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- PDB-1io8: Thermophilic cytochrome P450 (CYP119) from sulfolobus solfataricu... -

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Basic information

Entry
Database: PDB / ID: 1io8
TitleThermophilic cytochrome P450 (CYP119) from sulfolobus solfataricus: High resolution structural origin of its thermostability and functional properties
ComponentsCYTOCHROME P450 CYP119
KeywordsOXIDOREDUCTASE / Thermophilic / Cytochromo P450 / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / peroxidase / lactoperoxidase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding / cytoplasm
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 119
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPark, S.-Y. / Yamane, K. / Adachi, S. / Shiro, Y. / Sligar, S.G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Inorg.Biochem. / Year: 2002
Title: Thermophilic cytochrome P450 (CYP119) from Sulfolobus solfataricus: high resolution structure and functional properties
Authors: Park, S.Y. / Yamane, K. / Adachi, S. / Shiro, Y. / Weiss, K.E. / Maves, S.A. / Sligar, S.G.
History
DepositionFeb 8, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME P450 CYP119
B: CYTOCHROME P450 CYP119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0134
Polymers85,7802
Non-polymers1,2332
Water5,098283
1
A: CYTOCHROME P450 CYP119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5062
Polymers42,8901
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYTOCHROME P450 CYP119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5062
Polymers42,8901
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: CYTOCHROME P450 CYP119
hetero molecules

A: CYTOCHROME P450 CYP119
hetero molecules

B: CYTOCHROME P450 CYP119
hetero molecules

B: CYTOCHROME P450 CYP119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,0268
Polymers171,5604
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation2_664-x+1,-y+1,z-1/21
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area11300 Å2
ΔGint-137 kcal/mol
Surface area59680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.522, 85.522, 221.462
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CYTOCHROME P450 CYP119


Mass: 42890.012 Da / Num. of mol.: 2 / Mutation: F24L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: PKWS119 / Production host: Escherichia coli (E. coli) / Strain (production host): TB-1
References: UniProt: Q55080, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one ...References: UniProt: Q55080, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG4000, 0.2M sodium thiocyanate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 48 %
Crystal grow
*PLUS
Temperature: 293 K / pH: 6.4 / Details: Park, S.Y., (2000) Acta Crystallogr., D56, 1173.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1200 mMsodium thiocyanate1reservoir
220 %(w/v)PEG40001reservoir
341 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å
DetectorType: MARRESEARCH / Detector: CCD / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 188348 / Num. obs: 53362 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 16.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.6 / % possible all: 86.2
Reflection
*PLUS
Num. measured all: 188348
Reflection shell
*PLUS
% possible obs: 86.2 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native CYP119

Resolution: 2→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.307 2694 -RANDOM
Rwork0.23 ---
all-53328 --
obs-53328 94.5 %-
Displacement parametersBiso mean: 35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5965 0 86 283 6334
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d25.4
X-RAY DIFFRACTIONx_improper_angle_d0.83
LS refinement shellResolution: 2→2.13 Å
RfactorNum. reflection% reflection
Rfree0.373 423 -
Rwork0.388 --
obs-7895 85.5 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.228 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.83
LS refinement shell
*PLUS
Highest resolution: 2 Å / Rfactor Rfree: 0.373 / Rfactor Rwork: 0.388

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