[English] 日本語
Yorodumi
- PDB-1u2w: Crystal Structure of the Staphylococcus aureus pI258 CadC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u2w
TitleCrystal Structure of the Staphylococcus aureus pI258 CadC
ComponentsCadmium efflux system accessory protein
KeywordsDNA BINDING PROTEIN / cadmium / lead / repressor / soft metal ion resistance / ArsR/SmtB family
Function / homology
Function and homology information


response to cadmium ion / DNA-binding transcription factor activity / DNA binding / metal ion binding
Similarity search - Function
ArsR-type transcription regulator, HTH motif / Bacterial regulatory proteins, arsR family signature. / : / Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...ArsR-type transcription regulator, HTH motif / Bacterial regulatory proteins, arsR family signature. / : / Bacterial regulatory protein, arsR family / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cadmium resistance transcriptional regulatory protein CadC
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsYe, J. / Kandegedara, A. / Martin, P. / Rosen, B.P.
CitationJournal: J.Bacteriol. / Year: 2005
Title: Crystal structure of the Staphylococcus aureus pI258 CadC Cd(II)/Pb(II)/Zn(II)-responsive repressor
Authors: Ye, J. / Kandegedara, A. / Martin, P. / Rosen, B.P.
History
DepositionJul 20, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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 / _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.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.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cadmium efflux system accessory protein
B: Cadmium efflux system accessory protein
C: Cadmium efflux system accessory protein
D: Cadmium efflux system accessory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2127
Polymers55,0164
Non-polymers1963
Water8,467470
1
A: Cadmium efflux system accessory protein
B: Cadmium efflux system accessory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6394
Polymers27,5082
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-111 kcal/mol
Surface area10590 Å2
MethodPISA
2
C: Cadmium efflux system accessory protein
D: Cadmium efflux system accessory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5733
Polymers27,5082
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-72 kcal/mol
Surface area9570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.536, 116.536, 41.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
DetailsThe biological assembly is a dimer consisting Chain A and B or Chain C and D.

-
Components

#1: Protein
Cadmium efflux system accessory protein / CadC repressor


Mass: 13753.957 Da / Num. of mol.: 4 / Mutation: C11G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cadC / Plasmid: pYSCM2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20047
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulfate, sodium citrate, methanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9000, 0.9795, 0.9793, 0.9563
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 22, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97951
30.97931
40.95631
ReflectionResolution: 1.9→119 Å / Num. all: 44819 / Num. obs: 40693 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.045 / Net I/σ(I): 28
Reflection shellResolution: 1.9→1.95 Å / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→32.63 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.475 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26112 2152 5 %RANDOM
Rwork0.20496 ---
all0.236 44819 --
obs0.20774 40693 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2--0.91 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 3 470 3624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223180
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9594281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1545398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7825.168149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.24315607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7191519
X-RAY DIFFRACTIONr_chiral_restr0.1480.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022311
X-RAY DIFFRACTIONr_nbd_refined0.2370.21756
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22279
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2333
X-RAY DIFFRACTIONr_metal_ion_refined0.160.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.230
X-RAY DIFFRACTIONr_mcbond_it1.2611.52055
X-RAY DIFFRACTIONr_mcangle_it1.99623193
X-RAY DIFFRACTIONr_scbond_it3.39431246
X-RAY DIFFRACTIONr_scangle_it4.9624.51088
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 165 -
Rwork0.278 3039 -
obs--99.5 %
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)
10.46360.0390.25280.46430.60062.0697-0.0683-0.0010.0519-0.13760.01320.0806-0.8340.05970.0550.15740.0297-0.0164-0.16480.0316-0.024229.70147.4260.813
21.2415-0.5715-1.40481.37510.94934.918-0.09430.0328-0.07110.19190.0878-0.0879-0.17150.55550.0065-0.0423-0.0322-0.0146-0.0420.0338-0.004236.69635.82-1.513
31.5358-0.83921.94741.5708-1.54376.21430.42250.1875-0.2326-0.15210.00240.13921.43990.198-0.42490.19160.0374-0.0949-0.1188-0.06470.034827.5313.247-20.916
40.4404-0.5831-0.28652.2964-1.79963.30060.03490.1103-0.17910.05740.29510.29840.4095-0.5713-0.3301-0.1201-0.08880.0316-0.05990.07470.060317.31525.215-23.536
50.0005-0.00040.00010.0004-0.00020.0005000-0.00010-0.00010000.0001-0.00010.0001-0.0002-0.0001-0.000220.68546.891-5.026
62.52440.1541-1.24330.0484-0.21781.12850.15861.044-0.41931.042-0.019-0.26070.5598-0.6145-0.13950.03020.05590.0356-0.08840.04710.01630.13430.1414.33
70.88580.5573-0.31560.5799-0.13220.13170.0090.27870.1937-0.01950.06720.14630.09280.2213-0.07620.07320.08170.01270.0572-0.030.003223.70630.569-16.301
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 11911 - 119
2X-RAY DIFFRACTION2BB11 - 11711 - 117
3X-RAY DIFFRACTION3CC17 - 11417 - 114
4X-RAY DIFFRACTION4DD11 - 11811 - 118
5X-RAY DIFFRACTION5AE5011
6X-RAY DIFFRACTION6BF5021
7X-RAY DIFFRACTION7CG5031

+
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