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- PDB-2rfc: Ligand bound (4-phenylimidazole) Crystal Structure of a Cytochrom... -

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Basic information

Entry
Database: PDB / ID: 2rfc
TitleLigand bound (4-phenylimidazole) Crystal Structure of a Cytochrome P450 from the Thermoacidophilic Archaeon Picrophilus Torridus
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / CYTOCHROME P450 THERMOPHILE / Heme / Iron / Metal-binding / Monooxygenase
Function / homology
Function and homology information


unspecific monooxygenase / aromatase activity / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / 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
PROTOPORPHYRIN IX CONTAINING FE / 4-PHENYL-1H-IMIDAZOLE / Cytochrome P450
Similarity search - Component
Biological speciesPicrophilus torridus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHo, W.W. / Li, H. / Poulos, T.L. / Nishida, C.R. / Ortiz de Montellano, P.R.
CitationJournal: Biochemistry / Year: 2008
Title: Crystal Structure and Properties of CYP231A2 from the Thermoacidophilic Archaeon Picrophilus torridus.
Authors: Ho, W.W. / Li, H. / Nishida, C.R. / Ortiz de Montellano, P.R. / Poulos, T.L.
History
DepositionSep 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: Cytochrome P450
B: Cytochrome P450
C: Cytochrome P450
D: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,50012
Polymers158,4584
Non-polymers3,0438
Water34219
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3753
Polymers39,6141
Non-polymers7612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3753
Polymers39,6141
Non-polymers7612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3753
Polymers39,6141
Non-polymers7612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3753
Polymers39,6141
Non-polymers7612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.520, 141.010, 101.030
Angle α, β, γ (deg.)90.00, 90.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cytochrome P450


Mass: 39614.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Picrophilus torridus (archaea) / Plasmid: pCWori / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6KZ68, unspecific monooxygenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-PIM / 4-PHENYL-1H-IMIDAZOLE


Mass: 144.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05M sodium chloride, 0.1M HEPES, 30% polyethyleneglycol 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 4, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→41.85 Å / Num. obs: 23827 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 8.72
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 1.93 / Num. unique all: 1211 / Rsym value: 0.471 / % possible all: 98.1

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→41.85 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 718335.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.334 1141 4.8 %RANDOM
Rwork0.229 ---
obs0.229 23572 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.7006 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 42 Å2
Baniso -1Baniso -2Baniso -3
1--7.6 Å20 Å2-7.39 Å2
2--2.92 Å20 Å2
3---4.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.81 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 3.1→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10995 0 216 19 11230
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_mcbond_it7.291.5
X-RAY DIFFRACTIONc_mcangle_it11.32
X-RAY DIFFRACTIONc_scbond_it7.722
X-RAY DIFFRACTIONc_scangle_it11.192.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.424 214 5.4 %
Rwork0.312 3777 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2param19x.heme2water.top
X-RAY DIFFRACTION3water_rep.paramtoph19x.heme2
X-RAY DIFFRACTION4all.parall.top

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