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

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Basic information

Entry
Database: PDB / ID: 8yyp
TitleCrystal structure of PtmB in complex with cyclo-(L-Trp-L-Trp) and Adenine
ComponentsPtmB
KeywordsOXIDOREDUCTASE / P450 oxidoreductase
Function / homologyADENINE / PROTOPORPHYRIN IX CONTAINING FE / Chem-UYM
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 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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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)92,4747
Polymers90,5992
Non-polymers1,8765
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-52 kcal/mol
Surface area30630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.453, 84.453, 133.377
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-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-UYM / (3S,6S)-3,6-bis[(1H-indol-3-yl)methyl]piperazine-2,5-dione


Mass: 372.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C22H20N4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.62 Å3/Da / Density % sol: 53.14 %
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: 2.6→25.01 Å / Num. obs: 28724 / % possible obs: 99.87 % / Redundancy: 13.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1549 / Net I/σ(I): 17.29
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 13.8 % / Num. unique obs: 2865 / CC1/2: 0.851 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→25.01 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.111 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.931 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 1439 5 %RANDOM
Rwork0.2064 ---
obs0.17102 28724 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å2-0 Å2-0 Å2
2--0.73 Å2-0 Å2
3----1.47 Å2
Refinement stepCycle: 1 / Resolution: 2.6→25.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5916 0 134 201 6251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136400
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156104
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.6468736
X-RAY DIFFRACTIONr_angle_other_deg1.2881.57213992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.355786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.55219.896386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.05715998
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4621568
X-RAY DIFFRACTIONr_chiral_restr0.0730.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027374
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021492
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8824.1893150
X-RAY DIFFRACTIONr_mcbond_other3.8824.1893149
X-RAY DIFFRACTIONr_mcangle_it5.9546.2773934
X-RAY DIFFRACTIONr_mcangle_other5.9536.2763935
X-RAY DIFFRACTIONr_scbond_it3.9584.463250
X-RAY DIFFRACTIONr_scbond_other3.9574.4613251
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.046.5744803
X-RAY DIFFRACTIONr_long_range_B_refined8.63649.3767124
X-RAY DIFFRACTIONr_long_range_B_other8.64549.3757090
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 110 -
Rwork0.204 2013 -
obs--100 %

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