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

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Basic information

Entry
Database: PDB / ID: 8abo
TitleCrystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a fragment
ComponentsCYPX
KeywordsOXIDOREDUCTASE / CYP / CYPX / Staphylococcus aureus / CLL / Pulcherremin / P450
Function / homology4-PHENYL-1H-IMIDAZOLE / PROTOPORPHYRIN IX CONTAINING FE / NITRATE ION
Function and homology information
Biological speciesStaphylococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 4, 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 ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYPX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8595
Polymers45,9751
Non-polymers8854
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-27 kcal/mol
Surface area17060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.080, 104.425, 104.688
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 CYPX


Mass: 45974.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus (bacteria) / Plasmid: pET47b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
#2: Chemical ChemComp-231 / 4-PHENYL-1H-IMIDAZOLE


Mass: 144.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8N2 / 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: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Ammonium nitrate, 0.1M Bis-Tris propane pH 8.5, 18% 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: 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: 1.97→53.68 Å / Num. obs: 30618 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 34.01 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.02 / Net I/σ(I): 17.5
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2129 / CC1/2: 0.967 / Rpim(I) all: 0.213 / % 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: 1.97→53.68 Å / SU ML: 0.2367 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.0004
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2269 1577 5.17 %
Rwork0.1786 28946 -
obs0.181 30523 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.38 Å2
Refinement stepCycle: LAST / Resolution: 1.97→53.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 62 236 3452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013375
X-RAY DIFFRACTIONf_angle_d1.02964584
X-RAY DIFFRACTIONf_chiral_restr0.0605508
X-RAY DIFFRACTIONf_plane_restr0.0078586
X-RAY DIFFRACTIONf_dihedral_angle_d7.753465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.030.32381310.32082589X-RAY DIFFRACTION99.42
2.03-2.110.3211330.27252606X-RAY DIFFRACTION99.53
2.11-2.190.25021470.21682569X-RAY DIFFRACTION99.56
2.19-2.290.2761340.22292624X-RAY DIFFRACTION99.49
2.29-2.410.2511610.19512582X-RAY DIFFRACTION99.82
2.41-2.560.29121580.18992599X-RAY DIFFRACTION99.82
2.56-2.760.20571430.17422614X-RAY DIFFRACTION99.93
2.76-3.040.24611450.19222637X-RAY DIFFRACTION100
3.04-3.480.21061350.17772660X-RAY DIFFRACTION99.96
3.48-4.380.21341300.14852703X-RAY DIFFRACTION100
4.38-53.680.19221600.15552763X-RAY DIFFRACTION99.93
Refinement TLS params.Method: refined / Origin x: -16.5499592451 Å / Origin y: -22.2090157304 Å / Origin z: -5.93775278281 Å
111213212223313233
T0.317606437473 Å2-0.0340497380333 Å20.0206442678824 Å2-0.27043531743 Å20.0116264172446 Å2--0.170213953881 Å2
L1.3668559059 °20.335172741479 °20.915472261705 °2-1.14749000772 °20.521376686989 °2--2.88719074851 °2
S-0.0716873676814 Å °0.112590641094 Å °0.00631548733612 Å °-0.0994728453992 Å °0.0454078980378 Å °-0.0140724979266 Å °-0.0796422531807 Å °0.083527337692 Å °0.0256336221082 Å °
Refinement TLS groupSelection details: all

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