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- PDB-8yy7: Crystal structure of PtmB in complex with cyclo-(L-Trp-L-Trp) and... -

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Basic information

Entry
Database: PDB / ID: 8yy7
TitleCrystal structure of PtmB in complex with cyclo-(L-Trp-L-Trp) and Hypoxanthine
ComponentsPtmB
KeywordsOXIDOREDUCTASE / P450 oxidoreductase
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / HYPOXANTHINE / Chem-UYM
Function and homology information
Biological speciesKitasatospora mediocidica KCTC 9733 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 3, 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
B: PtmB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8498
Polymers90,5992
Non-polymers2,2506
Water12,196677
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-53 kcal/mol
Surface area28890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.970, 84.970, 136.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein PtmB


Mass: 45299.418 Da / Num. of mol.: 2
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-UYM / (3S,6S)-3,6-bis[(1H-indol-3-yl)methyl]piperazine-2,5-dione


Mass: 372.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H20N4O2
#3: Chemical ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / 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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Bis-Tris pH 5.5 0.2M Ammonium acetate 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: 2.1→31.61 Å / Num. obs: 56291 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.996 / Net I/σ(I): 11.5
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 1.216 / Num. unique obs: 4167

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→31.61 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2244 2779 -
Rwork0.1945 --
obs-56241 99.94 %
Refinement stepCycle: LAST / Resolution: 2.1→31.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6134 0 0 677 6811
LS refinement shellResolution: 2.1→2.175 Å
RfactorNum. reflection
Rfree0.255 301
Rwork0.207 -
all-5629

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