[English] 日本語
Yorodumi
- PDB-4ek1: Crystal Structure of Electron-Spin Labeled Cytochrome P450cam -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ek1
TitleCrystal Structure of Electron-Spin Labeled Cytochrome P450cam
ComponentsCamphor 5-monooxygenase
KeywordsOXIDOREDUCTASE / electron spin / MTSL / double electron electron resonance / camphor / Cytochrome P450 fold / Monooxidase / Putidaredoxin
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
CAMPHOR / PROTOPORPHYRIN IX CONTAINING FE / : / Chem-MTN / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsLee, Y.-T. / Goodin, D.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Double electron-electron resonance shows cytochrome P450cam undergoes a conformational change in solution upon binding substrate.
Authors: Stoll, S. / Lee, Y.T. / Zhang, M. / Wilson, R.F. / Britt, R.D. / Goodin, D.B.
History
DepositionApr 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Camphor 5-monooxygenase
B: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,45811
Polymers93,0492
Non-polymers2,4099
Water7,440413
1
A: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8616
Polymers46,5251
Non-polymers1,3375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5975
Polymers46,5251
Non-polymers1,0724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.020, 101.530, 72.980
Angle α, β, γ (deg.)90.000, 107.390, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Camphor 5-monooxygenase / / Cytochrome P450-cam / Cytochrome P450cam


Mass: 46524.688 Da / Num. of mol.: 2 / Mutation: S48C,C58S,C85S,C136S,S190C,C285S,C334A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00183, camphor 5-monooxygenase

-
Non-polymers , 5 types, 422 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CAM / CAMPHOR / Camphor


Mass: 152.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL / MTSL


Mass: 264.385 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H18NO3S2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 279 K / Method: sitting-drop vapor diffusion / pH: 7.4
Details: 12% PEG 8000, 0.1M Tris, pH 7.4, 0.2M KCl, 1mM camphor, sitting-drop vapor diffusion, temperature 279K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2012
RadiationMonochromator: SIDE SCATTERING I-BEAM BENT SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 1.97→47.303 Å / Num. all: 55395 / Num. obs: 54475 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 20.33 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.97-2.0730.4161.82417979410.41698.6
2.07-2.23.10.2942.62364875250.29499.1
2.2-2.353.20.2273.32247870880.22798.7
2.35-2.543.20.1814.12097566000.18198.9
2.54-2.783.20.1355.51936660590.13598.6
2.78-3.113.20.0997.21760254960.09998.5
3.11-3.593.20.068101539148070.06898.2
3.59-4.43.20.05610.71287240740.05697.5
4.4-6.223.10.05410960930810.05495.3
6.22-47.3033.40.0459.5611518040.04599.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.15 Å47.3 Å
Translation2.15 Å47.3 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→10 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.1743 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8515 / SU B: 4.387 / SU ML: 0.123 / SU R Cruickshank DPI: 0.2017 / SU Rfree: 0.1729 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.202 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2738 5.1 %RANDOM
Rwork0.204 ---
obs0.207 53689 98.34 %-
all-54938 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 46.06 Å2 / Biso mean: 20.3927 Å2 / Biso min: 8.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0 Å2-1.46 Å2
2---1.29 Å20 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.97→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6390 0 146 413 6949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226786
X-RAY DIFFRACTIONr_angle_refined_deg1.4922.0179289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.495830
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24123.951324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.857151113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6021553
X-RAY DIFFRACTIONr_chiral_restr0.0960.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215277
X-RAY DIFFRACTIONr_mcbond_it0.5721.54087
X-RAY DIFFRACTIONr_mcangle_it1.07726636
X-RAY DIFFRACTIONr_scbond_it1.9132699
X-RAY DIFFRACTIONr_scangle_it3.0744.52641
LS refinement shellResolution: 1.97→2.015 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 207 -
Rwork0.242 3639 -
all-3846 -
obs--98.31 %

+
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