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- PDB-4mt1: Crystal Structure of the Neisseria gonorrhoeae MtrD Inner Membran... -

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Basic information

Entry
Database: PDB / ID: 4mt1
TitleCrystal Structure of the Neisseria gonorrhoeae MtrD Inner Membrane Multidrug Efflux Pump
ComponentsDrug efflux proteinEfflux (microbiology)
Keywordsmembrane protein / tranport protein / transmembrane helix
Function / homology
Function and homology information


Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / Hydrophobe/amphiphile efflux-1 HAE1 ...Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Efflux pump membrane transporter
Similarity search - Component
Biological speciesNeisseria gonorrhoeae PID332 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.54 Å
AuthorsSu, C.-C. / Bolla, J.R. / Yu, E.W.
CitationJournal: Plos One / Year: 2014
Title: Crystal structure of the open state of the Neisseria gonorrhoeae MtrE outer membrane channel.
Authors: Lei, H.T. / Chou, T.H. / Su, C.C. / Bolla, J.R. / Kumar, N. / Radhakrishnan, A. / Long, F. / Delmar, J.A. / Do, S.V. / Rajashankar, K.R. / Shafer, W.M. / Yu, E.W.
History
DepositionSep 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Drug efflux protein


Theoretical massNumber of molelcules
Total (without water)112,9571
Polymers112,9571
Non-polymers00
Water0
1
A: Drug efflux protein

A: Drug efflux protein

A: Drug efflux protein


Theoretical massNumber of molelcules
Total (without water)338,8723
Polymers338,8723
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area19760 Å2
ΔGint-65 kcal/mol
Surface area114190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.995, 152.995, 360.746
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Drug efflux protein / Efflux (microbiology)


Mass: 112957.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae PID332 (bacteria)
Gene: NGJG_01522 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: D1E405

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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: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 30% PEG400, 0.05M CaCl2, 0.1M Bicine, pH 8.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2013
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.54→50 Å / Num. all: 18421 / Num. obs: 18421 / % possible obs: 90.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 127.17 Å2 / Rmerge(I) obs: 0.077 / Χ2: 1.4 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.54-3.682.90.49920580.635192.9
3.68-3.852.80.35421110.712194.4
3.85-4.052.80.2520730.908193.1
4.05-4.312.90.17720641.176193
4.31-4.6430.13420411.603191.4
4.64-5.12.80.10420551.842191.2
5.1-5.842.90.09620551.721191.5
5.84-7.3630.07419951.908187.7
7.36-502.80.04419692.148182.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.54→48.798 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6462 / SU ML: 0.61 / σ(F): 1.36 / Phase error: 40.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3331 961 5.22 %RANDOM
Rwork0.2796 ---
obs0.2824 18396 90.68 %-
all-18396 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 222.99 Å2 / Biso mean: 94.6161 Å2 / Biso min: 14.22 Å2
Refinement stepCycle: LAST / Resolution: 3.54→48.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7667 0 0 0 7667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037806
X-RAY DIFFRACTIONf_angle_d0.79410594
X-RAY DIFFRACTIONf_chiral_restr0.0541259
X-RAY DIFFRACTIONf_plane_restr0.0031346
X-RAY DIFFRACTIONf_dihedral_angle_d16.1232783
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5349-3.72120.40811390.30312525266493
3.7212-3.95420.38321430.27792528267193
3.9542-4.25940.39821450.26342527267293
4.2594-4.68770.31881230.23912484260791
4.6877-5.36530.31841340.262511264591
5.3653-6.75690.44431370.342489262690
6.7569-48.80240.27341400.27812371251183

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