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- PDB-2rfb: Crystal Structure of a Cytochrome P450 from the Thermoacidophilic... -

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Basic information

Entry
Database: PDB / ID: 2rfb
TitleCrystal 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 / Cytochrome P450
Similarity search - Component
Biological speciesPicrophilus torridus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 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: Advisory / Refinement description / 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,07710
Polymers118,8433
Non-polymers2,2347
Water2,432135
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5195
Polymers39,6141
Non-polymers9054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2312
Polymers39,6141
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3273
Polymers39,6141
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.790, 168.460, 88.230
Angle α, β, γ (deg.)90.00, 96.25, 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.: 3
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2M ammonium sulfate, 0.1M HEPES, 2% polyethylene glycol 400, pH 7.5, 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: 1.7400, 1.6475
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 17, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.741
21.64751
ReflectionResolution: 2.5→48.51 Å / Num. obs: 48305 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 31.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 2 / Rsym value: 0.661 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→48.51 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.917 / SU B: 20.72 / SU ML: 0.228 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.453 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26844 2414 5 %RANDOM
Rwork0.21147 ---
obs0.21434 45855 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.811 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å2-2.13 Å2
2--2.21 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8181 0 149 135 8465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228510
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6192.01611516
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55851000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57524.412408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.58151557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9761549
X-RAY DIFFRACTIONr_chiral_restr0.1090.21231
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026400
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.23957
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.25759
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2345
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7271.55147
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23428128
X-RAY DIFFRACTIONr_scbond_it1.73333809
X-RAY DIFFRACTIONr_scangle_it2.5744.53382
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.495→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 152 -
Rwork0.302 3327 -
obs--95.24 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.85580.4318-0.22031.5456-0.09742.76470.0106-0.5086-0.15210.1418-0.04880.001-0.05480.03090.0382-0.41190.06570.0331-0.33480.0242-0.2694-14.078633.2443-42.8779
22.8836-0.5371.98682.44990.54227.5056-0.1718-0.0945-0.0449-0.2589-0.21410.2967-0.3178-1.03760.3859-0.09680.0754-0.0043-0.022-0.1001-0.1361-16.51354.805-83.8507
33.16810.0407-0.07343.9920.91812.38870.05580.0775-0.08280.30720.301-0.15780.38790.3977-0.35690.30870.1949-0.3147-0.1587-0.24540.12921.452381.3368-40.989
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 352
2X-RAY DIFFRACTION2B10 - 352
3X-RAY DIFFRACTION3C12 - 352

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