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- PDB-4hx4: Structure of MNTR mutant E11K complexed with Mn2+ -

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Basic information

Entry
Database: PDB / ID: 4hx4
TitleStructure of MNTR mutant E11K complexed with Mn2+
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 / 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: 1.65 Å
AuthorsGlasfeld, A. / McGuire, A.
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_asym_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_asym_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)33,4224
Polymers33,3122
Non-polymers1102
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-31 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.427, 46.081, 74.892
Angle α, β, γ (deg.)90.00, 92.96, 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 (bacteria) / Strain: 168 / Gene: BACILLUS SUBTILIS, BSU24520, MNTR, YQHN / Plasmid: PHB7506 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)AI / References: UniProt: P54512
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% ETHYLENE GLYCOL, 55 MM LITHIUM SULFATE, 2 MM MANGANESE CHLORIDE, 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: Aug 14, 2007
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.65→74.79 Å / Num. obs: 40214 / % possible obs: 98.8 % / Redundancy: 3.56 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 22.2
Reflection shellResolution: 1.65→1.74 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.2 / % possible all: 97.4

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F5D

2f5d


Resolution: 1.65→30.33 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.109 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26444 2021 5 %RANDOM
Rwork0.23377 ---
obs0.23534 38181 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.787 Å2
Baniso -1Baniso -2Baniso -3
1-5.38 Å20 Å2-2.67 Å2
2---3.14 Å20 Å2
3----2.08 Å2
Refinement stepCycle: LAST / Resolution: 1.65→30.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 2 112 2212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192194
X-RAY DIFFRACTIONr_bond_other_d0.0010.022184
X-RAY DIFFRACTIONr_angle_refined_deg1.121.9812947
X-RAY DIFFRACTIONr_angle_other_deg0.7235053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.725266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.77624.679109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5915456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7861515
X-RAY DIFFRACTIONr_chiral_restr0.0630.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02467
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21536
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2119
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7331.51346
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04422099
X-RAY DIFFRACTIONr_scbond_it1.9243963
X-RAY DIFFRACTIONr_scangle_it2.9564.5843
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 145 -
Rwork0.385 2641 -
obs--94.83 %
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)
14.40710.3138-0.44452.62810.89259.02220.075-0.37960.19580.5997-0.05350.28280.0198-0.3034-0.02150.147-0.03710.07530.219-0.01960.162218.063625.08082.5288
29.54273.9304-0.91516.6421.65567.3737-0.12280.0062-0.2489-0.10550.02760.07810.5037-0.08430.09520.0826-0.00060.05630.2019-0.02180.170916.253318.0322-6.1036
33.38740.77730.84436.3393-2.30134.070.1183-0.16390.03750.3645-0.03660.7047-0.0832-0.5491-0.08180.1648-0.00920.12760.4092-0.02170.28318.760525.86541.2337
46.8949-3.29385.31754.3684-2.95348.3935-0.03450.14210.2752-0.1049-0.0240.0958-0.0876-0.10.05850.0511-0.00810.05560.1633-0.00040.127321.788630.7698-1.8354
52.63140.47890.6452.90840.6172.50890.09110.1446-0.1155-0.0867-0.02470.0070.16210.0277-0.06640.03040.00790.01790.1476-0.010.060531.864723.794413.4849
68.5322-2.40811.56882.1406-5.304516.46830.17580.4256-0.3047-0.3071-0.23840.04540.87830.48890.06260.20150.01350.22310.2775-0.04780.336448.221721.503315.6695
714.2096-3.8032-6.06614.2286-3.904317.8963-0.0602-0.4087-0.90170.63440.14150.43810.5894-0.4288-0.08120.1910.07530.05670.35130.03820.322944.859114.470524.7366
84.6618-0.46920.75242.16541.00837.83760.13880.2167-0.2021-0.53230.05910.19490.3151-0.0482-0.19780.1891-0.0099-0.02690.14060.02050.153416.574525.695334.1261
96.5436-0.68655.61670.9945-0.32228.91660.0956-0.26750.0602-0.2080.04630.1159-0.1003-0.4119-0.14190.06370.00940.03120.22390.00770.190710.299332.259337.7667
107.67590.34471.0183.9495-0.22577.608-0.09490.1878-0.022-0.57590.11070.65050.1314-0.4235-0.01580.1626-0.0505-0.02520.23550.0630.2568.635418.806637.9196
117.4054.5424-6.06913.9378-4.2075.483-0.189-0.1748-0.2766-0.2150.0359-0.09770.25210.15760.15310.04660.02390.03490.1691-0.0030.110821.696719.425938.345
122.9889-0.3312-0.13133.32140.2242.40380.0385-0.09790.00480.2074-0.04390.06230.0101-0.08010.00540.0232-0.00680.02350.1251-0.01030.042629.892427.407225.2246
137.76521.69950.24792.4819-0.05151.23450.2708-0.4062-0.21880.667-0.2434-0.5404-0.01370.2836-0.02740.2257-0.0427-0.09290.24030.04450.202345.845128.253425.3102
1420.3726-7.0868-4.981217.2939-3.209813.9209-0.37840.59780.5449-0.26910.1822-0.0035-0.52210.11540.19620.2554-0.0815-0.01480.350.04070.288345.7836.888115.1655
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 17
2X-RAY DIFFRACTION2A18 - 29
3X-RAY DIFFRACTION3A30 - 51
4X-RAY DIFFRACTION4A52 - 76
5X-RAY DIFFRACTION5A77 - 119
6X-RAY DIFFRACTION6A120 - 130
7X-RAY DIFFRACTION7A131 - 135
8X-RAY DIFFRACTION8B3 - 17
9X-RAY DIFFRACTION9B18 - 41
10X-RAY DIFFRACTION10B42 - 60
11X-RAY DIFFRACTION11B61 - 75
12X-RAY DIFFRACTION12B76 - 115
13X-RAY DIFFRACTION13B116 - 130
14X-RAY DIFFRACTION14B131 - 135

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