[English] 日本語
Yorodumi
- PDB-5nc0: The 0.91 A resolution structure of the L16G mutant of cytochrome ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nc0
TitleThe 0.91 A resolution structure of the L16G mutant of cytochrome c prime from Alcaligenes xylosoxidans, complexed with nitric oxide
ComponentsCytochrome c'
KeywordsOXIDOREDUCTASE / nitric oxide / cytochrome / homodimer
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, class II / Cytochrome c prime / Cytochrome C' / Cytochrome c class II profile. / 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 / NITRITE ION / NITRATE ION / Cytochrome c'
Similarity search - Component
Biological speciesAlcaligenes xylosoxydans xylosoxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.91 Å
AuthorsStrange, R. / Hough, M. / Antonyuk, S. / Rustage, N.
CitationJournal: Inorg Chem / Year: 2017
Title: Distinguishing Nitro vs Nitrito Coordination in Cytochrome c' Using Vibrational Spectroscopy and Density Functional Theory.
Authors: Nilsson, Z.N. / Mandella, B.L. / Sen, K. / Kekilli, D. / Hough, M.A. / Moenne-Loccoz, P. / Strange, R.W. / Andrew, C.R.
History
DepositionMar 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,94813
Polymers13,5751
Non-polymers1,37312
Water4,143230
1
A: Cytochrome c'
hetero molecules

A: Cytochrome c'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,89726
Polymers27,1512
Non-polymers2,74624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area7270 Å2
ΔGint-141 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.430, 52.430, 183.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Cytochrome c'


Mass: 13575.336 Da / Num. of mol.: 1 / Mutation: L16G
Source method: isolated from a genetically manipulated source
Details: residue PCA is pyroglutamic acid - 2-pyrrolidone-5-carboxylic acid
Source: (gene. exp.) Alcaligenes xylosoxydans xylosoxydans (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P00138

-
Non-polymers , 7 types, 242 molecules

#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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: AMMONIUM SULPHATE, TRIS PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.7872 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7872 Å / Relative weight: 1
ReflectionResolution: 0.91→44.07 Å / Num. obs: 106845 / % possible obs: 99.5 % / Redundancy: 8 % / CC1/2: 0.999 / Rpim(I) all: 0.023 / Net I/σ(I): 16.1
Reflection shellResolution: 0.91→0.93 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4889 / CC1/2: 0.547 / Rpim(I) all: 0.564 / % possible all: 93.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDS20161101data reduction
Aimless0.5.27data scaling
REFMAC5.8.0158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YL7

2yl7


Resolution: 0.91→44.07 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.378 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.014 / ESU R Free: 0.014 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13177 5378 5 %RANDOM
Rwork0.12453 ---
obs0.1249 101466 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 8.977 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.07 Å20 Å2
2---0.15 Å20 Å2
3---0.48 Å2
Refinement stepCycle: 1 / Resolution: 0.91→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 87 230 1253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021091
X-RAY DIFFRACTIONr_bond_other_d0.0030.02991
X-RAY DIFFRACTIONr_angle_refined_deg2.4712.0771484
X-RAY DIFFRACTIONr_angle_other_deg1.07532306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.755138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77424.3941
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.01715170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.307155
X-RAY DIFFRACTIONr_chiral_restr0.0960.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211264
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02209
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_it0.7160.598521
X-RAY DIFFRACTIONr_mcbond_other0.6230.593518
X-RAY DIFFRACTIONr_mcangle_it0.9760.9653
X-RAY DIFFRACTIONr_mcangle_other0.9840.904654
X-RAY DIFFRACTIONr_scbond_it1.530.839570
X-RAY DIFFRACTIONr_scbond_other1.530.839570
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8161.169827
X-RAY DIFFRACTIONr_long_range_B_refined2.5789.4241366
X-RAY DIFFRACTIONr_long_range_B_other2.5779.431367
X-RAY DIFFRACTIONr_rigid_bond_restr5.07532081
X-RAY DIFFRACTIONr_sphericity_free19.6535156
X-RAY DIFFRACTIONr_sphericity_bonded6.35452149
LS refinement shellResolution: 0.91→0.934 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 359 -
Rwork0.273 7086 -
obs--95.31 %

+
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