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- PDB-4mt0: Crystal Structure of the Open State of the Neisseria gonorrhoeae ... -

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Basic information

Entry
Database: PDB / ID: 4mt0
TitleCrystal Structure of the Open State of the Neisseria gonorrhoeae MtrE Outer Membrane Channel
ComponentsMtrE protein
Keywordsmembrane protein / tranport protein / beta barrel
Function / homology
Function and homology information


efflux transmembrane transporter activity / plasma membrane
Similarity search - Function
Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / RND efflux system, outer membrane lipoprotein, NodT / Outer membrane efflux protein / Outer membrane efflux protein / Single Sheet / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle ...Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / Outer membrane efflux proteins (OEP) / RND efflux system, outer membrane lipoprotein, NodT / Outer membrane efflux protein / Outer membrane efflux protein / Single Sheet / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.292 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 / 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: MtrE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6252
Polymers48,5291
Non-polymers961
Water1267
1
A: MtrE protein
hetero molecules

A: MtrE protein
hetero molecules

A: MtrE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,8746
Polymers145,5863
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area14560 Å2
ΔGint-132 kcal/mol
Surface area60850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.096, 94.096, 392.368
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein MtrE protein


Mass: 48528.516 Da / Num. of mol.: 1 / Fragment: unp residues 21-467
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: SK2 / Gene: mtrE / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q51006
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 5.17 Å3/Da / Density % sol: 76.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: 30% PEG400, 0.05M Mg(Ac)2, 0.1M NaAc, pH 5.0, 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: 3.29→50 Å / Num. all: 27283 / Num. obs: 27283 / % possible obs: 92.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 64.01 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.29-3.4120.429194.7
3.41-3.5420.354194.9
3.54-3.7120.229194.4
3.71-3.920.187194.1
3.9-4.142.10.131193.4
4.14-4.4620.109193.2
4.46-4.912.10.116192.8
4.91-5.622.10.11190.8
5.62-7.082.10.086189.1
7.08-502.20.035185.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DPSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.292→46.182 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.44 / σ(F): 1.35 / Phase error: 32.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3169 765 4.98 %
Rwork0.2807 --
obs0.2824 15374 92.42 %
all-15374 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.7282 Å2
Refinement stepCycle: LAST / Resolution: 3.292→46.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 5 7 3418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023465
X-RAY DIFFRACTIONf_angle_d0.6124692
X-RAY DIFFRACTIONf_dihedral_angle_d15.6471278
X-RAY DIFFRACTIONf_chiral_restr0.039527
X-RAY DIFFRACTIONf_plane_restr0.002621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2921-3.54620.40231370.35972894X-RAY DIFFRACTION94
3.5462-3.90290.30731570.30582896X-RAY DIFFRACTION94
3.9029-4.46730.32121650.2562881X-RAY DIFFRACTION94
4.4673-5.62670.26731660.24362907X-RAY DIFFRACTION93
5.6267-46.18660.32641400.27753031X-RAY DIFFRACTION88

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