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- PDB-4hx7: Structure of MNTR E11K mutant complexed with Cd2+ -

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Basic information

Entry
Database: PDB / ID: 4hx7
TitleStructure of MNTR E11K mutant complexed with Cd2+
ComponentsTranscriptional regulator MntR
KeywordsTRANSCRIPTION / WINGED HELIX-TURN-HELIX / TRANSCRIPTION REGULATOR
Function / homology
Function and homology information


intracellular manganese ion homeostasis / manganese ion binding / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / 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 / Helix-turn-helix diphteria tox regulatory element ...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 subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGlasfeld, A. / Cuthbert, B.J.
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
DepositionNov 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Sep 20, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

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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)33,5374
Polymers33,3122
Non-polymers2252
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-36 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.119, 46.252, 74.142
Angle α, β, γ (deg.)90.00, 92.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transcriptional regulator MntR / Manganese transport regulator


Mass: 16656.000 Da / Num. of mol.: 2 / Mutation: E11K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: mntR, yqhN, BSU24520 / References: UniProt: P54512
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 40% ETHYLENE GLYCOL, 10% PEG 3000, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.9→74 Å / Num. obs: 25216 / % possible obs: 95.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 6.4
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.5 / % possible all: 78.4

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Processing

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

2f5d


Resolution: 1.9→74 Å / SU ML: 0.34 / Cross valid method: THROUGOUT / σ(F): 0 / Phase error: 27.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2858 1189 4.86 %RANDOM
Rwork0.2439 ---
obs0.2459 24461 92.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.304 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.6412 Å2-0 Å2-2.3546 Å2
2---3.4007 Å20 Å2
3----3.2405 Å2
Refinement stepCycle: LAST / Resolution: 1.9→74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2121 0 2 58 2181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072152
X-RAY DIFFRACTIONf_angle_d0.8812881
X-RAY DIFFRACTIONf_dihedral_angle_d13.695840
X-RAY DIFFRACTIONf_chiral_restr0.062319
X-RAY DIFFRACTIONf_plane_restr0.003360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.98650.31041240.27192046X-RAY DIFFRACTION66
1.9865-2.09130.32231440.2362810X-RAY DIFFRACTION90
2.0913-2.22230.26731430.22922938X-RAY DIFFRACTION94
2.2223-2.39390.2841480.22073009X-RAY DIFFRACTION96
2.3939-2.63480.26631620.23173032X-RAY DIFFRACTION97
2.6348-3.01610.25941630.23783075X-RAY DIFFRACTION98
3.0161-3.80.29661600.24933142X-RAY DIFFRACTION99
3.8-74.09750.29471450.2573220X-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)
11.3265-0.01180.71770.2185-0.03290.49460.06180.4708-0.208-0.1146-0.0198-0.0278-0.01550.1625-0.02980.03270.03460.01230.1490.02680.116629.2227-2.639538.343
20.75960.6915-0.64771.0459-0.30950.9274-0.2582-0.4686-0.438-0.00290.051-0.31530.19790.32630.19530.21870.13120.07150.30210.01470.190437.9855-7.484635.0564
30.4106-0.18540.38551.4086-0.41651.3676-0.01980.33170.32610.069-0.2763-0.2042-0.10660.60290.26870.1814-0.04670.06290.29680.03410.191935.89166.51339.6267
43.7661.24881.00142.93710.10031.3061-0.2695-0.09970.26880.51520.35570.4067-0.41720.1183-0.11570.23660.0734-0.00640.1583-0.06310.202523.23516.848737.4283
50.8858-0.0468-0.74930.2268-0.3712.0536-0.1757-0.11160.1004-0.13890.0499-0.1290.02130.32240.08110.1031-0.0084-0.04880.0193-0.00180.103317.3414-5.424424.8686
61.47290.86950.19990.831-0.24990.45580.140.0501-0.22440.18540.0429-0.15180.0023-0.0592-0.13560.11280.0025-0.00270.1219-0.00770.09716.0088-0.476320.6484
70.9756-0.1785-0.10762.71340.76190.8943-0.0829-0.18230.19360.4540.0265-0.16350.04380.1713-0.00340.053-0.0099-0.00980.10230.01090.091132.33334.2990.5512
80.60650.94210.23672.36320.12790.1549-0.0862-0.0528-0.35920.55390.2802-1.02520.00510.1219-0.21450.21230.0772-0.13120.1943-0.03810.292842.0417-0.37973.3196
91.0477-0.35170.3921.4832-0.31310.60080.018-0.0245-0.48130.1629-0.0799-0.28320.29950.01560.09310.15230.01520.0230.1253-0.00670.21536.1307-6.8409-4.0322
101.4703-0.292-0.60051.04880.04090.7067-0.24930.4369-0.16230.11720.07840.07280.4314-0.07370.110.14230.00630.00360.1302-0.04130.093420.3725-1.70834.3669
111.0723-0.6437-0.37231.1501-0.27910.46450.0071-0.14870.35980.17940.0556-0.2859-0.23440.0844-0.11260.14420.03520.04030.0845-0.01380.092919.19817.456714.2022
120.92690.33310.5830.3788-0.33951.62250.1177-0.2541-0.0153-0.09930.00880.05870.2656-0.261-0.11770.071-0.0004-0.0170.13-0.02290.0815.67671.092914.4152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:25)
2X-RAY DIFFRACTION2(chain A and resid 26:40)
3X-RAY DIFFRACTION3(chain A and resid 41:64)
4X-RAY DIFFRACTION4(chain A and resid 65:73)
5X-RAY DIFFRACTION5(chain A and resid 74:103)
6X-RAY DIFFRACTION6(chain A and resid 104:136)
7X-RAY DIFFRACTION7(chain B and resid 3:34)
8X-RAY DIFFRACTION8(chain B and resid 35:47)
9X-RAY DIFFRACTION9(chain B and resid 48:64)
10X-RAY DIFFRACTION10(chain B and resid 65:83)
11X-RAY DIFFRACTION11(chain B and resid 84:104)
12X-RAY DIFFRACTION12(chain B and resid 105:136)

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