[English] 日本語
Yorodumi
- PDB-5agf: Nitrosyl complex of the D121Q variant of cytochrome c prime from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5agf
TitleNitrosyl complex of the D121Q variant of cytochrome c prime from Alcaligenes xylosoxidans
ComponentsCYTOCHROME C PRIME
KeywordsOXIDOREDUCTASE / PROXIMAL NO / CYTOCHROME / GAS SENSING / NITRIC OXIDE
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c prime, subgroup / Cytochrome c prime / Cytochrome c class II profile. / Cytochrome c, class II / Cytochrome C' / Cytochrome c/b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / NITRIC OXIDE / Cytochrome c'
Similarity search - Component
Biological speciesACHROMOBACTER XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.09 Å
AuthorsGahfoor, D.D. / Kekilli, D. / Abdullah, G.H. / Dworkowski, F.S.N. / Hassan, H.G. / Wilson, M.T. / Hough, M.A. / Strange, R.W.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2015
Title: Hydrogen Bonding of the Dissociated Histidine Ligand is not Required for Formation of a Proximal No Adduct in Cytochrome C'.
Authors: Ghafoor, D.D. / Kekilli, D. / Abdullah, G.H. / Dworkowski, F.S.N. / Hassan, H.G. / Wilson, M.T. / Strange, R.W. / Hough, M.A.
History
DepositionJan 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Atomic model / Other
Revision 1.2Dec 7, 2016Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 2.0Mar 11, 2020Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_status ...entity_poly / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYTOCHROME C PRIME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3894
Polymers13,6441
Non-polymers7453
Water3,495194
1
A: CYTOCHROME C PRIME
hetero molecules

A: CYTOCHROME C PRIME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7788
Polymers27,2892
Non-polymers1,4896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area1460 Å2
ΔGint-28.6 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.239, 53.239, 180.539
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2039-

HOH

21A-2057-

HOH

-
Components

#1: Protein CYTOCHROME C PRIME


Mass: 13644.483 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACHROMOBACTER XYLOSOXIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00138
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.64 Å3/Da / Density % sol: 53.4 % / Description: NONE
Crystal growpH: 7.5 / Details: AMMONIUM SULFATE, HEPES, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2013 / Details: MIRRORS
RadiationMonochromator: SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.09→15.5 Å / Num. obs: 62452 / % possible obs: 97 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.4
Reflection shellResolution: 1.09→1.13 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.2 / % possible all: 76

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.09→46.11 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.351 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18521 3155 5.1 %RANDOM
Rwork0.1695 ---
obs0.17029 59145 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0.2 Å20 Å2
2---0.39 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.09→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms941 0 50 194 1185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021156
X-RAY DIFFRACTIONr_bond_other_d0.0030.021062
X-RAY DIFFRACTIONr_angle_refined_deg2.272.041594
X-RAY DIFFRACTIONr_angle_other_deg1.80132463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8395157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03825.20848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89515181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.558154
X-RAY DIFFRACTIONr_chiral_restr0.1050.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211429
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02257
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6261.515571
X-RAY DIFFRACTIONr_mcbond_other3.6261.513569
X-RAY DIFFRACTIONr_mcangle_it4.8152.308722
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2591.606585
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.28932218
X-RAY DIFFRACTIONr_sphericity_free70.497523
X-RAY DIFFRACTIONr_sphericity_bonded15.87452355
LS refinement shellResolution: 1.09→1.118 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 145 -
Rwork0.295 3163 -
obs--71.66 %

+
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://pdbjlvh1.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