber of molelcules
Total (without water)74,0362
Polymers74,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-28 kcal/mol
Surface area22520 Å2
MethodPISA
3
E: ChlB3
F: ChlB3


Theoretical massNumber of molelcules
Total (without water)74,0362
Polymers74,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-27 kcal/mol
Surface area22840 Å2
MethodPISA
4
G: ChlB3
H: ChlB3


Theoretical massNumber of molelcules
Total (without water)74,0362
Polymers74,0362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-23 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.473, 186.583, 189.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ChlB3


Mass: 37017.992 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces antibioticus (bacteria)
Production host: Streptomyces antibioticus JCM 4620 (bacteria)
References: UniProt: Q0R4P5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M HEPS pH 7.0, 1.4 M sodium acetate-trihydrate

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 0.939 Å
DetectorType: DECTRIS MYTHEN2 R 1K / Detector: PIXEL / Date: Oct 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 74294 / % possible obs: 99.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.051 / Rrim(I) all: 0.126 / Χ2: 0.936 / Net I/σ(I): 7.2 / Num. measured all: 442810
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.155.90.58936450.8840.2610.6450.96799.9
3.15-3.215.90.56435890.8930.2490.6180.959100
3.21-3.276.30.45936470.9340.1940.4990.97100
3.27-3.346.30.34836490.9560.1470.3790.987100
3.34-3.416.30.30236200.960.1280.3290.98899.8
3.41-3.496.20.25336130.9680.1080.2761.03799.8
3.49-3.586.20.22536850.9750.0960.2450.99999.7
3.58-3.686.20.18736250.9780.080.2030.99499.9
3.68-3.786.10.15836320.9810.0690.1730.9999.9
3.78-3.9160.14236500.9830.0630.1550.98299.9
3.91-4.045.60.12136510.9840.0560.1340.95999.7
4.04-4.215.80.11136530.9880.050.1220.97399.8
4.21-4.46.20.10436710.9880.0450.1130.95999.7
4.4-4.636.30.09536570.9910.040.1030.91399.6
4.63-4.926.20.09136580.9890.0390.0990.88699.5
4.92-5.36.10.08936870.9910.0390.0980.8599.4
5.3-5.835.80.0936910.9880.040.0980.81699.4
5.83-6.675.80.08637340.990.0380.0940.8299.4
6.67-8.46.20.07937070.9910.0340.0870.77898.5
8.4-505.50.08238370.990.0370.090.88796.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-3000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xsa

4xsa


Resolution: 3.1→50 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25604 3931 5 %RANDOM
Rwork0.2262 ---
obs0.22773 74294 99.41 %-
Displacement parametersBiso max: 166.21 Å2 / Biso mean: 66.5365 Å2 / Biso min: 33.56 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19057 0 0 85 19142
LS refinement shellResolution: 3.1→3.181 Å
RfactorNum. reflection% reflection
Rfree0.32 247 -
Rwork0.296 --
obs-5107 93.41 %

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