[English] 日本語
Yorodumi
- PDB-2y3b: Co-bound form of Cupriavidus metallidurans CH34 CnrXs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y3b
TitleCo-bound form of Cupriavidus metallidurans CH34 CnrXs
ComponentsNICKEL AND COBALT RESISTANCE PROTEIN CNRR
KeywordsMETAL BINDING PROTEIN
Function / homologyHeavy-metal resistance protein / Heavy-metal resistance / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1490 / Four Helix Bundle (Hemerythrin (Met), subunit A) / periplasmic space / Up-down Bundle / Mainly Alpha / : / Nickel and cobalt resistance protein CnrR
Function and homology information
Biological speciesCUPRIAVIDUS METALLIDURANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.554 Å
AuthorsTrepreau, J. / Girard, E. / Maillard, A.P. / de Rosny, E. / Petit-Haertlein, I. / Kahn, R. / Coves, J.
Citation
#1: Journal: FEBS Lett. / Year: 2008
Title: X-Ray Structure of the Metal-Sensor Cnrx in Both the Apo-and Copper-Bound Forms.
Authors: Pompidor, G. / Maillard, A.P. / Girard, E. / Gambarelli, S. / Kahn, R. / Coves, J.
History
DepositionDec 20, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_dist_value / _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_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_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: NICKEL AND COBALT RESISTANCE PROTEIN CNRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6475
Polymers13,3121
Non-polymers3354
Water2,756153
1
A: NICKEL AND COBALT RESISTANCE PROTEIN CNRR
hetero molecules

A: NICKEL AND COBALT RESISTANCE PROTEIN CNRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,29410
Polymers26,6242
Non-polymers6708
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3770 Å2
ΔGint-21.4 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.033, 33.033, 196.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2102-

HOH

21A-2103-

HOH

-
Components

#1: Protein NICKEL AND COBALT RESISTANCE PROTEIN CNRR / NICKEL AND COBALT RESISTANCE PROTEIN CNRX


Mass: 13311.874 Da / Num. of mol.: 1 / Fragment: METAL-SENSOR DOMAIN, RESIDUES 31-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CUPRIAVIDUS METALLIDURANS (bacteria) / Strain: CH34 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37975
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 28 % / Description: NONE
Crystal growpH: 8
Details: 0.1M TRIS PH8, 1.6M AMMONIUM SULFATE, 15% GLYCEROL.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.033
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 18, 2009 / Details: KB FOCUSING MIRRORS
RadiationMonochromator: SI111 CHANNEL-CUT / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.55→33.04 Å / Num. obs: 16626 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 14.75 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.2
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.4 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.554→32.575 Å / SU ML: 0.17 / σ(F): 1.37 / Phase error: 17.61 / Stereochemistry target values: ML / Details: RESIDUES 31-37 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2038 829 5 %
Rwork0.1762 --
obs0.1776 16579 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.412 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.2983 Å20 Å20 Å2
2---6.2983 Å20 Å2
3----14.0547 Å2
Refinement stepCycle: LAST / Resolution: 1.554→32.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms884 0 19 153 1056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017942
X-RAY DIFFRACTIONf_angle_d1.5831273
X-RAY DIFFRACTIONf_dihedral_angle_d17.856374
X-RAY DIFFRACTIONf_chiral_restr0.605139
X-RAY DIFFRACTIONf_plane_restr0.009174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5541-1.65140.26631290.21332455X-RAY DIFFRACTION95
1.6514-1.77890.22631340.18762554X-RAY DIFFRACTION100
1.7789-1.95790.22681380.17442620X-RAY DIFFRACTION100
1.9579-2.24120.18051380.15992614X-RAY DIFFRACTION100
2.2412-2.82340.19971410.17092673X-RAY DIFFRACTION100
2.8234-32.58180.18931490.1732834X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.83630.4101-0.24041.47680.3149-0.12980.1353-0.2850.22140.2624-0.07910.1925-0.2174-0.1514-0.06120.2807-0.01340.01210.2426-0.03160.246617.41259.99335.8741
2-0.00220.03040.04620.2844-0.24040.49860.1056-0.0689-0.0287-0.0463-0.05740.27790.1065-0.2849-0.05270.2463-0.0317-0.02780.2638-0.01090.272811.8077-0.770626.9364
30.11810.02880.00560.06170.08620.4250.02880.0196-0.08390.06360.0906-0.0780.676-0.4111-0.11440.3557-0.0901-0.01890.3210.02870.252218.1578-4.256445.9756
40.24430.00370.05620.11770.09650.26540.0501-0.03790.09070.1184-0.0225-0.06160.1550.0085-0.00320.2879-0.0198-0.00830.2617-0.00920.275427.4549-1.768265.7921
50.07030.10210.1098-0.18090.05180.7752-0.08760.00970.05960.07030.0481-0.13680.31060.3702-0.00540.30750.0787-0.04170.2737-0.01470.243329.7236-2.151750.4038
60.1102-0.1036-0.0833-0.0162-0.0389-0.02020.03260.02070.0512-0.017-0.00160.0562-0.062-0.0221-0.02080.2202-0.0103-0.0150.20620.00410.224122.54356.760527.6112
70.6672-0.21570.47751.68140.21350.32510.1434-0.46820.01560.2341-0.0555-0.01090.1377-0.218-0.15350.3-0.0363-0.02880.31740.00220.255627.097212.680739.3689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 38:50)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 51:65)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 66:80)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 81:98)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 99:114)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 115:142)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 143:148)

+
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