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- PDB-3vib: Structural basis for multidrug recognition and antimicrobial resi... -

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Basic information

Entry
Database: PDB / ID: 3vib
TitleStructural basis for multidrug recognition and antimicrobial resistance by MTRR, an efflux pump regulator from Neisseria Gonorrhoeae
ComponentsMtrR
KeywordsDNA BINDING PROTEIN / HELIX-TURN-HELIX MOTIF / DNA BINDING
Function / homology
Function and homology information


: / Transcription regulator MAATS, C-terminal / MAATS-type transcriptional repressor, C-terminal region / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type ...: / Transcription regulator MAATS, C-terminal / MAATS-type transcriptional repressor, C-terminal region / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / MtrR / HTH-type transcriptional regulator MtrR
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / molecular replacement / Resolution: 2.4 Å
AuthorsKumaraswami, M. / Shafer, W.M. / Brennan, R.G.
CitationJournal: TO BE PUBLISHED
Title: Structural basis for multidrug recognitionand antimicrobial resistance by MTRR, an efflux pump regulator from Neisseria Gonorrhoeae
Authors: Kumaraswami, M. / Shafer, W.M. / Brennan, R.G.
History
DepositionSep 27, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: MtrR
B: MtrR
C: MtrR
D: MtrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,70115
Polymers97,1514
Non-polymers1,55011
Water8,287460
1
A: MtrR
B: MtrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3037
Polymers48,5762
Non-polymers7285
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-20 kcal/mol
Surface area16810 Å2
MethodPISA
2
C: MtrR
D: MtrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3988
Polymers48,5762
Non-polymers8236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-21 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.300, 84.600, 58.100
Angle α, β, γ (deg.)90.000, 103.900, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
MtrR / HTH-TYPE TRANSCRIPTIONAL REGULATOR MTRR / Multiple transferable resistance repressor


Mass: 24287.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: mtrR / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: C0ITL7, UniProt: P39897*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 10.5
Details: 1.7M NA/K PHOSPHATE, 0.18M LITHIUM SULFATE, 0.1M CAPS, PH 10.5, VAPOR DIFFUSION, HANGING DROP,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9797, 0.9798, 1.02
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2008
RadiationMonochromator: DOUBLE FLAT CRYSTAL, SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97981
31.021
ReflectionResolution: 2.4→45.46 Å / Num. obs: 39412 / % possible obs: 97.8 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.4→2.55 Å / % possible all: 98.4

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Phasing

Phasing
Method
MAD
molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
PHASERphasing
SOLVEphasing
RESOLVEphasing
CNS1.1refinement
PDB_EXTRACT3.1data extraction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→45.46 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.256 3981 RANDOM
Rwork0.212 --
obs-39412 -
Displacement parametersBiso max: 153.03 Å2 / Biso mean: 48.4034 Å2 / Biso min: 16.54 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.4→45.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6313 0 91 460 6864
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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