[English] 日本語
Yorodumi
- PDB-1k2o: Cytochrome P450Cam with Bound BIS(2,2'-BIPYRIDINE)-(5-METHYL-2-2'... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k2o
TitleCytochrome P450Cam with Bound BIS(2,2'-BIPYRIDINE)-(5-METHYL-2-2'-BIPYRIDINE)-C2-ADAMANTANE RUTHENIUM (II)
ComponentsCytochrome P450CAM
KeywordsOXIDOREDUCTASE / P450 / monooxygenase / electron transfer / energy transfer / fluorinated aromatics / biphenyl / adamantane / ruthenium channel / substrate-binding
Function / homology
Function and homology information


camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor 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
CACODYLATE ION / PROTOPORPHYRIN IX CONTAINING FE / Chem-RFA / Chem-RFB / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsDunn, A.R. / Dmochowski, I.J. / Bilwes, A.M. / Gray, H.B. / Crane, B.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Probing the open state of cytochrome P450cam with ruthenium-linker substrates.
Authors: Dunn, A.R. / Dmochowski, I.J. / Bilwes, A.M. / Gray, H.B. / Crane, B.R.
History
DepositionSep 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome P450CAM
B: Cytochrome P450CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,33313
Polymers93,1142
Non-polymers6,21911
Water12,502694
1
A: Cytochrome P450CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5986
Polymers46,5571
Non-polymers3,0415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7357
Polymers46,5571
Non-polymers3,1786
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.870, 67.050, 72.520
Angle α, β, γ (deg.)71.16, 65.20, 62.31
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Cytochrome P450CAM / Camphor 5-monooxygenase


Mass: 46556.816 Da / Num. of mol.: 2 / Mutation: C334A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): TBY / References: UniProt: P00183, camphor 5-monooxygenase

-
Non-polymers , 5 types, 705 molecules

#2: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-RFA / DELTA-BIS(2,2'-BIPYRIDINE)-(5-METHYL-2-2'-BIPYRIDINE)-C2-ADAMANTANE RUTHENIUM (II)


Mass: 1075.277 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C54H75F8N7Ru
#5: Chemical ChemComp-RFB / LAMBDA-BIS(2,2'-BIPYRIDINE)-(5-METHYL-2-2'-BIPYRIDINE)-C2-ADAMANTANE RUTHENIUM (II)


Mass: 1075.277 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C54H75F8N7Ru
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 277 K / Method: slow cooling / pH: 7.5
Details: Hepes, PEG, KCL, DTT, pH 7.5, slow cooling, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.396 mMprotein1drop
220 mMHEPES1drop
3100 mM1dropKCl
41 mMdithiothreitol1drop
50.1 Msodium cacodylate1reservoir
6200 mM1reservoirKCl
78-15 %(w/v)PEG80001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.72 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 24, 2000
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72 Å / Relative weight: 1
ReflectionResolution: 1.65→28 Å / Num. all: 111741 / Num. obs: 111741 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19 Å2 / Rsym value: 0.038 / Net I/σ(I): 16.4
Reflection shellResolution: 1.65→1.71 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.292 / % possible all: 97
Reflection
*PLUS
Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.292

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2cpp

2cpp


Resolution: 1.65→19.81 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 819940.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 8939 8 %RANDOM
Rwork0.21 ---
all-111741 --
obs-111741 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.6776 Å2 / ksol: 0.349301 e/Å3
Displacement parametersBiso mean: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.47 Å2-1.46 Å2-4.58 Å2
2---3.8 Å22.63 Å2
3---0.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.65→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6424 0 386 694 7504
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d1.32
X-RAY DIFFRACTIONc_mcbond_it0.411.5
X-RAY DIFFRACTIONc_mcangle_it0.732
X-RAY DIFFRACTIONc_scbond_it0.522
X-RAY DIFFRACTIONc_scangle_it0.762.5
LS refinement shellResolution: 1.65→1.71 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.287 940 8.5 %
Rwork0.292 10099 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM19X.HEMEWATER.TOP
X-RAY DIFFRACTION3WATER.PARAMRFA.TOP
X-RAY DIFFRACTION4RFA.PARRFB.TOP
X-RAY DIFFRACTION5RFB.PARION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 8 % / Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.32
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.287 / % reflection Rfree: 8.5 % / Rfactor Rwork: 0.292

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more