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- PDB-3hrs: Crystal Structure of the Manganese-activated Repressor ScaR: apo form -

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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 / negative regulation of DNA-templated transcription / 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 / Winged helix DNA-binding domain superfamily / Roll / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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