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- PDB-3r61: Structure of the MntR Co2+ Complex -

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Basic information

Entry
Database: PDB / ID: 3r61
TitleStructure of the MntR Co2+ Complex
ComponentsTranscriptional regulator mntR
KeywordsTRANSCRIPTION REGULATOR / Winged helix-turn-helix
Function / homology
Function and homology information


intracellular manganese ion homeostasis / manganese ion binding / protein dimerization activity / DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
HTH-type transcription regulator MntR / Iron dependent repressor, metal binding and dimerisation domain / : / 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 ...HTH-type transcription regulator MntR / Iron dependent repressor, metal binding and dimerisation domain / : / 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 / Diphtheria Toxin Repressor; domain 2 / 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
: / HTH-type transcriptional regulator MntR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9002 Å
AuthorsGlasfeld, A. / Brophy, M.B. / Kliegman, J.I. / Griner, S.L. / Nix, J.C.
CitationJournal: Biochemistry / Year: 2013
Title: Roles of the A and C Sites in the Manganese-Specific Activation of MntR.
Authors: McGuire, A.M. / Cuthbert, B.J. / Ma, Z. / Grauer-Gray, K.D. / Brunjes Brophy, M. / Spear, K.A. / Soonsanga, S. / Kliegman, J.I. / Griner, S.L. / Helmann, J.D. / Glasfeld, A.
History
DepositionMar 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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: Transcriptional regulator mntR
B: Transcriptional regulator mntR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9066
Polymers33,3122
Non-polymers5944
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-39 kcal/mol
Surface area14330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.930, 75.013, 96.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcriptional regulator mntR / Manganese transport regulator


Mass: 16655.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: Bacillus subtilis, BSU24520, mntR, yqhN / Plasmid: pHB7506 / Production host: Escherichia coli (E. coli) / References: UniProt: P54512
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES, pH 7.0, 50 mM Lithium Sulfate, 20% 1,2-Propanediol, 0.5 mM Cobalt(II) Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Feb 10, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→41.45 Å / Num. obs: 26945 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 18.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
EPMRphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F5D

2f5d


Resolution: 1.9002→41.445 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 1240 4.88 %RANDOM
Rwork0.2135 ---
obs0.2157 25409 94.47 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.874 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.8589 Å2-0 Å20 Å2
2---6.7319 Å2-0 Å2
3---14.5908 Å2
Refinement stepCycle: LAST / Resolution: 1.9002→41.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 0 32 122 2256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072225
X-RAY DIFFRACTIONf_angle_d0.8592988
X-RAY DIFFRACTIONf_dihedral_angle_d15.32906
X-RAY DIFFRACTIONf_chiral_restr0.062324
X-RAY DIFFRACTIONf_plane_restr0.003373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9002-1.97630.34161230.32072338X-RAY DIFFRACTION83
1.9763-2.06630.31571550.24582488X-RAY DIFFRACTION90
2.0663-2.17520.28271270.23092621X-RAY DIFFRACTION93
2.1752-2.31150.34831180.22442558X-RAY DIFFRACTION91
2.3115-2.48990.2621390.20962712X-RAY DIFFRACTION96
2.4899-2.74040.27181430.22182751X-RAY DIFFRACTION97
2.7404-3.13690.29041330.20862826X-RAY DIFFRACTION99
3.1369-3.95160.21591460.19722880X-RAY DIFFRACTION100
3.9516-41.45530.22651560.19942995X-RAY DIFFRACTION99
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)
10.774-0.11970.40140.6027-0.56711.0319-0.04650.0199-0.3309-0.15970.3766-0.40330.0640.4423-0.00020.2709-0.07980.03640.3131-0.16490.380416.306719.550463.2376
21.3491.4634-1.89482.0564-1.73182.87540.45881.81180.2743-1.93330.35290.97940.0264-1.47610.15750.7241-0.0844-0.05910.5862-0.24660.45448.230418.434154.224
30.4908-0.0425-0.69650.72980.07880.8640.15490.14470.08420.04580.23780.6314-0.038-0.17130.00090.15870.0115-0.06460.20520.07570.37856.729419.554869.4401
40.98540.5279-0.92782.2116-0.69441.3614-0.0656-0.04250.168-0.04840.0639-0.2611-0.03450.127300.1884-0.011-0.04780.1504-0.00010.172218.09015.701877.286
50.66580.4533-0.91211.51030.02941.54740.0273-0.07020.43330.1141-0.1732-0.01220.12540.025-0.00010.15870.0059-0.02880.1496-0.08310.097411.9534.596389.671
61.3496-0.88660.25420.7714-0.18250.47410.16670.17320.3529-0.1024-0.0114-0.06650.0949-0.3592-00.2328-0.039-0.02740.25840.09650.18447.8024-18.939365.0715
70.18930.36460.1991.46771.00880.94360.42120.5330.8798-0.7789-0.313-0.92820.1056-0.1155-0.00080.36290.1090.20460.4530.3370.473612.2514-16.357756.7446
80.8258-0.64770.41770.5121-0.37390.52530.23850.00810.04120.19520.193-0.74470.06050.18640.00080.21430.0025-0.04610.2036-0.03460.461417.1974-20.024869.647
91.40180.70340.1631.57340.49112.26680.08120.005-0.191-0.1338-0.04150.26670.0882-0.037300.0978-0.0352-0.03980.1179-0.03960.13526.0191-5.035977.3669
100.78391.37510.3252.3794-0.04091.88680.0232-0.0396-0.29410.2939-0.29410.02480.2812-0.3029-0.00040.2207-0.0474-0.02780.19470.00690.078710.7302-2.020989.9751
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:36)
2X-RAY DIFFRACTION2(chain A and resid 37:49)
3X-RAY DIFFRACTION3(chain A and resid 50:79)
4X-RAY DIFFRACTION4(chain A and resid 80:104)
5X-RAY DIFFRACTION5(chain A and resid 105:136)
6X-RAY DIFFRACTION6(chain B and resid 4:29)
7X-RAY DIFFRACTION7(chain B and resid 30:52)
8X-RAY DIFFRACTION8(chain B and resid 53:75)
9X-RAY DIFFRACTION9(chain B and resid 76:104)
10X-RAY DIFFRACTION10(chain B and resid 105:136)

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