[English] 日本語
Yorodumi
- PDB-1osd: crystal structure of Oxidized MerP from Ralstonia metallidurans CH34 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1osd
Titlecrystal structure of Oxidized MerP from Ralstonia metallidurans CH34
Componentshypothetical protein MerP
KeywordsMETAL BINDING PROTEIN / Mercury resistance / Perisplasm / structural genomics
Function / homologyAlpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSerre, L. / Rossy, E. / Pebay-Peyroula, E. / Cohen-Addad, C. / Coves, J.
CitationJournal: J.MOL.BIOL. / Year: 2004
Title: Crystal Structure of the Oxidized Form of the Periplasmic Mercury-binding Protein MerP from Ralstonia metallidurans CH34
Authors: Serre, L. / Rossy, E. / Pebay-Peyroula, E. / Cohen-Addad, C. / Coves, J.
History
DepositionMar 19, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 4, 2018Group: Data collection / Category: diffrn_source / struct_biol / Item: _diffrn_source.type
Revision 1.4Oct 25, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein MerP
B: hypothetical protein MerP


Theoretical massNumber of molelcules
Total (without water)15,0612
Polymers15,0612
Non-polymers00
Water2,252125
1
A: hypothetical protein MerP


Theoretical massNumber of molelcules
Total (without water)7,5311
Polymers7,5311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein MerP


Theoretical massNumber of molelcules
Total (without water)7,5311
Polymers7,5311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.810, 52.612, 60.006
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 5 / Auth seq-ID: 1 - 70 / Label seq-ID: 1 - 70

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological assembly is a monomer

-
Components

#1: Protein hypothetical protein MerP / MerP


Mass: 7530.622 Da / Num. of mol.: 2 / Fragment: residues 1-72
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / Gene: MerP / Plasmid: pET-3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: GenBank: 22980851
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEGMME5000, Sodium acetate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: osmic multi-layer mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 9437 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.048 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.1 / Num. unique all: 655 / Rsym value: 0.282 / % possible all: 97

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(SCALA)data scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AFI

1afi


Resolution: 2→39.53 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.418 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26754 938 9.9 %RANDOM
Rwork0.1923 ---
all0.19976 ---
obs0.1997 8498 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.569 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 0 125 1215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0221103
X-RAY DIFFRACTIONr_bond_other_d0.0020.021043
X-RAY DIFFRACTIONr_angle_refined_deg2.3061.9711496
X-RAY DIFFRACTIONr_angle_other_deg1.21332466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1365142
X-RAY DIFFRACTIONr_chiral_restr0.1480.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021157
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02177
X-RAY DIFFRACTIONr_nbd_refined0.2140.2234
X-RAY DIFFRACTIONr_nbd_other0.2550.21198
X-RAY DIFFRACTIONr_nbtor_other0.0910.2744
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.217
X-RAY DIFFRACTIONr_mcbond_it1.4841.5728
X-RAY DIFFRACTIONr_mcangle_it2.27321209
X-RAY DIFFRACTIONr_scbond_it3.5933375
X-RAY DIFFRACTIONr_scangle_it5.7974.5287
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
412medium positional0.180.5
511loose positional0.535
412medium thermal1.472
511loose thermal2.1610
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.44 71
Rwork0.255 599

+
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