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- PDB-2x79: Inward facing conformation of Mhp1 -

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Basic information

Entry
Database: PDB / ID: 2x79
TitleInward facing conformation of Mhp1
ComponentsHYDANTOIN TRANSPORT PROTEIN
KeywordsTRANSPORT PROTEIN / TRANSPORTER / MEMBRANE PROTEIN
Function / homology
Function and homology information


transmembrane transporter activity / membrane / metal ion binding
Similarity search - Function
Hydantoin permease / Hydantoin permease / Uracil/uridine/allantoin permease / Purine-cytosine permease / Permease for cytosine/purines, uracil, thiamine, allantoin / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMICROBACTERIUM LIQUEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.8 Å
AuthorsShimamura, T. / Weyand, S. / Beckstein, O. / Rutherford, N.G. / Hadden, J.M. / Sharples, D. / Sansom, M.S.P. / Iwata, S. / Henderson, P.J.F. / Cameron, A.D.
CitationJournal: Science / Year: 2010
Title: Molecular Basis of Alternating Access Membrane Transport by the Sodium-Hydantoin Transporter Mhp1.
Authors: Shimamura, T. / Weyand, S. / Beckstein, O. / Rutherford, N.G. / Hadden, J.M. / Sharples, D. / Sansom, M.S.P. / Iwata, S. / Henderson, P.J.F. / Cameron, A.D.
History
DepositionFeb 25, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYDANTOIN TRANSPORT PROTEIN


Theoretical massNumber of molelcules
Total (without water)55,5571
Polymers55,5571
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)173.888, 173.888, 74.502
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein HYDANTOIN TRANSPORT PROTEIN / MHP1


Mass: 55556.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONINE / Source: (gene. exp.) MICROBACTERIUM LIQUEFACIENS (bacteria) / Strain: AJ3912 / Plasmid: PSHP11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: D6R8X8*PLUS
Sequence detailsNOT PUBLISHED

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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: 7.2 Å3/Da / Density % sol: 83 % / Description: BUILDING WAS BASED ON PDB ENTRY 2JLN
Crystal growpH: 9 / Details: 24-28% PEG300, 100 MM NACL AND 100 MM BICINE PH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979147
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2004 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979147 Å / Relative weight: 1
ReflectionResolution: 3.8→40 Å / Num. obs: 47973 / % possible obs: 97 % / Observed criterion σ(I): -1 / Redundancy: 3.8 % / Biso Wilson estimate: 172.82 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.6
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.4 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.8→33.388 Å / SU ML: 0.83 / σ(F): 1.96 / Phase error: 39.94 / Stereochemistry target values: ML
Details: MODELLING WAS DONE WITH SHARPENED MAPS. IN THE SODIUM BINDING SITE BETWEEN RESIDUES ALA38 AND THR330 THERE IS ADDITIONAL DENSITY THAT HAS NOT BEEN MODELLED.
RfactorNum. reflection% reflection
Rfree0.3126 2204 9.9 %
Rwork0.2732 --
obs0.2773 22378 90.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 99 Å2 / ksol: 0.262 e/Å3
Displacement parametersBiso mean: 242 Å2
Baniso -1Baniso -2Baniso -3
1--32.6384 Å20 Å20 Å2
2---32.6384 Å2-0 Å2
3---53.8407 Å2
Refinement stepCycle: LAST / Resolution: 3.8→33.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3585 0 0 0 3585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.1153925
X-RAY DIFFRACTIONf_angle_d1.0375034
X-RAY DIFFRACTIONf_dihedral_angle_d17.5841246
X-RAY DIFFRACTIONf_chiral_restr0.061595
X-RAY DIFFRACTIONf_plane_restr0.005616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8002-3.88280.46521460.43461181X-RAY DIFFRACTION83
3.8828-3.97290.41651050.45391129X-RAY DIFFRACTION82
3.9729-4.07210.45681330.431143X-RAY DIFFRACTION82
4.0721-4.1820.40691390.41861196X-RAY DIFFRACTION84
4.182-4.30480.39621520.37061169X-RAY DIFFRACTION86
4.3048-4.44350.40211210.33761250X-RAY DIFFRACTION90
4.4435-4.60190.37361260.33531286X-RAY DIFFRACTION89
4.6019-4.78570.36671180.30811264X-RAY DIFFRACTION90
4.7857-5.00280.32891400.27121290X-RAY DIFFRACTION92
5.0028-5.26560.39811570.28351266X-RAY DIFFRACTION92
5.2656-5.5940.33911160.27291324X-RAY DIFFRACTION93
5.594-6.02360.28011180.2491360X-RAY DIFFRACTION95
6.0236-6.62560.34421440.25411332X-RAY DIFFRACTION96
6.6256-7.57450.25521620.20191368X-RAY DIFFRACTION98
7.5745-9.50650.17831580.16091376X-RAY DIFFRACTION99
9.5065-33.38970.32471690.27211240X-RAY DIFFRACTION91
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)
10.21252.0747-2.07311.7964-3.0455-0.31580.3908-0.70690.38530.5107-0.0458-0.79460.91440.0541-0.00032.75330.0812-0.00362.69440.0752.380435.47-34.301717.1569
20.7263-0.1078-1.17390.77523.74171.20870.36520.2368-1.31890.3941-0.576-0.77430.5555-0.1230.00072.408-0.0568-0.04662.22070.71512.760648.449-47.87888.6233
31.175-1.66150.2030.69130.6407-0.5274-1.4742-1.47173.33830.88230.7287-2.2437-0.8632-2.339-0.16282.3232-0.31020.68712.58660.61052.334934.1023-54.227820.2136
4-0.7126-0.13160.44550.7481-0.2851-1.99190.3549-1.1772-1.3407-0.66491.081-1.6591-0.06320.03590.00032.81090.37030.41542.80060.06083.105762.6161-32.94681.7312
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1RESSEQ 100:160 OR RESSEQ 295:358
2X-RAY DIFFRACTION2RESSEQ 8:99 OR RESSEQ 192:294
3X-RAY DIFFRACTION3RESSEQ 161:191
4X-RAY DIFFRACTION4RESSEQ 359:470

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