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- PDB-4hv6: Structure of MNTR H77A mutant in apo- and mn-bound forms -

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Basic information

Entry
Database: PDB / ID: 4hv6
TitleStructure of MNTR H77A mutant in apo- and mn-bound forms
ComponentsTranscriptional regulator MntR
KeywordsTRANSCRIPTION / WINGED HELIX-TURN-HELIX / TRANSCRIPTION REGULATOR / METALLOREGULATOR
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 subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGlasfeld, A. / Grauer-Gray, K. / 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 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 17, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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)33,3125
Polymers33,1782
Non-polymers1343
Water25214
1
A: Transcriptional regulator MntR
hetero molecules

A: Transcriptional regulator MntR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3976
Polymers33,1782
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+4/31
Buried area3050 Å2
ΔGint-44 kcal/mol
Surface area14970 Å2
MethodPISA
2
B: Transcriptional regulator MntR
hetero molecules

B: Transcriptional regulator MntR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2264
Polymers33,1782
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+5/31
Buried area2820 Å2
ΔGint-31 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.734, 51.734, 175.564
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Transcriptional regulator MntR / Manganese transport regulator


Mass: 16588.865 Da / Num. of mol.: 2 / Fragment: MNTR (unp residues 2-142) / Mutation: H77A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU24520, mntR, yqhN / Production host: Escherichia coli (E. coli) / 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16% ETHOXYETHANOL,4% ETHYLENE GLYCOL, 90 MM MGCL2, 60 MM TRIS HCL, 1 MM MNSO4, pH 8.5, 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
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2007
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→44.8 Å / Num. obs: 12767 / % possible obs: 99.4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
EPMRphasing
PHENIX(PHENIX.REFINE: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ON2

1on2


Resolution: 2.3→44.8 Å / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.317 --RANDOM
Rwork0.252 ---
obs-12767 99.4 %-
Refinement stepCycle: LAST / Resolution: 2.3→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2194 0 3 14 2211
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_deg1.08
LS refinement shellResolution: 2.3→2.42 Å /
Rfactor% reflection
Rfree0.317 -
Rwork0.252 -
obs-100 %
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)
16.8408-0.5059-0.77312.7633.71645.4277-0.1971-0.89811.09610.1846-0.01410.4641-0.5791-0.35540.17890.5587-0.071-0.01230.5929-0.01250.6463-21.915417.7153132.4947
28.3530.77026.06971.9911-1.86381.9957-0.5075-1.4096-0.9259-0.55670.9484-0.3927-1.0678-1.5028-0.2930.8083-0.2941-0.01510.83430.10740.6878-31.761616.3128142.6287
30.2158-2.2131-0.2423.80522.43532.9440.46860.09690.69250.25990.1779-0.39370.6916-0.4133-0.32420.3006-0.13930.02920.22750.15220.2627-23.0626.1486128.738
45.178-0.4426-0.70963.22220.86351.8287-0.1222-0.2665-0.00630.6902-0.10330.41610.2775-0.11090.22690.39310.0429-0.02830.27610.03420.2653-5.43814.892122.7536
55.3381-3.8009-1.08474.9126-5.30637.3785-0.7918-1.4783-0.4249-0.54580.4491-1.43121.70951.44530.07690.72180.3444-0.04180.7165-0.06620.50348.4672-4.5736122.1699
62.05940.39590.99674.71060.060.71240.5902-0.2734-0.20620.2574-0.5081-0.7516-0.53760.453-0.0770.7329-0.0145-0.07810.51650.05310.566529.315312.806164.7426
71.0244-1.1020.3315-1.2781-2.1833.61511.1689-1.15630.46420.8763-0.7439-0.38520.39310.0343-0.64680.82870.0134-0.04870.90280.04850.422731.998321.5388173.0485
83.0552-1.6531.1148-1.9945-0.82920.94730.08880.0890.6390.2646-0.03460.2877-0.0817-0.2956-0.1210.56120.0154-0.0920.3956-0.02240.420219.317817.4146158.5185
92.2018-1.1641.06014.89190.90195.1351-0.33-0.20310.2670.46510.1186-0.2351-0.2999-0.1240.17290.26850.0366-0.00050.31110.03050.334110.30722.3816151.996
100.49590.2684-3.26848.14764.66543.4593-0.07040.9023-0.24410.9514-0.19621.56510.5739-2.1822-0.05130.4125-0.13580.06160.72890.01520.4824-4.6915-6.5956150.8955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:53 )A2 - 53
2X-RAY DIFFRACTION2( CHAIN A AND RESID 54:60 )A54 - 60
3X-RAY DIFFRACTION3( CHAIN A AND RESID 61:75 )A61 - 75
4X-RAY DIFFRACTION4( CHAIN A AND RESID 76:122 )A76 - 122
5X-RAY DIFFRACTION5( CHAIN A AND RESID 123:134 )A123 - 134
6X-RAY DIFFRACTION6( CHAIN B AND RESID 4:53 )B4 - 53
7X-RAY DIFFRACTION7( CHAIN B AND RESID 54:60 )B54 - 60
8X-RAY DIFFRACTION8( CHAIN B AND RESID 61:75 )B61 - 75
9X-RAY DIFFRACTION9( CHAIN B AND RESID 76:122 )B76 - 122
10X-RAY DIFFRACTION10( CHAIN B AND RESID 123:136 )B123 - 136

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