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- PDB-5mqq: Transcriptional repressor AmtR of corynebacterium glutamicum -

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Basic information

Entry
Database: PDB / ID: 5mqq
TitleTranscriptional repressor AmtR of corynebacterium glutamicum
ComponentsAmtR protein
KeywordsTRANSCRIPTION / transcription regulator / nitrogen regulation
Function / homology: / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / transcription cis-regulatory region binding / DNA-binding transcription factor activity / AmtR protein / Repressor of the high-affinity (Methyl) ammonium uptake system
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.093 Å
AuthorsSevvana, M. / Hasselt, K. / Muller, Y.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB473 Germany
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Similarities in the structure of the transcriptional repressor AmtR in two different space groups suggest a model for the interaction with GlnK.
Authors: Sevvana, M. / Hasselt, K. / Grau, F.C. / Burkovski, A. / Muller, Y.A.
History
DepositionDec 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AmtR protein
B: AmtR protein
C: AmtR protein
D: AmtR protein
E: AmtR protein
F: AmtR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,8458
Polymers137,6526
Non-polymers1922
Water10,647591
1
A: AmtR protein
B: AmtR protein


Theoretical massNumber of molelcules
Total (without water)45,8842
Polymers45,8842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-19 kcal/mol
Surface area17710 Å2
MethodPISA
2
C: AmtR protein
D: AmtR protein


Theoretical massNumber of molelcules
Total (without water)45,8842
Polymers45,8842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-29 kcal/mol
Surface area18310 Å2
MethodPISA
3
E: AmtR protein
F: AmtR protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0764
Polymers45,8842
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-42 kcal/mol
Surface area17850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.783, 160.638, 51.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-346-

HOH

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Components

#1: Protein
AmtR protein


Mass: 22942.072 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: First three residues were not modeled due to missing electron density. Last two residues were not modeled due to missing electron density. First residue is not A, but K. Side chain could not ...Details: First three residues were not modeled due to missing electron density. Last two residues were not modeled due to missing electron density. First residue is not A, but K. Side chain could not be built due to missing electron density.
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: amtR / Plasmid: pMALc2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H7C699, UniProt: Q79VH8*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / 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: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: AmtR (12 mg/ml) in 20 mM Tris HCl, pH 8.0, 0.2 M NaCl Crystals obtained under the conditions: 0.1 M Bis-Tris pH 5.8, 20 % PEG 3350 and 0.2 M (NH4)2SO4 with a protein to drop ratio of 1:1 microliters

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.09→33.24 Å / Num. obs: 73411 / % possible obs: 98.8 % / Redundancy: 4.05 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.5
Reflection shellResolution: 2.09→2.22 Å / Redundancy: 3.86 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 2.6 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.093→33.24 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.97
RfactorNum. reflection% reflection
Rfree0.2497 3693 5.04 %
Rwork0.2091 --
obs0.2112 73341 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.093→33.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9410 0 10 591 10011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059622
X-RAY DIFFRACTIONf_angle_d0.93913106
X-RAY DIFFRACTIONf_dihedral_angle_d13.2423574
X-RAY DIFFRACTIONf_chiral_restr0.041556
X-RAY DIFFRACTIONf_plane_restr0.0051692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0934-2.12090.33581030.30122255X-RAY DIFFRACTION83
2.1209-2.150.37641410.30242664X-RAY DIFFRACTION100
2.15-2.18070.3841370.29342616X-RAY DIFFRACTION100
2.1807-2.21320.34061500.28432699X-RAY DIFFRACTION100
2.2132-2.24780.30011230.27042702X-RAY DIFFRACTION99
2.2478-2.28470.32551290.25732623X-RAY DIFFRACTION99
2.2847-2.3240.27661410.24852703X-RAY DIFFRACTION100
2.324-2.36630.27571380.25242681X-RAY DIFFRACTION100
2.3663-2.41180.30711630.24352636X-RAY DIFFRACTION100
2.4118-2.4610.30081300.25142701X-RAY DIFFRACTION100
2.461-2.51450.27421420.23872652X-RAY DIFFRACTION100
2.5145-2.5730.29781360.22072721X-RAY DIFFRACTION100
2.573-2.63730.24631350.23312679X-RAY DIFFRACTION100
2.6373-2.70860.29681310.22332722X-RAY DIFFRACTION100
2.7086-2.78820.26851410.22192654X-RAY DIFFRACTION100
2.7882-2.87820.26451380.22552695X-RAY DIFFRACTION100
2.8782-2.9810.29461730.2132669X-RAY DIFFRACTION100
2.981-3.10020.28371720.21562657X-RAY DIFFRACTION100
3.1002-3.24120.2561420.21422711X-RAY DIFFRACTION99
3.2412-3.4120.27191500.21182698X-RAY DIFFRACTION99
3.412-3.62550.25131490.19642682X-RAY DIFFRACTION99
3.6255-3.9050.21981230.18162742X-RAY DIFFRACTION99
3.905-4.29720.18941310.16162727X-RAY DIFFRACTION99
4.2972-4.91740.20621490.16392722X-RAY DIFFRACTION99
4.9174-6.18880.21021620.20772767X-RAY DIFFRACTION99
6.1888-33.24820.18061640.17412870X-RAY DIFFRACTION98

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