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- PDB-8yxt: Crystal structure of PtmB -

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Basic information

Entry
Database: PDB / ID: 8yxt
TitleCrystal structure of PtmB
ComponentsPtmB
KeywordsOXIDOREDUCTASE / P450 oxidoreductase
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesKitasatospora mediocidica KCTC 9733 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhang, Z.Y. / Qu, X.D. / Duan, B.R. / Wei, G.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800052 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: A nucleobase-driven P450 peroxidase system enables regio- and stereo-specific formation of C─C and C─N bonds.
Authors: Wei, G. / Duan, B. / Zhou, T.P. / Tian, W. / Sun, C. / Lin, Z. / Deng, Z. / Wang, B. / Zhang, Z. / Qu, X.
History
DepositionApr 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: 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.name
Revision 1.2Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PtmB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9162
Polymers45,2991
Non-polymers6161
Water43224
1
A: PtmB
hetero molecules

A: PtmB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8324
Polymers90,5992
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area4740 Å2
ΔGint-55 kcal/mol
Surface area31700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.712, 88.712, 139.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein PtmB


Mass: 45299.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Kitasatospora medicidica KCTC 9733 strain (TAX ID 1449347) is not available in UniProt at the time of biocuration. Kitasatospora medicidica KCTC 9733: NCBI RefSeq ...Details: Sequence reference for Kitasatospora medicidica KCTC 9733 strain (TAX ID 1449347) is not available in UniProt at the time of biocuration. Kitasatospora medicidica KCTC 9733: NCBI RefSeq assembly is GCF_000744225.1 and GenBank assembly is GCA_000744225.1.
Source: (gene. exp.) Kitasatospora mediocidica KCTC 9733 (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M BIS-Tris pH 5.5 0.2M Ammonium sulfate 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.6→24.97 Å / Num. obs: 17583 / % possible obs: 98.4 % / Redundancy: 25.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 26.7
Reflection shellResolution: 2.6→2.72 Å / Num. unique obs: 2136 / CC1/2: 0.912

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→24.97 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2613 864 -
Rwork0.2269 --
obs-17524 98.15 %
Refinement stepCycle: LAST / Resolution: 2.6→24.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2981 0 0 24 3005
LS refinement shellResolution: 2.6→2.693 Å
RfactorNum. reflection
Rfree0.3306 84
Rwork0.2827 -
all-1753

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