[English] 日本語
Yorodumi
- PDB-1cp4: FORMATION, CRYSTAL STRUCTURE, AND REARRANGEMENT OF A CYTOCHROME P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cp4
TitleFORMATION, CRYSTAL STRUCTURE, AND REARRANGEMENT OF A CYTOCHROME P450-CAM IRON-PHENYL COMPLEX
ComponentsCYTOCHROME P450-CAM
KeywordsOXIDOREDUCTASE(OXYGENASE)
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
BENZENE / PROTOPORPHYRIN IX CONTAINING FE / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsRaag, R. / Poulos, T.L.
Citation
Journal: Biochemistry / Year: 1990
Title: Formation, crystal structure, and rearrangement of a cytochrome P-450cam iron-phenyl complex.
Authors: Raag, R. / Swanson, B.A. / Poulos, T.L. / Ortiz de Montellano, P.R.
#1: Journal: To be Published
Title: X-Ray Crystallographic Structural Studies of Cytochrome P450-Cam+
Authors: Raag, R. / Poulos, T.L.
#2: Journal: Biochemistry / Year: 1991
Title: Crystal Structures of Cytochrome P450-Cam Complexed with Camphane, Thiocamphor, and Adamantane: Factors Controlling P450 Substrate Hydroxylation
Authors: Raag, R. / Poulos, T.L.
#3: Journal: Biochemistry / Year: 1989
Title: Crystal Structure of the Carbon Monoxy-Substrate-Cytochrome P450-Cam Ternary Complex
Authors: Raag, R. / Poulos, T.L.
#4: Journal: Biochemistry / Year: 1989
Title: The Structural Basis for Substrate-Induced Changes in Redox Potential and Spin Equilibrium in Cytochrome P450(Cam)
Authors: Raag, R. / Poulos, T.L.
History
DepositionJun 4, 1991Processing site: BNL
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYTOCHROME P450-CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2833
Polymers46,5891
Non-polymers6952
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.670, 103.900, 36.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES PRO 89, PRO 100, AND PRO 106 ARE CIS PROLINES.

-
Components

#1: Protein CYTOCHROME P450-CAM


Mass: 46588.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / 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-BNZ / BENZENE


Mass: 78.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal grow
*PLUS
Temperature: 12-15 ℃ / Method: batch method / Details: took Poulos et al., 1982 from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.05 mlprotein11
20.05 mlammonium sulfate11

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.87 Å / % possible obs: 55 % / Num. measured all: 128716 / Rmerge(I) obs: 0.074

-
Processing

SoftwareName: PROFFT / Classification: refinement
RefinementRfactor obs: 0.199 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3215 0 43 209 3467
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.031
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection all: 27666 / Num. reflection obs: 20765 / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_dihedral_angle_d / Dev ideal: 0.036

+
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