[English] 日本語
Yorodumi
- PDB-3hrs: Crystal Structure of the Manganese-activated Repressor ScaR: apo form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hrs
TitleCrystal Structure of the Manganese-activated Repressor ScaR: apo form
ComponentsMetalloregulator ScaR
KeywordsTRANSCRIPTION / DtxR/MntR family member
Function / homology
Function and homology information


transition metal ion binding / protein dimerization activity / DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
FeoA domain / Ferrous iron transport protein A (FeoA) / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / : / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain ...FeoA domain / Ferrous iron transport protein A (FeoA) / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / : / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element / Transcriptional repressor, C-terminal / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Manganese transport regulator
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD/SIR / Resolution: 2.7 Å
AuthorsStoll, K.E. / Draper, W.E. / Kliegman, J.I. / Golynskiy, M.V. / Brew-Appiah, R.A.T. / Brown, H.K. / Breyer, W.A. / Jakubovics, N.S. / Jenkinson, H.F. / Brennan, R.B. ...Stoll, K.E. / Draper, W.E. / Kliegman, J.I. / Golynskiy, M.V. / Brew-Appiah, R.A.T. / Brown, H.K. / Breyer, W.A. / Jakubovics, N.S. / Jenkinson, H.F. / Brennan, R.B. / Cohen, S.M. / Glasfeld, A.
CitationJournal: Biochemistry / Year: 2009
Title: Characterization and structure of the manganese-responsive transcriptional regulator ScaR.
Authors: Stoll, K.E. / Draper, W.E. / Kliegman, J.I. / Golynskiy, M.V. / Brew-Appiah, R.A. / Phillips, R.K. / Brown, H.K. / Breyer, W.A. / Jakubovics, N.S. / Jenkinson, H.F. / Brennan, R.G. / Cohen, S.M. / Glasfeld, A.
History
DepositionJun 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Metalloregulator ScaR
B: Metalloregulator ScaR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7876
Polymers49,4032
Non-polymers3844
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-72 kcal/mol
Surface area23580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.600, 70.600, 301.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Metalloregulator ScaR


Mass: 24701.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Gene: scaR / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RFN3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.78 Å3/Da / Density % sol: 67.48 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 6
Details: 1.6 M lithium sulfate, 0.05 M sodium cacodylate in the presence of 1 mM MnCl2 and 1 mM duplex DNA containing operator sequence, pH 6.0, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1
DetectorDetector: CCD / Date: Jul 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→45.852 Å / Num. obs: 21511 / % possible obs: 97.5 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 7.674
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.7-2.853.50.3172.4982827710.31790.7
2.85-3.024.10.2293.21189128800.22998.2
3.02-3.234.60.1624.41268127820.16299
3.23-3.494.50.11161163225720.11199.5
3.49-3.824.50.0886.91092624140.08899.2
3.82-4.274.40.0688.9971221960.06899.5
4.27-4.934.40.05710.7856319680.05799.6
4.93-6.044.30.05211727916830.05299.2
6.04-8.544.20.04312.8559613440.04399.1
8.54-45.853.40.03816.424167020.03886.6

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
SCALA3.1.20data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
SOLVEphasing
MOSFLMdata reduction
RefinementMethod to determine structure: SAD/SIR / Resolution: 2.7→20 Å / Occupancy max: 1 / Occupancy min: 1
RfactorNum. reflection% reflection
Rfree0.272 2063 -
Rwork0.227 --
obs-21434 97.7 %
Displacement parametersBiso max: 246.67 Å2 / Biso mean: 108.445 Å2 / Biso min: 29.89 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3447 0 20 14 3481
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg1.22
X-RAY DIFFRACTIONf_bond_d0.008
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)
11.92470.16380.6180.89524.3472.73180.3406-0.0421-0.1731-0.1359-0.50440.57230.67-0.29520.00030.9448-0.1488-0.04120.11610.00210.585240.551977.656328.5465
20.7466-0.0842-0.2117-1.7101-0.50650.90970.2926-0.08360.3319-0.089-0.2852-0.0532-0.7462-0.2655-0.28830.74-0.09680.1114-0.9689-0.06440.408850.608360.816639.2986
36.81941.70631.2983.06620.74111.78520.95961.6836-0.53030.07380.01760.38620.65560.2341-0.72511.08260.2032-0.26370.5964-0.17570.463545.974452.554916.7733
40.7221-0.47670.773-0.6728-1.2270.55620.2174-0.05760.6951-0.3096-0.2104-0.1914-0.58510.03440.19682.3319-0.03720.64950.5472-0.15230.974433.95160.16469.8128
53.52050.2862-0.4138-1.07770.0630.68841.2130.06792.43610.5939-1.1494-0.1205-0.41330.2518-0.08252.47780.06790.2471.04460.04291.798628.100364.678374.4642
60.5182-0.20020.6233-0.42760.37551.9918-0.0684-0.0332-0.0313-0.6821.02650.0514-1.4589-0.5417-0.89361.5032-0.27560.39181.18620.25640.816227.694452.461771.9501
73.37150.4232-0.5870.64830.27043.78310.3373-0.52370.41570.97310.0333-0.26540.0797-0.1563-0.26921.2318-0.22230.12630.1821-0.03440.493347.205555.036258.7057
80.4491-0.8760.34342.8362-1.23411.00010.0341-0.64820.33720.51270.18470.00650.14540.0547-0.23771.4584-0.21510.13071.1791-0.28910.541356.432160.577881.2195
90.67060.07910.91974.558-0.35292.0826-0.0359-0.35470.38040.435-0.5058-0.37991.604-1.07630.63341.7986-0.26350.15130.9239-0.24250.883852.029557.951580.9221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:69)A2 - 69
2X-RAY DIFFRACTION2(chain A and resid 70:140)A70 - 140
3X-RAY DIFFRACTION3(chain A and resid 141:215)A141 - 215
4X-RAY DIFFRACTION4(chain B and resid 6:15)B6 - 15
5X-RAY DIFFRACTION5(chain B and resid 16:46)B16 - 46
6X-RAY DIFFRACTION6(chain B and resid 47:71)B47 - 71
7X-RAY DIFFRACTION7(chain B and resid 72:138)B72 - 138
8X-RAY DIFFRACTION8(chain B and resid 139:202)B139 - 202
9X-RAY DIFFRACTION9(chain B and resid 203:215)B203 - 215

+
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