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- PDB-8ae8: Crystal structure of a staphylococcal orthologue of CYP134A1 (CYP... -

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Basic information

Entry
Database: PDB / ID: 8ae8
TitleCrystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a heme-coordinated fragment
ComponentsCytochrome P450 protein
KeywordsOXIDOREDUCTASE / CLL / Pulcherrimin / CYP134A1 / fragment / heme / iron / CYPX / P450 / cytochrome / staphylococcus
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 / 1~{H}-indol-5-ylmethanamine / Cytochrome P450 protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsSnee, M. / Katariya, M.
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 heme-coordinated fragment
Authors: Snee, M. / Katariya, M.
History
DepositionJul 12, 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)46,7373
Polymers45,9751
Non-polymers7632
Water2,864159
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)80.889, 107.841, 105.695
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 / Plasmid: pET47b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: A0A380DQV1, pulcherriminic acid synthase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-LUU / 1~{H}-indol-5-ylmethanamine


Mass: 146.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.05M Magnesium chloride hexahydrate, 0.05M sodium citrate tribasic, 0.1M Bis-tris propane pH 7.8, 22.5% 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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.92→55.19 Å / Num. obs: 35640 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 37.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.027 / Net I/σ(I): 13.1
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.661 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2358 / CC1/2: 0.936 / Rpim(I) all: 0.472 / % 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→55.19 Å / SU ML: 0.2642 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2269 1775 5.02 %
Rwork0.1923 33610 -
obs0.1941 35385 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.16 Å2
Refinement stepCycle: LAST / Resolution: 1.92→55.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3149 0 54 159 3362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00963326
X-RAY DIFFRACTIONf_angle_d0.90314512
X-RAY DIFFRACTIONf_chiral_restr0.0502498
X-RAY DIFFRACTIONf_plane_restr0.0079575
X-RAY DIFFRACTIONf_dihedral_angle_d7.4647451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.42471210.38032535X-RAY DIFFRACTION98.81
1.97-2.030.37221520.32422528X-RAY DIFFRACTION98.86
2.03-2.10.31181350.28522532X-RAY DIFFRACTION98.81
2.1-2.170.28341510.23132542X-RAY DIFFRACTION98.79
2.17-2.260.25611240.21522565X-RAY DIFFRACTION99.12
2.26-2.360.23761230.19652557X-RAY DIFFRACTION99.15
2.36-2.480.28321360.21072556X-RAY DIFFRACTION99.23
2.48-2.640.2881370.21672580X-RAY DIFFRACTION99.38
2.64-2.840.26491350.21412599X-RAY DIFFRACTION99.74
2.84-3.130.2911420.22112598X-RAY DIFFRACTION99.93
3.13-3.580.21211410.19422627X-RAY DIFFRACTION99.93
3.58-4.510.16241350.14962647X-RAY DIFFRACTION100
4.51-55.190.17681430.16072744X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: -17.3249465673 Å / Origin y: -23.1245692334 Å / Origin z: -5.89876145513 Å
111213212223313233
T0.192305733547 Å2-0.0172474759716 Å20.00781336353596 Å2-0.419175694503 Å20.0397962111261 Å2--0.252455554492 Å2
L0.866117233574 °20.0612282793232 °20.476159163791 °2-0.787686172562 °20.361282627594 °2--4.01360137628 °2
S0.00391256566511 Å °0.0280992840725 Å °0.0945984185893 Å °-0.0894045881831 Å °-0.029179881177 Å °-0.0214077982644 Å °-0.362989424378 Å °0.064205828895 Å °0.0265886393112 Å °
Refinement TLS groupSelection details: all

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