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- PDB-4fmx: Crystal Structure of Substrate-Bound P450cin -

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Basic information

Entry
Database: PDB / ID: 4fmx
TitleCrystal Structure of Substrate-Bound P450cin
ComponentsP450cin1,8-Cineole 2-endo-monooxygenase
KeywordsOXIDOREDUCTASE / P450 / HEME / MONOOXYGENASE / CINDOXIN
Function / homology
Function and homology information


1,8-cineole 2-endo-monooxygenase / carbazole catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,3,3-TRIMETHYL-2-OXABICYCLO[2.2.2]OCTANE / PROTOPORPHYRIN IX CONTAINING FE / 1,8-cineole 2-endo-monooxygenase
Similarity search - Component
Biological speciesCitrobacter braakii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.554 Å
AuthorsMadrona, Y. / Tripathi, S.M. / Huiying, L. / Poulos, T.L.
CitationJournal: Biochemistry / Year: 2012
Title: Crystal structures of substrate-free and nitrosyl cytochrome p450cin: implications for o(2) activation.
Authors: Madrona, Y. / Tripathi, S. / Li, H. / Poulos, T.L.
History
DepositionJun 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2May 28, 2014Group: Data collection
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P450cin
B: P450cin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,58611
Polymers89,5762
Non-polymers2,0109
Water15,781876
1
A: P450cin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8396
Polymers44,7881
Non-polymers1,0515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: P450cin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7475
Polymers44,7881
Non-polymers9594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.551, 69.259, 122.608
Angle α, β, γ (deg.)90.00, 97.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein P450cin / 1,8-Cineole 2-endo-monooxygenase


Mass: 44787.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter braakii (bacteria) / Gene: CIN A, cinA / Plasmid: pCWori-P450cin / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha / References: UniProt: Q8VQF6

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Non-polymers , 5 types, 885 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CNL / 1,3,3-TRIMETHYL-2-OXABICYCLO[2.2.2]OCTANE / 1,8-CINEOLE / Eucalyptol


Mass: 154.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18O
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 876 / 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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 6-9% PEG 3350, 100mM BisTris pH 6.2, 100mM Lithium Sulfate, 5mM Cineole, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 28, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 136152 / Num. obs: 136152 / % possible obs: 99.2 % / Observed criterion σ(F): 0.02 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 17.1 Å2 / Rsym value: 0.074 / Net I/σ(I): 20.1
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.11 / Num. unique all: 6791 / Rsym value: 0.583 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T2B

1t2b


Resolution: 1.554→34.995 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.47 / Stereochemistry target values: ML
Details: In the B subunit, the carboxyl group of Asp227 comes within covalent bonding distance of the hydroxyl group in Tyr101. The 2mFo-DFc map is continuous in this region. This observation is ...Details: In the B subunit, the carboxyl group of Asp227 comes within covalent bonding distance of the hydroxyl group in Tyr101. The 2mFo-DFc map is continuous in this region. This observation is likely due to an X-ray induced structural change and is not present in the A subunit
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 6849 5.03 %RANDOM
Rwork0.175 ---
obs0.1773 136107 98.96 %-
all-136129 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.24 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6767 Å2-0 Å2-1.2643 Å2
2---0.8227 Å20 Å2
3---0.146 Å2
Refinement stepCycle: LAST / Resolution: 1.554→34.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6298 0 136 876 7310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066633
X-RAY DIFFRACTIONf_angle_d1.1219059
X-RAY DIFFRACTIONf_dihedral_angle_d12.9392420
X-RAY DIFFRACTIONf_chiral_restr0.06981
X-RAY DIFFRACTIONf_plane_restr0.0061166
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.554-1.57170.32352120.25113957416992
1.5717-1.59020.32482350.241642914526100
1.5902-1.60960.31172300.234943544584100
1.6096-1.630.29462160.221443024518100
1.63-1.65140.27382270.19943384565100
1.6514-1.6740.26822370.200542954532100
1.674-1.6980.25442030.193843914594100
1.698-1.72330.24782500.178942694519100
1.7233-1.75020.25511940.182443284522100
1.7502-1.77890.24412230.17784306452999
1.7789-1.80960.26132120.177743494561100
1.8096-1.84250.22642620.15774288455099
1.8425-1.87790.21042130.15944348456199
1.8779-1.91630.22512460.16254306455299
1.9163-1.95790.23551970.15994305450299
1.9579-2.00350.23442460.16624291455299
2.0035-2.05360.21232390.16294325456499
2.0536-2.10910.20952520.15874251450399
2.1091-2.17110.21292560.16124277453399
2.1711-2.24120.21192320.16194349458199
2.2412-2.32130.21832070.15614324453199
2.3213-2.41420.21312280.16044274450299
2.4142-2.52410.19342250.158543614586100
2.5241-2.65710.21792490.157743524601100
2.6571-2.82350.20212440.16764313455799
2.8235-3.04140.21762170.17244369458699
3.0414-3.34720.20832440.16264314455899
3.3472-3.83110.20622270.17054293452097
3.8311-4.82470.18512100.1664311452198
4.8247-34.9950.22672160.23194427464398

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