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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


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / 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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