[English] 日本語
Yorodumi
- PDB-1b0y: MUTANT H42Q OF HIPIP FROM CHROMATIUM VINOSUM AT 0.93A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b0y
TitleMUTANT H42Q OF HIPIP FROM CHROMATIUM VINOSUM AT 0.93A
ComponentsPROTEIN (HIPIP)
KeywordsELECTRON TRANSPORT / ELECTRON TRANSFER PROTEIN / ATOMIC RESOLUTION / DIRECT METHODS IRON-SULPHUR CLUSTER / METALLOPROTEIN
Function / homology
Function and homology information


aerobic electron transport chain / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / metal ion binding
Similarity search - Function
High potential iron-sulphur protein / High-Potential Iron-Sulfur Protein; Chain A / High potential iron-sulfur protein / High potential iron-sulphur protein / High potential iron-sulphur protein superfamily / High potential iron-sulfur proteins family profile. / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Few Secondary Structures / Irregular
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / High-potential iron-sulfur protein
Similarity search - Component
Biological speciesAllochromatium vinosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 0.93 Å
AuthorsSheldrick, G.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Ab initio solution and refinement of two high-potential iron protein structures at atomic resolution.
Authors: Parisini, E. / Capozzi, F. / Lubini, P. / Lamzin, V. / Luchinat, C. / Sheldrick, G.M.
#1: Journal: J.Biol.Chem. / Year: 1974
Title: Two-Angstrom Crystal Structure of Oxidized Chromatium High Potential Iron Protein
Authors: Carter, C.W. / Kraut, J. / Freer, S.T. / Xuong, N.-H. / Alden, R.A. / Bartsch, R.G.
History
DepositionNov 15, 1998Processing site: RCSB
Revision 1.0Dec 16, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 17, 2016Group: Atomic model / Derived calculations
Revision 1.4Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (HIPIP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2542
Polymers8,9021
Non-polymers3521
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.681, 41.675, 41.913
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PROTEIN (HIPIP)


Mass: 8901.924 Da / Num. of mol.: 1 / Mutation: H42Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allochromatium vinosum (bacteria) / Strain: XL1BLUE / Plasmid: PLEHP20 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1BLUE / References: UniProt: P00260
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 30 %
Crystal growpH: 5.3 / Details: 2M AMMONIUM SULPHATE, 40 MM TRI 180 MM KCL, pH 5.3
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
220 mMTris-HCl1drop
390 mM1dropKCl
41 Mammonium sulfate1drop
52 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9116
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 24, 1996 / Details: BENT CRYSTAL
RadiationMonochromator: GE SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 0.93→20 Å / Num. obs: 39854 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.5
Reflection shellResolution: 0.93→0.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.1 / % possible all: 88.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 402616
Reflection shell
*PLUS
Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 5.3

-
Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 0.93→20 Å / Num. parameters: 7536 / Num. restraintsaints: 8810 / Cross valid method: FREE R / σ(F): 0
StereochEM target val spec case: NO RESTRAINTS ON PROSTHETIC GROUP (RESIDUE 87)
Stereochemistry target values: ENGH AND HUBER
Details: NO RESTRAINTS ON PROSTHETIC GROUP B23 (A**2) : ESTIMATED OVERALL COORDINATE ERROR.
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 2097 5 %RANDOM
all0.1548 41951 --
obs0.1529 -93 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 37 / Occupancy sum hydrogen: 594 / Occupancy sum non hydrogen: 800
Refinement stepCycle: LAST / Resolution: 0.93→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms623 0 8 206 837
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_zero_chiral_vol0.116
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.064
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.033
X-RAY DIFFRACTIONs_approx_iso_adps0.077
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.136 / Rfactor Rwork: 0.153
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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