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- PDB-4hv5: Structure of the MNTR FE2+ complex with E site metal binding -

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Basic information

Entry
Database: PDB / ID: 4hv5
TitleStructure of the MNTR FE2+ complex with E site metal binding
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 / 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. / Brophy, M.B. / Kliegman, J.I. / Griner, S.L.
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 14, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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)34,0128
Polymers33,3122
Non-polymers7006
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-65 kcal/mol
Surface area14090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.980, 75.230, 97.400
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 subsp. subtilis (bacteria)
Strain: 168 / Gene: BACILLUS SUBTILIS, BSU24520, mntR, yqhN / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P54512
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


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


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 100 MM HEPES, 7.0, 90 MM LITHIUM SULFATE, 20% 1,2-PROPANEDIOL, 10 MM ASCORBIC ACID, 1 MM FERROUS SULFATE , VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.2131
DetectorType: NOIR-1 / Detector: CCD / Date: Oct 5, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2131 Å / Relative weight: 1
ReflectionResolution: 1.9→22 Å / Num. obs: 26399 / % possible obs: 96.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 9.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.7 / % possible all: 97.4

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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: MNTR

Resolution: 1.9→21.99 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 31.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.283 1213 4.91 %
Rwork0.23 --
obs0.233 24688 90.3 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.19 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.0356 Å2-0 Å20 Å2
2---2.2218 Å2-0 Å2
3---11.2574 Å2
Refinement stepCycle: LAST / Resolution: 1.9→21.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 34 220 2337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072144
X-RAY DIFFRACTIONf_angle_d0.912875
X-RAY DIFFRACTIONf_dihedral_angle_d15.139842
X-RAY DIFFRACTIONf_chiral_restr0.061313
X-RAY DIFFRACTIONf_plane_restr0.003357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.97610.38561040.30822222X-RAY DIFFRACTION78
1.9761-2.06590.31381710.25812618X-RAY DIFFRACTION93
2.0659-2.17480.27461270.23712653X-RAY DIFFRACTION93
2.1748-2.31090.32071180.24282468X-RAY DIFFRACTION86
2.3109-2.48910.30391250.24982533X-RAY DIFFRACTION89
2.4891-2.73910.31470.25292561X-RAY DIFFRACTION89
2.7391-3.13450.32861280.23052673X-RAY DIFFRACTION92
3.1345-3.94540.26351390.21042791X-RAY DIFFRACTION96
3.9454-21.98770.23481540.20632956X-RAY DIFFRACTION97
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)
10.37950.1813-0.50240.2836-0.12890.7282-0.1037-0.0113-0.26610.0425-0.02120.08050.0618-0.06880.11950.12560.04140.1310.12380.06230.20196.887820.787132.6229
20.2735-0.02360.40871.84720.02810.61410.1352-0.2357-0.02150.0536-0.0283-0.2181-0.0401-0.0649-0.0910.1027-0.01950.07050.16670.08380.170915.443922.002839.1676
30.1852-0.0671-0.1160.44740.14280.14510.1414-0.01820.2478-0.07170.0799-0.2937-0.0810.0294-0.21340.1076-0.01170.11940.0291-0.03760.224614.615617.015921.9677
40.69660.3209-0.57190.82430.05670.62760.15560.00440.2422-0.02560.03250.1215-0.1393-0.0229-0.18310.10890.01910.08440.05410.01670.1354.82316.211719.1388
50.87871.002-0.5961.2157-0.54410.65070.16120.06890.26110.15650.15150.2623-0.0769-0.0508-0.24140.03840.01040.0506-0.01920.15490.046511.52555.58457.0139
61.76431.40070.44161.17330.00642.13250.30780.02620.36620.0785-0.11130.25110.00740.2242-0.18560.01190.06310.1388-0.0055-0.11790.072515.1482-18.561631.5484
70.27930.1349-0.10320.36650.37170.6270.08520.02850.0440.1582-0.13590.1510.1074-0.06450.05710.1282-0.05390.12970.2305-0.2750.169912.0747-15.212540.6015
80.04460.0656-0.10460.2591-0.17550.26560.0764-0.00430.01140.050.11770.3275-0.0282-0.0694-0.17720.0415-0.00940.07060.08010.01740.35865.5151-20.062529.1846
90.05190.12710.08780.3875-0.00890.84020.0458-0.0891-0.1635-0.0292-0.0801-0.23390.0180.18120.06130.0791-0.00320.08080.10340.0610.206917.3251-4.434918.9622
100.2584-0.354-0.43170.85080.34760.8704-0.0178-0.0383-0.1136-0.121-0.06340.1464-0.11050.04460.08070.14370.01030.05520.06820.03060.127111.4814-2.5116.8269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 4:34)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 35:65)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 66:79)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 80:104)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 105:134)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 4:29)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 30:49)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 50:75)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 76:104)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 105:134)

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