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- PDB-8twu: Crystal structure of Cytochrome P450 AspB bound to N1-methylated ... -

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Basic information

Entry
Database: PDB / ID: 8twu
TitleCrystal structure of Cytochrome P450 AspB bound to N1-methylated cyclo-L-Trp-L-Pro
ComponentsCytochrome P450 AspB
KeywordsOXIDOREDUCTASE / dimerase
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / Chem-RQB
Function and homology information
Biological speciesStreptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsGering, H.E. / Li, X. / Tang, H. / Swartz, P.D. / Chang, W.-C. / Makris, T.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135315 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127588 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: A Ferric-Superoxide Intermediate Initiates P450-Catalyzed Cyclic Dipeptide Dimerization.
Authors: Gering, H.E. / Li, X. / Tang, H. / Swartz, P.D. / Chang, W.C. / Makris, T.M.
History
DepositionAug 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 AspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8365
Polymers44,5591
Non-polymers1,2774
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.710, 120.999, 46.223
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Cytochrome P450 AspB


Mass: 44559.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces (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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-RQB / (3S,5S,8aS)-3-[(1-methyl-1H-indol-3-yl)methyl]hexahydropyrrolo[1,2-a]pyrazine-1,4-dione


Mass: 297.352 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 15% PEG 3350 50 mM Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→39.73 Å / Num. obs: 38294 / % possible obs: 99.59 % / Redundancy: 7.3 % / Biso Wilson estimate: 22.35 Å2 / CC1/2: 0.993 / Net I/σ(I): 24.7
Reflection shellResolution: 1.84→1.91 Å / Num. unique obs: 38156 / CC1/2: 0.865

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→39.73 Å / SU ML: 0.1897 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.379
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2091 1998 5.24 %
Rwork0.1635 36158 -
obs0.1658 38156 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.22 Å2
Refinement stepCycle: LAST / Resolution: 1.84→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3093 0 88 345 3526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753416
X-RAY DIFFRACTIONf_angle_d1.02954697
X-RAY DIFFRACTIONf_chiral_restr0.0564505
X-RAY DIFFRACTIONf_plane_restr0.0099626
X-RAY DIFFRACTIONf_dihedral_angle_d13.0327502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.890.29081360.22872441X-RAY DIFFRACTION96.44
1.89-1.940.30481400.2382542X-RAY DIFFRACTION99.52
1.94-20.25391420.19042544X-RAY DIFFRACTION99.78
2-2.060.25271390.18442534X-RAY DIFFRACTION99.74
2.06-2.140.23511410.17822549X-RAY DIFFRACTION99.78
2.14-2.220.21321420.1582571X-RAY DIFFRACTION99.67
2.22-2.320.25771430.18212589X-RAY DIFFRACTION99.89
2.32-2.450.2131410.15542555X-RAY DIFFRACTION99.81
2.45-2.60.20651420.17022578X-RAY DIFFRACTION99.89
2.6-2.80.21561430.1662584X-RAY DIFFRACTION99.89
2.8-3.080.24711440.16312618X-RAY DIFFRACTION99.93
3.08-3.530.18591450.15592620X-RAY DIFFRACTION100
3.53-4.440.17281460.13312643X-RAY DIFFRACTION99.96
4.45-39.730.18191540.15952790X-RAY DIFFRACTION99.9

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