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- PDB-8yz8: Crystal structure of PtmB in complex with Adenine -

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Basic information

Entry
Database: PDB / ID: 8yz8
TitleCrystal structure of PtmB in complex with Adenine
ComponentsPtmB
KeywordsOXIDOREDUCTASE / P450 oxidoreductase
Function / homologyADENINE / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesKitasatospora mediocidica KCTC 9733 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 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 6, 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

Downloads & links

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Assembly

Deposited unit
A: PtmB
B: PtmB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1026
Polymers90,5992
Non-polymers1,5034
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-46 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.406, 145.406, 129.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5
Has ligand of interestY
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: 3.77 Å3/Da / Density % sol: 67.36 %
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: 2.86→30.27 Å / Num. obs: 31057 / % possible obs: 99.87 % / Redundancy: 13.5 % / CC1/2: 0.996 / Net I/σ(I): 7.95
Reflection shellResolution: 2.86→2.962 Å / Num. unique obs: 3125 / CC1/2: 0.639

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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: 2.86→30.27 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2713 1521 4.9 %
Rwork0.2078 --
obs0.2109 31048 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.86→30.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5764 0 106 0 5870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096368
X-RAY DIFFRACTIONf_angle_d1.1388691
X-RAY DIFFRACTIONf_dihedral_angle_d7.454960
X-RAY DIFFRACTIONf_chiral_restr0.053956
X-RAY DIFFRACTIONf_plane_restr0.011177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-2.950.35141300.29672705X-RAY DIFFRACTION100
2.95-3.060.33951180.29222648X-RAY DIFFRACTION100
3.06-3.180.33451380.26892696X-RAY DIFFRACTION100
3.18-3.320.29671200.25322691X-RAY DIFFRACTION100
3.32-3.50.29831570.23682664X-RAY DIFFRACTION100
3.5-3.720.26481460.21572660X-RAY DIFFRACTION100
3.72-40.25791490.19562669X-RAY DIFFRACTION100
4.01-4.410.25541560.18332668X-RAY DIFFRACTION100
4.41-5.040.2091150.17552709X-RAY DIFFRACTION100
5.04-6.340.2921530.19662684X-RAY DIFFRACTION100
6.35-30.270.24361390.16732733X-RAY DIFFRACTION100

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