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- PDB-8a91: Crystal structure of a staphylococcal orthologue of CYP134A1 (CYP... -

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Basic information

Entry
Database: PDB / ID: 8a91
TitleCrystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a heme-coordinated fragment
ComponentsCytochrome P450 protein
KeywordsOXIDOREDUCTASE / CYPX / CYP134 / staphylococcus / fragment / heme / cyclic leucine / CLL / diketopiperazine / iron
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 / 1H-indol-3-ylmethanamine / Cytochrome P450 protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 heme-coordinated fragment
Authors: Snee, M.
History
DepositionJun 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 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)46,9295
Polymers45,9751
Non-polymers9554
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-40 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.154, 108.574, 105.768
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-LC9 / 1H-indol-3-ylmethanamine


Mass: 146.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.15M Lithium sulfate, 0.05M Magnesium chloride hexahydrate, 0.1M HEPES pH 7.8, 20% v/v PEG Smear High
Temp details: 4C

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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: 1.85→55.38 Å / Num. obs: 40202 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 30.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.032 / Rrim(I) all: 0.115 / Net I/σ(I): 12.6
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 13.4 % / Rmerge(I) obs: 2 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2451 / CC1/2: 0.793 / Rpim(I) all: 0.785 / % 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: 7OW9

7ow9


Resolution: 1.85→55.38 Å / SU ML: 0.2587 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.2682
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2279 2042 5.1 %
Rwork0.2058 37996 -
obs0.2069 40038 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.55 Å2
Refinement stepCycle: LAST / Resolution: 1.85→55.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 64 209 3438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283356
X-RAY DIFFRACTIONf_angle_d0.49954557
X-RAY DIFFRACTIONf_chiral_restr0.0379503
X-RAY DIFFRACTIONf_plane_restr0.0044578
X-RAY DIFFRACTIONf_dihedral_angle_d6.9776457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.41791310.36012490X-RAY DIFFRACTION99.54
1.89-1.940.39121250.34252503X-RAY DIFFRACTION99.51
1.94-1.990.34031430.33042510X-RAY DIFFRACTION99.21
1.99-2.050.33111290.28592502X-RAY DIFFRACTION99.62
2.05-2.120.23811480.252468X-RAY DIFFRACTION99.02
2.12-2.190.23411500.22552499X-RAY DIFFRACTION99.7
2.19-2.280.24131320.21292494X-RAY DIFFRACTION99.55
2.28-2.390.25691380.20812523X-RAY DIFFRACTION99.59
2.39-2.510.23641390.21662529X-RAY DIFFRACTION99.59
2.51-2.670.30231360.22592513X-RAY DIFFRACTION99.89
2.67-2.870.24081260.21672548X-RAY DIFFRACTION99.89
2.87-3.160.25161370.21542549X-RAY DIFFRACTION99.96
3.16-3.620.21071330.19112572X-RAY DIFFRACTION100
3.62-4.560.15951390.16082594X-RAY DIFFRACTION100
4.56-55.380.19321360.17892702X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: -17.7483680921 Å / Origin y: -23.356345485 Å / Origin z: -6.03811596646 Å
111213212223313233
T0.196155140957 Å2-0.00983436366957 Å20.00879152017983 Å2-0.304495483846 Å20.0463197803216 Å2--0.235772408233 Å2
L0.945410722446 °20.118248700521 °20.279523698 °2-0.75973998647 °20.496718134232 °2--3.90291742891 °2
S-0.00767243745431 Å °0.090706970379 Å °0.13781099591 Å °-0.109458189917 Å °-0.00440906716319 Å °-0.030049507835 Å °-0.388090284762 Å °0.110762136015 Å °0.00844984636279 Å °
Refinement TLS groupSelection details: all

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