[English] 日本語
Yorodumi
- PDB-2je3: Cytochrome P460 from Nitrosomonas europaea - probable physiologic... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2je3
TitleCytochrome P460 from Nitrosomonas europaea - probable physiological form
ComponentsCYTOCHROME P460
KeywordsMETAL BINDING PROTEIN / HEME P460 / CYTOCHROME P460 / CROSS-LINKED HEME
Function / homology
Function and homology information


Cytochrome P460 / Chalcone isomerase / Cytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HEME C / PHOSPHATE ION / Cytochrome P460
Similarity search - Component
Biological speciesNITROSOMONAS EUROPAEA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPearson, A.R. / Elmore, B.O. / Yang, C. / Ferrara, J.D. / Hooper, A.B. / Wilmot, C.M.
CitationJournal: Biochemistry / Year: 2007
Title: The Crystal Structure of Cytochrome P460 of Nitrosomonas Europaea Reveals a Novel Cytochrome Fold and Heme-Protein Cross-Link.
Authors: Pearson, A.R. / Elmore, B.O. / Yang, C. / Ferrara, J.D. / Hooper, A.B. / Wilmot, C.M.
History
DepositionJan 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYTOCHROME P460
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4325
Polymers20,5281
Non-polymers9034
Water2,486138
1
A: CYTOCHROME P460
hetero molecules

A: CYTOCHROME P460
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,86310
Polymers41,0562
Non-polymers1,8078
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)53.256, 53.256, 127.033
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein CYTOCHROME P460


Mass: 20528.113 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-198
Source method: isolated from a genetically manipulated source
Details: PROTEIN-HEME CROSS-LINK FROM NZ OF LYS 70 TO CHA OF HEC 200. PROTEIN-HEME CROSSLINK FROM SG OF CYS 136 TO CAB OF HEC 200. PROTEIN-HEME CROSSLINK FROM SG OF CYS 139 TO CAC OF HEC 200
Source: (gene. exp.) NITROSOMONAS EUROPAEA (bacteria)
Description: CONTAINS ADDITIONAL N-TERMINAL METHIONINE AND AT THE TERMINUS THE ADDITIONS RESIDUES KLAAALEHHHHHH
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q50927
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRECOMBINANT PROTEIN CONTAINS ADDITIONAL N-TERMINAL METHIONINE AND C-TERMINAL TAG KLAAALEHHHHHH

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.08 %
Description: THE STRUCTURE WAS SOLVED BY SAD USING A DATASET COLLECTED AT CR K-ALPHA. PHASED USING SHELX AND SHARP. THE INITIAL MODEL WAS THEN USED TO PHASE THE HIGHER RESOLUTION CU K-ALPHA DATASET
Crystal growpH: 5.2 / Details: pH 5.20

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: May 5, 2005 / Details: VARIMAX CONFOCAL MAXFLUX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.69→43 Å / Num. obs: 17344 / % possible obs: 80.1 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.1
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 2.8 / % possible all: 15

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INITIAL MODEL FROM SULPHUR SAD STRUCTURE

Resolution: 1.8→43.35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 31-40 AND 82-85 ARE NOT VISIBLE IN THE ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 921 5 %RANDOM
Rwork0.195 ---
obs0.197 17341 91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 58 138 1419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221336
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6532.0571837
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6885162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3824.21157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86615201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.111156
X-RAY DIFFRACTIONr_chiral_restr0.1410.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021024
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.260.2646
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2901
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2104
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0061.5807
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72921277
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2063622
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3674.5554
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 44
Rwork0.296 775

+
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