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- PDB-8adr: Crystal structure of a staphylococcal orthologue of CYP134A1 (CYP... -

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Basic information

Entry
Database: PDB / ID: 8adr
TitleCrystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a fragment
ComponentsCytochrome P450 protein
KeywordsOXIDOREDUCTASE / CYP / CYPX / Staphylococcus aureus / CLL / Pulcherremin / P450
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / pyridin-3-ylboronic acid / Cytochrome P450 protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsSnee, M. / Katariya, M. / Levy, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a fragment
Authors: Snee, M. / Katariya, M.
History
DepositionJul 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 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 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7143
Polymers45,9751
Non-polymers7392
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-23 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.016, 108.244, 105.779
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Cytochrome P450 protein / cypX


Mass: 45974.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cypX_1, NCTC5664_01270, cypX / Production host: Escherichia coli (E. coli)
References: UniProt: A0A380DQV1, pulcherriminic acid synthase
#2: Chemical ChemComp-LS9 / pyridin-3-ylboronic acid


Mass: 122.918 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6BNO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.15M Lithium sulphate, 0.05M Magnesium chloride hexahydrate, 0.1M HEPES pH7.8, 20% v/v PEG smear high

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.92→55.29 Å / Num. obs: 35867 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 32.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.036 / Net I/σ(I): 10.7
Reflection shellResolution: 1.92→1.97 Å / Rmerge(I) obs: 1.607 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2372 / CC1/2: 0.935 / Rpim(I) all: 0.456 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PQ1

7pq1


Resolution: 1.92→52.89 Å / SU ML: 0.2302 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1194
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2413 1779 5.03 %
Rwork0.2098 33601 -
obs0.2114 35380 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.91 Å2
Refinement stepCycle: LAST / Resolution: 1.92→52.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3161 0 52 193 3406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00873325
X-RAY DIFFRACTIONf_angle_d0.81554508
X-RAY DIFFRACTIONf_chiral_restr0.0464498
X-RAY DIFFRACTIONf_plane_restr0.0058575
X-RAY DIFFRACTIONf_dihedral_angle_d7.0074446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.41911260.38732544X-RAY DIFFRACTION98.23
1.97-2.030.35291440.29182510X-RAY DIFFRACTION97.57
2.03-2.10.2351370.27572543X-RAY DIFFRACTION98.06
2.1-2.170.2671510.23022538X-RAY DIFFRACTION98.39
2.17-2.260.3821270.31932515X-RAY DIFFRACTION96.53
2.26-2.360.28121240.24382537X-RAY DIFFRACTION97.72
2.36-2.480.28961310.21332547X-RAY DIFFRACTION98.67
2.48-2.640.24561410.22422587X-RAY DIFFRACTION98.88
2.64-2.840.26131290.2172611X-RAY DIFFRACTION99.46
2.84-3.130.26891450.2192612X-RAY DIFFRACTION99.82
3.13-3.580.22061420.21022632X-RAY DIFFRACTION99.89
3.58-4.510.19271360.17172669X-RAY DIFFRACTION99.93
4.51-52.890.21011460.17522756X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: -17.6815669303 Å / Origin y: -23.04652623 Å / Origin z: -5.68092413672 Å
111213212223313233
T0.221026449989 Å2-0.0138823203203 Å20.0119600700158 Å2-0.376691911803 Å20.0339086160219 Å2--0.21148089955 Å2
L0.909504894169 °2-0.021141887963 °20.37414192268 °2-0.65077319685 °20.25865957523 °2--3.58271826602 °2
S0.023731313009 Å °0.0523126629792 Å °0.10452556437 Å °-0.10636495944 Å °-0.0167292372677 Å °-0.0166812789234 Å °-0.345818885666 Å °0.0554341523762 Å °-0.00634821322287 Å °
Refinement TLS groupSelection details: all

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