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- PDB-9j6e: Crystal structure of BioZ from Agrobacterium tumefaciens in compl... -

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Basic information

Entry
Database: PDB / ID: 9j6e
TitleCrystal structure of BioZ from Agrobacterium tumefaciens in complex with galutaryl-CoA
Components3-oxopimeloyl-[acyl-carrier-protein] synthase
KeywordsBIOSYNTHETIC PROTEIN / Biotin synthesis
Function / homology
Function and homology information


biotin biosynthetic process / secondary metabolite biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process
Similarity search - Function
3-oxopimeloyl-[acyl-carrier-protein] synthase / 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-like
Similarity search - Domain/homology
COENZYME A / 3-oxopimeloyl-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsZhang, L. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077081 China
CitationJournal: To Be Published
Title: Crystal structure of BioZ from Agrobacterium tumefaciens in complex with galutaryl-CoA
Authors: Zhang, L. / Zhang, L.
History
DepositionAug 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxopimeloyl-[acyl-carrier-protein] synthase
B: 3-oxopimeloyl-[acyl-carrier-protein] synthase
C: 3-oxopimeloyl-[acyl-carrier-protein] synthase
D: 3-oxopimeloyl-[acyl-carrier-protein] synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,2068
Polymers137,1364
Non-polymers3,0704
Water6,449358
1
A: 3-oxopimeloyl-[acyl-carrier-protein] synthase
B: 3-oxopimeloyl-[acyl-carrier-protein] synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1034
Polymers68,5682
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-31 kcal/mol
Surface area22100 Å2
MethodPISA
2
C: 3-oxopimeloyl-[acyl-carrier-protein] synthase
D: 3-oxopimeloyl-[acyl-carrier-protein] synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1034
Polymers68,5682
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-35 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.681, 126.691, 84.856
Angle α, β, γ (deg.)90.00, 102.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-oxopimeloyl-[acyl-carrier-protein] synthase / 3-oxopimeloyl-[ACP] synthase / 3-ketoacyl-ACP synthase / 3-oxoacyl-(acyl-carrier-protein) synthase ...3-oxopimeloyl-[ACP] synthase / 3-ketoacyl-ACP synthase / 3-oxoacyl-(acyl-carrier-protein) synthase / Beta-ketoacyl-ACP synthase


Mass: 34283.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Gene: bioZ, fabH2, Atu4001 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7CTU0, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% v/v Glycerol, 10% w/v PEG 4000, and 100 mM MES monohydrate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.15→69.26 Å / Num. obs: 64224 / % possible obs: 95.6 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.062 / Rrim(I) all: 0.164 / Χ2: 0.99 / Net I/σ(I): 10.6 / Num. measured all: 440854
Reflection shellResolution: 2.15→2.26 Å / % possible obs: 80.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.138 / Num. measured all: 53582 / Num. unique obs: 7893 / CC1/2: 0.727 / Rpim(I) all: 0.465 / Rrim(I) all: 1.231 / Χ2: 0.94 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→53.54 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2308 3080 4.81 %
Rwork0.1905 --
obs0.1925 64070 95.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→53.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9564 0 192 358 10114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099896
X-RAY DIFFRACTIONf_angle_d1.23713456
X-RAY DIFFRACTIONf_dihedral_angle_d14.3493532
X-RAY DIFFRACTIONf_chiral_restr0.0581576
X-RAY DIFFRACTIONf_plane_restr0.0081748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.180.29261660.24092856X-RAY DIFFRACTION100
2.18-2.210.29971460.23122894X-RAY DIFFRACTION100
2.21-2.240.323810.29231709X-RAY DIFFRACTION89
2.26-2.290.29331190.23982261X-RAY DIFFRACTION96
2.29-2.340.2991260.22382878X-RAY DIFFRACTION100
2.34-2.390.25941320.22252946X-RAY DIFFRACTION100
2.39-2.440.29151700.20552849X-RAY DIFFRACTION100
2.44-2.490.2581380.21652947X-RAY DIFFRACTION100
2.49-2.560.24961470.21172852X-RAY DIFFRACTION100
2.56-2.630.2871400.20252901X-RAY DIFFRACTION100
2.63-2.70.2711040.22311951X-RAY DIFFRACTION67
2.7-2.790.27591540.20932890X-RAY DIFFRACTION100
2.79-2.890.27221390.19132883X-RAY DIFFRACTION100
2.89-3.010.25281490.1962902X-RAY DIFFRACTION100
3.01-3.140.23161750.18842900X-RAY DIFFRACTION100
3.14-3.310.22381410.18632908X-RAY DIFFRACTION100
3.31-3.520.19621370.17832914X-RAY DIFFRACTION100
3.52-3.790.22171380.18422897X-RAY DIFFRACTION100
3.79-4.170.19891370.17712909X-RAY DIFFRACTION100
4.17-4.770.17461490.15282924X-RAY DIFFRACTION100
4.77-6.010.20611380.18842942X-RAY DIFFRACTION100
6.01-53.540.20911540.17252877X-RAY DIFFRACTION97

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