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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


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 / 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

Downloads & links

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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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