[English] 日本語
Yorodumi
- PDB-7c90: Crystal structure of Cytochrome CL from the marine methylotrophic... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c90
TitleCrystal structure of Cytochrome CL from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT (Ma-CytcL)
ComponentsCytochrome c, mono-and diheme variant
KeywordsELECTRON TRANSPORT / Methanol Oxidation system / Marine Bacterium / Methylophaga aminisulfidivorans MPT
Function / homology
Function and homology information


periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome cL / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
: / HEME C / Cytochrome c, mono-and diheme variant
Similarity search - Component
Biological speciesMethylophaga aminisulfidivorans MP (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsGhosh, S. / Dhanasingh, I. / Lee, S.H.
CitationJournal: J Microbiol Biotechnol. / Year: 2020
Title: Crystal Structure of CytochromecLfrom the Aquatic Methylotrophic BacteriumMethylophaga aminisulfidivoransMPT.
Authors: Ghosh, S. / Dhanasingh, I. / Ryu, J. / Kim, S.W. / Lee, S.H.
History
DepositionJun 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.2Nov 29, 2023Group: 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 1.3Oct 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 c, mono-and diheme variant
B: Cytochrome c, mono-and diheme variant
C: Cytochrome c, mono-and diheme variant
D: Cytochrome c, mono-and diheme variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,75731
Polymers86,4864
Non-polymers4,27127
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The peak elutes with a molecular weight corresponding to monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14050 Å2
ΔGint-297 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.760, 76.060, 66.440
Angle α, β, γ (deg.)90.000, 106.850, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Cytochrome c, mono-and diheme variant


Mass: 21621.459 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylophaga aminisulfidivorans MP (bacteria)
Gene: MAMP_01204 / Production host: Methylophaga aminisulfidivorans (bacteria) / References: UniProt: F5SWR8

-
Non-polymers , 7 types, 399 molecules

#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Fe
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1600 mM sodium/potassium phosphate monobasic, 100 mM HEPES/sodium hydroxide pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97941 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 32914 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.042 / Rrim(I) all: 0.111 / Χ2: 2.836 / Net I/σ(I): 11.7 / Num. measured all: 237733
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.13-2.177.40.6315950.9010.2480.6781.74100
2.17-2.217.50.56516680.9190.2210.6071.816100
2.21-2.257.40.51316280.9190.2020.5512.036100
2.25-2.297.50.47816540.940.1870.5131.931100
2.29-2.347.50.38816320.9580.1520.4171.89100
2.34-2.47.50.3416310.9620.1330.3662.079100
2.4-2.467.50.28616530.9710.1120.3072.207100
2.46-2.537.50.25216150.9810.0990.2712.253100
2.53-2.67.50.22616430.9810.0890.2432.398100
2.6-2.687.40.20216590.9840.080.2172.604100
2.68-2.787.40.17516520.9860.0690.1882.671100
2.78-2.897.40.14516470.990.0570.1562.861100
2.89-3.027.30.12716300.9920.0510.1373.189100
3.02-3.187.20.10816490.9930.0430.1173.597100
3.18-3.387.10.09516420.9950.0390.1033.775100
3.38-3.646.90.08116730.9950.0330.0874.111100
3.64-4.016.80.0716380.9960.0290.0764.16999.9
4.01-4.596.80.06316510.9970.0260.0684.11599.9
4.59-5.786.70.0616780.9970.0250.0653.905100
5.78-506.10.0616760.9960.0260.0654.16697.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D0W

2d0w


Resolution: 2.13→30.58 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.622 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1998 1953 6.1 %RANDOM
Rwork0.1478 ---
obs0.1509 30244 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.04 Å2 / Biso mean: 37.923 Å2 / Biso min: 17.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20.06 Å2
2---0.42 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: final / Resolution: 2.13→30.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4683 0 266 372 5321
Biso mean--41.96 49.2 -
Num. residues----597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135097
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184424
X-RAY DIFFRACTIONr_angle_refined_deg2.1131.7296945
X-RAY DIFFRACTIONr_angle_other_deg1.3651.64610316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6615593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2524.685254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14515788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.281512
X-RAY DIFFRACTIONr_chiral_restr0.1170.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025708
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021044
LS refinement shellResolution: 2.13→2.185 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 128 -
Rwork0.164 2041 -
all-2169 -
obs--89.96 %

+
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