[English] 日本語
Yorodumi
- PDB-4ggg: Crystal structure of V66A/L68V CzrA in the Zn(II)bound state. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ggg
TitleCrystal structure of V66A/L68V CzrA in the Zn(II)bound state.
ComponentsRepressor protein
KeywordsTRANSCRIPTION regulator / Zn(II) binding protein / transcriptional regulator / ArsR/SmtB family of transcriptional regulators / Zn(II) sensing transcriptional regulator
Function / homology
Function and homology information


DNA-binding transcription factor activity / metal ion binding
Similarity search - Function
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
Repressor protein / Repressor protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsCampanello, G.C. / Ma, Z. / Grossoehme, N.E. / Chakrovorty, D.K. / Guerra, A.J. / Ye, Y. / Dann III, C.E. / Merz Jr., K.M. / Giedroc, D.P.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Allosteric inhibition of a zinc-sensing transcriptional repressor: insights into the arsenic repressor (ArsR) family.
Authors: Campanello, G.C. / Ma, Z. / Grossoehme, N.E. / Guerra, A.J. / Ward, B.P. / Dimarchi, R.D. / Ye, Y. / Dann, C.E. / Giedroc, D.P.
History
DepositionAug 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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: Repressor protein
B: Repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8696
Polymers23,6372
Non-polymers2324
Water2,036113
1
A: Repressor protein
hetero molecules

A: Repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9698
Polymers23,6372
Non-polymers3336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3180 Å2
ΔGint-106 kcal/mol
Surface area9530 Å2
MethodPISA
2
B: Repressor protein
hetero molecules

B: Repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7684
Polymers23,6372
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3180 Å2
ΔGint-105 kcal/mol
Surface area9450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.286, 50.198, 85.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-322-

HOH

21A-340-

HOH

-
Components

#1: Protein Repressor protein /


Mass: 11818.431 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: N315 / Gene: czrA, SA1947 / Plasmid: pET-CzrA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q7A4C3, UniProt: A0A0H3JNF1*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PEG 8000, NaCl, Ches, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293 K, temperature 293.K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: Osmic mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.998→26.669 Å / Num. all: 14056 / Num. obs: 13543 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.2 % / % possible all: 94.2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1R1V

1r1v


Resolution: 1.998→26.669 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 1358 9.95 %Random
Rwork0.1727 ---
all0.1778 14056 --
obs0.1778 -96.78 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.446 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.4294 Å2-0 Å20 Å2
2---6.6904 Å20 Å2
3---1.261 Å2
Refinement stepCycle: LAST / Resolution: 1.998→26.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 4 113 1565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051476
X-RAY DIFFRACTIONf_angle_d0.8031985
X-RAY DIFFRACTIONf_dihedral_angle_d13.997542
X-RAY DIFFRACTIONf_chiral_restr0.057236
X-RAY DIFFRACTIONf_plane_restr0.003250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9984-2.06980.30531130.24841069X-RAY DIFFRACTION87
2.0698-2.15260.25971340.20991175X-RAY DIFFRACTION95
2.1526-2.25060.28111360.17781188X-RAY DIFFRACTION96
2.2506-2.36920.2541390.17961212X-RAY DIFFRACTION97
2.3692-2.51750.23611320.17651236X-RAY DIFFRACTION98
2.5175-2.71170.22141360.17571225X-RAY DIFFRACTION98
2.7117-2.98420.22451380.17691253X-RAY DIFFRACTION99
2.9842-3.41530.22221460.18131270X-RAY DIFFRACTION100
3.4153-4.30.21221420.15511284X-RAY DIFFRACTION100
4.3-26.67140.19171420.15831381X-RAY DIFFRACTION100
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)
16.0688-5.9383-4.18145.87584.40215.1489-0.06610.7762-0.903-0.2994-0.30860.77270.6988-0.76320.34950.3316-0.0135-0.04780.293-0.02990.226-8.4168-5.24831.163
23.455-0.4571.60467.69951.18467.9507-0.04190.18160.1176-0.32710.0665-0.1394-0.16420.3992-0.02810.14050.00070.03380.171-0.02780.13074.7309-3.7926-16.3102
38.6837-5.288-5.91217.45845.25484.6534-0.07720.1106-0.4274-0.1256-0.25760.91490.3118-0.19830.33780.23880.0094-0.02990.1939-0.01710.2533-3.5823-9.8673-15.6269
45.997-0.3264.66577.3199-1.15034.0461-0.08460.53320.0711-0.14540.04860.1643-0.9438-0.49860.14810.15670.0431-0.0060.214-0.05570.1297-8.58890.4744-16.9186
52.22133.29453.63035.20665.59946.0660.19480.33520.0265-0.10780.2320.0095-0.23790.3847-0.28420.20290.045-0.04680.2327-0.01330.2187-6.38820.9988-19.8343
69.2375-3.23962.96938.8965-0.00954.95470.16250.05850.026-0.0482-0.043-0.43490.21110.3714-0.11130.1808-0.02790.060.17990.01320.09226.00894.9441-1.0819
78.3237-3.351.65777.9237-3.20151.9735-0.1475-0.38740.82990.94810.1364-0.5257-0.85630.01880.22270.3435-0.0438-0.0130.2067-0.06780.26716.0842-23.4017.1908
86.77770.1877-2.02526.8179-2.25847.7598-0.01580.1557-0.1235-0.2513-0.0063-0.02780.1091-0.11960.01420.1445-0.0154-0.02170.13410.00320.10986.4883-24.5113-15.5733
95.60690.9559-0.01026.9103-5.00663.7206-0.2481-0.35440.3330.5529-0.1983-0.6968-0.60720.27380.39790.214-0.00560.00180.1687-0.03050.203112.4199-18.4076-10.0022
105.8232.4251-4.79594.5677-1.96547.5067-0.0276-0.2498-0.3334-0.5862-0.2697-0.52210.33231.12380.24010.21550.04770.04530.28530.03760.151916.7313-28.0721-7.2923
115.24625.7471-6.56656.6875-7.60199.24890.15240.22040.09010.37520.0425-0.3365-0.5255-0.1409-0.26090.23280.03910.07380.2770.01560.323817.0753-28.267-11.311
123.7214-3.97685.09556.4761-3.5478.71560.53290.0208-0.108-0.4387-0.22940.0267-0.0594-0.1852-0.24450.26480.02080.0310.1452-0.02340.101-2.9004-33.4103-4.7968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 11:23)
2X-RAY DIFFRACTION2chain 'A' and (resseq 24:52)
3X-RAY DIFFRACTION3chain 'A' and (resseq 53:65)
4X-RAY DIFFRACTION4chain 'A' and (resseq 66:74)
5X-RAY DIFFRACTION5chain 'A' and (resseq 75:84)
6X-RAY DIFFRACTION6chain 'A' and (resseq 85:102)
7X-RAY DIFFRACTION7chain 'B' and (resseq 9:23)
8X-RAY DIFFRACTION8chain 'B' and (resseq 24:52)
9X-RAY DIFFRACTION9chain 'B' and (resseq 53:65)
10X-RAY DIFFRACTION10chain 'B' and (resseq 66:74)
11X-RAY DIFFRACTION11chain 'B' and (resseq 75:84)
12X-RAY DIFFRACTION12chain 'B' and (resseq 85:101)

+
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