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- PDB-6n6q: Crystal structure of a Cytochrome P450 (CYP102L1) -

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Basic information

Entry
Database: PDB / ID: 6n6q
TitleCrystal structure of a Cytochrome P450 (CYP102L1)
ComponentsCytochrome P450 (CYP102L1)
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


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, E-class, group I / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CACODYLATE ION / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesMycobacterium phage Adler (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsFollmer, A.H. / Poulos, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM57353 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: On the occurrence of cytochrome P450 in viruses.
Authors: Lamb, D.C. / Follmer, A.H. / Goldstone, J.V. / Nelson, D.R. / Warrilow, A.G. / Price, C.L. / True, M.Y. / Kelly, S.L. / Poulos, T.L. / Stegeman, J.J.
History
DepositionNov 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 (CYP102L1)
B: Cytochrome P450 (CYP102L1)
C: Cytochrome P450 (CYP102L1)
D: Cytochrome P450 (CYP102L1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,74213
Polymers214,5914
Non-polymers3,1519
Water2,180121
1
A: Cytochrome P450 (CYP102L1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4013
Polymers53,6481
Non-polymers7532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 (CYP102L1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5384
Polymers53,6481
Non-polymers8903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P450 (CYP102L1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4013
Polymers53,6481
Non-polymers7532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytochrome P450 (CYP102L1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4013
Polymers53,6481
Non-polymers7532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.899, 174.090, 203.469
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-503-

CAC

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Components

#1: Protein
Cytochrome P450 (CYP102L1)


Mass: 53647.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium phage Adler (virus) / Gene: MaF1660_ph0012 / Production host: Escherichia coli (E. coli) / References: UniProt: V5UQK0
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Sodium Cacodylate pH 6.5, 1.26 M AmSO4, 4.2 % (v/v) Dextran Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.734 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2017
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.734 Å / Relative weight: 1
ReflectionResolution: 2.5→66.56 Å / Num. obs: 73160 / % possible obs: 99.16 % / Redundancy: 2 % / Biso Wilson estimate: 61.8981945929 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.05555 / Net I/av σ(I): 7.55 / Net I/σ(I): 7.55
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 2 % / Rmerge(I) obs: 0.8252 / Mean I/σ(I) obs: 0.83 / Num. unique obs: 7248 / CC1/2: 0.396 / % possible all: 99.49

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→66.56 Å / SU ML: 0.447753736588 / Cross valid method: FREE R-VALUE / σ(F): 1.32681066748 / Phase error: 32.6464373538
RfactorNum. reflection% reflection
Rfree0.288701962304 3764 5.1479136179 %
Rwork0.230250244149 --
obs0.233229845074 73117 99.1672430864 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 69.0998341316 Å2
Refinement stepCycle: LAST / Resolution: 2.5→66.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14326 0 197 121 14644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022273291649814884
X-RAY DIFFRACTIONf_angle_d0.50704119409820252
X-RAY DIFFRACTIONf_chiral_restr0.03894362530782151
X-RAY DIFFRACTIONf_plane_restr0.003694695745912662
X-RAY DIFFRACTIONf_dihedral_angle_d14.21396508138861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.53170.3909041372541270.3624711946092595X-RAY DIFFRACTION99.5246800731
2.5317-2.5650.3849928080821530.3540721236862521X-RAY DIFFRACTION99.4791666667
2.565-2.60010.3948486338981310.3410496293312556X-RAY DIFFRACTION99.5922905856
2.6001-2.63730.4043646865671310.3173762059892531X-RAY DIFFRACTION99.1433891993
2.6373-2.67660.4328284425651150.3273814800812578X-RAY DIFFRACTION98.6808354709
2.6766-2.71850.3691617066111310.3085851833922545X-RAY DIFFRACTION99.1111111111
2.7185-2.7630.39804506241510.2994541987242513X-RAY DIFFRACTION98.6301369863
2.763-2.81070.3381733700471570.2938061148952504X-RAY DIFFRACTION98.5190670122
2.8107-2.86180.3208544948251360.277766022662551X-RAY DIFFRACTION99.3713017751
2.8618-2.91680.3301964712381460.2887385329422541X-RAY DIFFRACTION99.7031539889
2.9168-2.97640.3582054497811130.291338950232586X-RAY DIFFRACTION99.8520162782
2.9764-3.04110.3575202789741340.3014901450342580X-RAY DIFFRACTION99.4868035191
3.0411-3.11180.3426259812451390.290619730812581X-RAY DIFFRACTION99.5243322356
3.1118-3.18960.3242661352411550.2704716809892549X-RAY DIFFRACTION99.6315401621
3.1896-3.27590.3084810620251440.2662158032822544X-RAY DIFFRACTION99.7402597403
3.2759-3.37230.341472116241390.2630455220172538X-RAY DIFFRACTION98.8187523071
3.3723-3.48110.321128842311380.2546792585562554X-RAY DIFFRACTION98.6441920117
3.4811-3.60550.3359326751941470.2358996935932560X-RAY DIFFRACTION99.4854832782
3.6055-3.74990.286846387951370.2329120159892606X-RAY DIFFRACTION99.8543866036
3.7499-3.92050.2758427436451500.22221155632574X-RAY DIFFRACTION99.9633027523
3.9205-4.12720.2831379513251360.2052894626182583X-RAY DIFFRACTION99.6700879765
4.1272-4.38570.2662384303321450.1938815392312594X-RAY DIFFRACTION99.4914638576
4.3857-4.72430.2080795046761380.1715729202422580X-RAY DIFFRACTION98.6569872958
4.7243-5.19950.2843402769551350.1882316678082563X-RAY DIFFRACTION97.6828385228
5.1995-5.95150.2387167230921390.2143667747812599X-RAY DIFFRACTION99.0951863916
5.9515-7.49660.2424372041061430.2189851344522606X-RAY DIFFRACTION97.8988603989
7.4966-66.58710.2379743862191540.1859750564172721X-RAY DIFFRACTION98.4589041096

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