[English] 日本語
Yorodumi
- PDB-1stz: Crystal structure of a hypothetical protein at 2.2 A resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1stz
TitleCrystal structure of a hypothetical protein at 2.2 A resolution
ComponentsHeat-inducible transcription repressor hrcA homolog
KeywordsTRANSCRIPTION / Hrca / circe element / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


negative regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Heat-inducible transcription repressor hrca homolog; domain 3 / Heat-inducible transcription repressor HrcA / Heat-inducible transcription repressor HrcA, C-terminal / Winged helix-turn-helix transcription repressor, HrcA, inserted dimerising domain superfamily / HrcA protein C terminal domain / GAF domain / Enolase-like; domain 1 / GAF-like domain superfamily / Beta-Lactamase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...Heat-inducible transcription repressor hrca homolog; domain 3 / Heat-inducible transcription repressor HrcA / Heat-inducible transcription repressor HrcA, C-terminal / Winged helix-turn-helix transcription repressor, HrcA, inserted dimerising domain superfamily / HrcA protein C terminal domain / GAF domain / Enolase-like; domain 1 / GAF-like domain superfamily / Beta-Lactamase / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Heat-inducible transcription repressor HrcA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsLiu, J. / Adams, P.D. / Shin, D.-H. / Huang, C. / Yokota, H. / Jancarik, J. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of a heat-inducible transcriptional repressor HrcA from Thermotoga maritima: structural insight into DNA binding and dimerization.
Authors: Liu, J. / Huang, C. / Shin, D.H. / Yokota, H. / Jancarik, J. / Kim, J.S. / Adams, P.D. / Kim, R. / Kim, S.H.
History
DepositionMar 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heat-inducible transcription repressor hrcA homolog
B: Heat-inducible transcription repressor hrcA homolog
C: Heat-inducible transcription repressor hrcA homolog


Theoretical massNumber of molelcules
Total (without water)118,0963
Polymers118,0963
Non-polymers00
Water8,107450
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.295, 115.295, 185.148
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Heat-inducible transcription repressor hrcA homolog


Mass: 39365.496 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: HRCA, TM0851 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZV5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.61 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 50 mM Sodium Acetate, 2.0 M Sodium Formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 21, 2004
RadiationMonochromator: YALE MIRRORS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 72907 / Num. obs: 66929 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 2.2 Å / % possible all: 91.7

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.458 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25753 2983 5.1 %RANDOM
Rwork0.21494 ---
obs0.21709 55577 91.7 %-
all-60607 --
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: 21.613 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7716 0 0 450 8166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227841
X-RAY DIFFRACTIONr_bond_other_d0.0020.027477
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.99110540
X-RAY DIFFRACTIONr_angle_other_deg0.779317374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9575940
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.21200
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028466
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021623
X-RAY DIFFRACTIONr_nbd_refined0.2040.21690
X-RAY DIFFRACTIONr_nbd_other0.2220.28696
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.25027
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.2394
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.2157
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6121.54690
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1827610
X-RAY DIFFRACTIONr_scbond_it1.70633151
X-RAY DIFFRACTIONr_scangle_it2.9734.52930
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.306 203
Rwork0.238 4057
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)
15.56060.8292-0.29287.2249-0.30588.73680.0603-0.46820.69150.959-0.1511-0.2022-1.14540.4580.09080.3307-0.03160.01510.0942-0.02350.105221.419756.541166.7236
20.98090.0090.70715.05930.72595.14620.0652-0.0571-0.04070.1344-0.0045-0.24640.33910.3482-0.06060.25430.0736-0.01690.04220.03190.078519.167134.7117129.6629
39.986-3.7013-1.249511.701-1.42555.5004-0.5217-0.3542-1.25970.12190.31320.69911.08390.1330.20850.36630.2810.11640.34440.12450.329655.958316.928141.9808
40.81890.2370.28991.2109-0.30834.8313-0.04960.1855-0.0919-0.28720.07060.08110.35610.0965-0.0210.03140.02710.03130.02650.03850.072519.618444.4388128.1973
50.7936-0.44810.15385.58520.51290.76680.03660.02750.1123-0.3205-0.01610.1704-0.171-0.0143-0.02040.1415-0.0291-0.00470.09010.03880.062524.232394.8689128.8812
62.2695-2.06172.78542.7782-3.14164.288-0.09060.11580.1994-0.1349-0.1651-0.31070.06790.44350.25570.14330.09660.08580.18550.01520.138539.336548.36122.4929
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 9515 - 95
2X-RAY DIFFRACTION2BB15 - 9515 - 95
3X-RAY DIFFRACTION3CC15 - 9515 - 95
4X-RAY DIFFRACTION4AA111 - 335111 - 335
5X-RAY DIFFRACTION5BB111 - 335111 - 335
6X-RAY DIFFRACTION6CC111 - 335111 - 335

+
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://pdbjlvh1.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