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- PDB-2gu9: Crystal structure of XC5357 from Xanthomonas campestris: A putati... -

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Basic information

Entry
Database: PDB / ID: 2gu9
TitleCrystal structure of XC5357 from Xanthomonas campestris: A putative tetracenomycin polyketide synthesis protein adopting a novel cupin subfamily structure
Componentstetracenomycin polyketide synthesis protein
KeywordsIMMUNE SYSTEM / Xanthomonas campestris / cupin / tetracenomycin polyketide
Function / homology
Function and homology information


Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tetracenomycin polyketide synthesis protein
Similarity search - Component
Biological speciesXanthomonas campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsChin, K.-H. / Chou, C.C. / Wang, A.H.-J. / Chou, S.-H.
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of XC5357 from Xanthomonas campestris: A putative tetracenomycin polyketide synthesis protein adopting a novel cupin subfamily structure
Authors: Chin, K.-H. / Chou, C.C. / Wang, A.H.-J. / Chou, S.-H.
History
DepositionApr 28, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tetracenomycin polyketide synthesis protein
B: tetracenomycin polyketide synthesis protein


Theoretical massNumber of molelcules
Total (without water)24,3572
Polymers24,3572
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-20 kcal/mol
Surface area9730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.7, 43.68, 46.5
Angle α, β, γ (deg.)65.0, 64.9, 73.4
Int Tables number1
Space group name H-MP1

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Components

#1: Protein tetracenomycin polyketide synthesis protein


Mass: 12178.454 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris (bacteria) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8PBM3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 12

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M NaOAC, 1.6M LiSO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL12B210.97963, 0.96389
SYNCHROTRONSPring-8 BL12B220.97963
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 1, 2005
ADSC QUANTUM 42CCDJun 2, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Se-MetMADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979631
20.963891
ReflectionResolution: 1.4→30 Å / Num. all: 33553 / Num. obs: 32312 / % possible obs: 96.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.4→1.46 Å / % possible all: 96.3

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Processing

Software
NameClassification
ADSCdata collection
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.253 2854 Radom
Rwork0.22 --
all0.25 33553 -
obs0.231 32312 -
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1681 0 0 0 1681
Refine LS restraintsType: c_angle_deg / Dev ideal: 0.02

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