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- PDB-3b4x: Crystal Structure Analysis of Sulfolobus tokodaii strain7 cytochr... -

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Basic information

Entry
Database: PDB / ID: 3b4x
TitleCrystal Structure Analysis of Sulfolobus tokodaii strain7 cytochrom P450
Components367aa long hypothetical cytochrome P450
KeywordsOXIDOREDUCTASE / hem protein / Heme / Iron / Metal-binding / Monooxygenase
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / 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 tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsKamitori, S. / Yoshida, H. / Ohtaki, A. / Nakamura, N.
CitationJournal: To be Published
Title: Monooxygenation by Thermophilic Cytochrome P450 via Direct Electron Transfer from NADH without Redox Partner
Authors: Matsumura, H. / Nakamura, N. / Ohtaki, A. / Yoshida, H. / Kamitori, S. / Yohda, M. / Ohno, H.
History
DepositionOct 24, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 367aa long hypothetical cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0312
Polymers42,4151
Non-polymers6161
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.286, 55.168, 51.415
Angle α, β, γ (deg.)90.00, 93.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 367aa long hypothetical cytochrome P450


Mass: 42414.809 Da / Num. of mol.: 1 / Mutation: A367T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: Strain 7 / Gene: ST1148 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q972I2, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 20% PEG 4000, 0.2M ammonium sulphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 4, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→39.58 Å / Num. all: 26501 / Num. obs: 25507 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.5
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.277 / Num. unique all: 1862 / % possible all: 67

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UE8

1ue8


Resolution: 1.94→39.58 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 158941.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2509 9.8 %RANDOM
Rwork0.203 ---
all0.205 26501 --
obs0.203 25507 90.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.2546 Å2 / ksol: 0.387161 e/Å3
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1-8.48 Å20 Å2-8.56 Å2
2---6.35 Å20 Å2
3----2.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.94→39.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2985 0 43 85 3113
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 1.94→2.09 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.254 336 9 %
Rwork0.234 3382 -
obs-3718 66.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4hem.paramhem.top

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