[English] 日本語
Yorodumi
- PDB-1cno: STRUCTURE OF PSEUDOMONAS NAUTICA CYTOCHROME C552, BY MAD METHOD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cno
TitleSTRUCTURE OF PSEUDOMONAS NAUTICA CYTOCHROME C552, BY MAD METHOD
ComponentsCYTOCHROME C552
KeywordsELECTRON TRANSPORT / PSEUDOMONAS NAUTICA / X RAY STRUCTURE / MULTIWAVELENGTH ANOMALOUS DISPERSION / HEME / CYTOCHROME C
Function / homology
Function and homology information


periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c-552
Similarity search - Component
Biological speciesMarinobacter hydrocarbonoclasticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsBrown, K. / Nurizzo, D. / Cambillau, C.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: MAD structure of Pseudomonas nautica dimeric cytochrome c552 mimicks the c4 Dihemic cytochrome domain association.
Authors: Brown, K. / Nurizzo, D. / Besson, S. / Shepard, W. / Moura, J. / Moura, I. / Tegoni, M. / Cambillau, C.
History
DepositionAug 3, 1998Processing site: BNL
Revision 1.0Jul 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYTOCHROME C552
B: CYTOCHROME C552
C: CYTOCHROME C552
D: CYTOCHROME C552
E: CYTOCHROME C552
F: CYTOCHROME C552
G: CYTOCHROME C552
H: CYTOCHROME C552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,91019
Polymers69,6868
Non-polymers5,22411
Water13,115728
1
A: CYTOCHROME C552
B: CYTOCHROME C552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6584
Polymers17,4212
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-57 kcal/mol
Surface area7790 Å2
MethodPISA
2
C: CYTOCHROME C552
D: CYTOCHROME C552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6584
Polymers17,4212
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-54 kcal/mol
Surface area7900 Å2
MethodPISA
3
E: CYTOCHROME C552
F: CYTOCHROME C552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9357
Polymers17,4212
Non-polymers1,5135
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-54 kcal/mol
Surface area7750 Å2
MethodPISA
4
G: CYTOCHROME C552
H: CYTOCHROME C552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6584
Polymers17,4212
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-55 kcal/mol
Surface area7930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.800, 121.800, 136.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11F-294-

HOH

21G-297-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.95569, -0.284576, 0.075316), (-0.286032, 0.958177, -0.009077), (-0.069583, -0.030218, -0.997118)11.82894, 5.23245, 117.60955
2given(-0.974396, -0.135802, 0.179192), (0.145224, -0.98857, 0.040489), (0.171645, 0.065475, 0.982981)3.3046, 63.94316, -4.29454
3given(-0.796097, -0.352278, -0.492067), (-0.363452, 0.928452, -0.076676), (0.483872, 0.117801, -0.867174)52.6272, -16.57082, 101.27085

-
Components

#1: Protein
CYTOCHROME C552


Mass: 8710.734 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Details: C HEME IN EACH MONOMER LINKED BY CYS 14 AND 17 AND HIS 18 AND MET 60 AS AXIAL LIGANDS
Source: (natural) Marinobacter hydrocarbonoclasticus (bacteria)
Cellular location: PERIPLASM / Strain: 617 / References: UniProt: P82903
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 728 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE 3 C-TERMINAL SIDE CHAINS WERE NOT SEEN IN THE DENSITY MAP AND WERE REPLACED BY ALANINE. LEU 36 ...THE 3 C-TERMINAL SIDE CHAINS WERE NOT SEEN IN THE DENSITY MAP AND WERE REPLACED BY ALANINE. LEU 36 CHANGED TO LYS 36; GLY 79 CHANGED TO TYR 79 COMPARED TO REF. EURO. J. BIOL. (1994), 224, 1011-1017.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.36 Å3/Da / Density % sol: 72 %
Description: THE STARTING MODEL WAS THE C552 FROM PS. NAUTICA SOLVED BY MAD METHOD AT 2.8A RESOLUTION
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.7 Mammonium sulfate1reservoir
2100 mMsodium citrate1reservoirpH5.6
312 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.756
DetectorType: THOMPSON
Detector: X RAY IMAGE INTENSIFIER (THOMPSON) + PRINCETON CCD DETECTOR
Date: May 1, 1998 / Details: FOCUSED BEAM TOROIDAL
RadiationMonochromator: LAUE BRAGG / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.756 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 58183 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 18.84 Å2 / Rsym value: 0.108 / Net I/σ(I): 6.3
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2 / Rsym value: 0.246 / % possible all: 94.3
Reflection
*PLUS
Rmerge(I) obs: 0.094
Reflection shell
*PLUS
Rmerge(I) obs: 0.229

-
Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
DENZOdata reduction
PROWdata reduction
CCP4(SCALA)data scaling
X-PLOR3.843phasing
RefinementResolution: 2.2→15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 400000 / Data cutoff low absF: 1.0E-5 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1708 3 %RANDOM
Rwork0.1784 ---
obs0.1784 58148 99.31 %-
Displacement parametersBiso mean: 19.26 Å2
Refine analyzeLuzzati d res low obs: 2.2 Å / Luzzati sigma a obs: 0.13 Å
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4846 0 362 728 5936
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.269
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.59
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.841
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2374 220 3.02 %
Rwork0.2073 6730 -
obs--95.41 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2083
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.267 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.593
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.841

+
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