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- PDB-8aa7: Crystal structure of a staphylococcal orthologue of CYP134A1 (CYP... -

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Basic information

Entry
Database: PDB / ID: 8aa7
TitleCrystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a heme coordinated fragment
ComponentsCytochrome P450 protein
KeywordsOXIDOREDUCTASE / CYP / P450 / CYP134A1 / CLL / Cyclic / Diketopiperazine / pulcherrimin / staphylococcus / aureus
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 / 2,3,4,9-tetrahydro-1~{H}-pyrido[3,4-b]indole / Cytochrome P450 protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSnee, M. / Katariya, M. / Levy, C. / Leys, D.
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
DepositionJun 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)46,7633
Polymers45,9751
Non-polymers7892
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-23 kcal/mol
Surface area17170 Å2
Unit cell
Length a, b, c (Å)80.241, 106.412, 105.677
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-WYH / 2,3,4,9-tetrahydro-1~{H}-pyrido[3,4-b]indole


Mass: 172.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2 / 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.: 255 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.05M Magnesium chloride hexahydrate, 0.05M Sodium citrate tribasic dihydrate, 0.1M Bis-Tris propane pH7.8, 22.5 % v/v PEG Smear High

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 4C / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 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: 2.05→54.79 Å / Num. obs: 28754 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 37.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.027 / Rrim(I) all: 0.098 / Net I/σ(I): 15.4
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2190 / CC1/2: 0.941 / Rpim(I) all: 0.234 / Rrim(I) all: 0.82 / % 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: 2.05→47.52 Å / SU ML: 0.2294 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.7751
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2248 1380 4.81 %
Rwork0.1749 27282 -
obs0.1773 28662 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.95 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3181 0 56 255 3492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01053374
X-RAY DIFFRACTIONf_angle_d0.88954579
X-RAY DIFFRACTIONf_chiral_restr0.0493505
X-RAY DIFFRACTIONf_plane_restr0.0068582
X-RAY DIFFRACTIONf_dihedral_angle_d7.2155464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.120.3411530.28072644X-RAY DIFFRACTION99.33
2.12-2.210.27351500.21812681X-RAY DIFFRACTION99.61
2.21-2.310.21721290.19332712X-RAY DIFFRACTION99.47
2.31-2.430.22351420.18472676X-RAY DIFFRACTION99.65
2.43-2.580.24391240.19512726X-RAY DIFFRACTION99.79
2.58-2.780.22781300.17462729X-RAY DIFFRACTION100
2.78-3.060.23271500.18722703X-RAY DIFFRACTION99.93
3.06-3.510.22231260.17442766X-RAY DIFFRACTION99.97
3.51-4.410.20041330.15132771X-RAY DIFFRACTION100
4.42-47.520.21551430.1642874X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: -17.197048431 Å / Origin y: -22.7340135464 Å / Origin z: -5.66737327573 Å
111213212223313233
T0.229043965707 Å2-0.00819331615799 Å20.00710497119092 Å2-0.202964543571 Å20.0292579569446 Å2--0.277449803534 Å2
L1.07749320483 °20.0344138210394 °20.55283906469 °2-0.338641897917 °20.356504323535 °2--3.36950594604 °2
S0.00332705047456 Å °0.0216667659326 Å °0.10941888541 Å °-0.0673451563378 Å °-0.0160449987618 Å °-0.0110847013301 Å °-0.258179269242 Å °0.0148309725633 Å °0.0102287866288 Å °
Refinement TLS groupSelection details: all

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