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- PDB-1iwi: Putidaredoxin-Binding Stablilizes an Active Conformer of Cytochro... -

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Basic information

Entry
Database: PDB / ID: 1iwi
TitlePutidaredoxin-Binding Stablilizes an Active Conformer of Cytochrome P450cam in its Reduced State; Crystal Structure of Cytochrome P450cam
ComponentsCYTOCHROME P450-CAM
KeywordsOXIDOREDUCTASE / Putidaredoxin Binding site / Cytochrome P450cam / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / 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
CAMPHOR / PROTOPORPHYRIN IX CONTAINING FE / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsNagano, S. / Shimada, H. / Tarumi, A. / Hishiki, T. / Kimata-Ariga, Y. / Egawa, T. / Park, S.-Y. / Adachi, S. / Shiro, Y. / Ishimura, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Biochemistry / Year: 2003
Title: Infrared spectroscopic and mutational studies on putidaredoxin-induced conformational changes in ferrous CO-P450cam
Authors: Nagano, S. / Shimada, H. / Tarumi, A. / Hishiki, T. / Kimata-Ariga, Y. / Egawa, T. / Suematsu, M. / Park, S.-Y. / Adachi, S. / Shiro, Y. / Ishimura, Y.
History
DepositionMay 15, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.4Dec 27, 2023Group: 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.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_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-CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4893
Polymers46,7201
Non-polymers7692
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.160, 104.330, 36.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME P450-CAM


Mass: 46720.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: PUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00183, camphor 5-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: Chemical ChemComp-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 293 K / Method: small tubes / pH: 6
Details: ammonium sulfate, pH 6.0, SMALL TUBES, temperature 293K
Crystal grow
*PLUS
Temperature: 12-15 ℃ / pH: 7 / Method: unknown / Details: Poulos, T.L., (1982) J. Biol. Chem., 257, 10427.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mM11KPi
2250 mM11KCl
350 mMdithiothreitol11
466-70 %satammonium sulphate12

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 20, 2001 / Details: mirrors
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. all: 163126 / Num. obs: 27250 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 13.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 11 / Num. unique all: 3231 / % possible all: 79.8
Reflection
*PLUS
Num. measured all: 163126 / Rmerge(I) obs: 0.032
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 79.8 % / Rmerge(I) obs: 0.061

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
X-PLOR3.851refinement
CCP4(SCALA)data scaling
X-PLORphasing
RefinementResolution: 2→15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1367 5 %RANDOM
Rwork0.177 ---
obs-27147 94.5 %-
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 54 126 3388
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_improper_angle_d0.84
X-RAY DIFFRACTIONx_mcbond_it2.131.5
X-RAY DIFFRACTIONx_mcangle_it3.212
X-RAY DIFFRACTIONx_scbond_it4.312
X-RAY DIFFRACTIONx_scangle_it6.512.5
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 201 5.4 %
Rwork0.225 3512 -
obs--78.5 %
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 15 Å / Num. reflection obs: 27215 / % reflection Rfree: 5 % / Rfactor obs: 0.173 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.134
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.84
LS refinement shell
*PLUS
Rfactor obs: 0.225

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