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- PDB-2jln: Structure of Mhp1, a nucleobase-cation-symport-1 family transporter -

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Basic information

Entry
Database: PDB / ID: 2jln
TitleStructure of Mhp1, a nucleobase-cation-symport-1 family transporter
ComponentsMHP1
KeywordsMEMBRANE PROTEIN / HYDANTOIN / TRANSPORTER / NUCLEOBASE-CATION-SYMPORT-1 FAMILY
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
: / Hydantoin permease
Similarity search - Component
Biological speciesMICROBACTERIUM LIQUEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.85 Å
AuthorsWeyand, S. / Shimamura, T. / Yajima, S. / Suzuki, S. / Mirza, O. / Krusong, K. / Carpenter, E.P. / Rutherford, N.G. / Hadden, J.M. / O'Reilly, J. ...Weyand, S. / Shimamura, T. / Yajima, S. / Suzuki, S. / Mirza, O. / Krusong, K. / Carpenter, E.P. / Rutherford, N.G. / Hadden, J.M. / O'Reilly, J. / Ma, P. / Saidijam, M. / Patching, S.G. / Hope, R.J. / Norbertczak, H.T. / Roach, P.C.J. / Iwata, S. / Henderson, P.J.F. / Cameron, A.D.
CitationJournal: Science / Year: 2008
Title: Structure and Molecular Mechanism of a Nucleobase-Cation-Symport-1 Family Transporter.
Authors: Weyand, S. / Shimamura, T. / Yajima, S. / Suzuki, S. / Mirza, O. / Krusong, K. / Carpenter, E.P. / Rutherford, N.G. / Hadden, J.M. / O'Reilly, J. / Ma, P. / Saidijam, M. / Patching, S.G. / ...Authors: Weyand, S. / Shimamura, T. / Yajima, S. / Suzuki, S. / Mirza, O. / Krusong, K. / Carpenter, E.P. / Rutherford, N.G. / Hadden, J.M. / O'Reilly, J. / Ma, P. / Saidijam, M. / Patching, S.G. / Hope, R.J. / Norbertczak, H.T. / Roach, P.C.J. / Iwata, S. / Henderson, P.J.F. / Cameron, A.D.
History
DepositionSep 11, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8423
Polymers54,6191
Non-polymers2242
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.700, 109.140, 113.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHP1


Mass: 54618.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MICROBACTERIUM LIQUEFACIENS (bacteria) / Strain: AJ3912 / Plasmid: PSHP11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: D6R8X8*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg

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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: 4.5 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 31-33 % PEG 300, 100 MM NACL AND 100 MM NA-PHOSPHATE (PH 7.0), THAN SOAKED FOR 1 MINUTE IN 2.5 MM METHYL MERCURY ACETATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97925
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 10, 2004 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 22414 / % possible obs: 94 % / Observed criterion σ(I): -2.5 / Redundancy: 2.9 % / Biso Wilson estimate: 72.32 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.2
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1 / % possible all: 81

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Processing

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

Resolution: 2.85→29.014 Å / SU ML: 0.44 / σ(F): 1.89 / Phase error: 31.54 / Stereochemistry target values: ML / Details: THE MODEL WAS BUILT FROM RESIDUES 8- 470.
RfactorNum. reflection% reflection
Rfree0.2809 1981 5.03 %
Rwork0.2338 --
obs0.2362 39346 87.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.484 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.9434 Å2-0 Å20 Å2
2---11.3656 Å2-0 Å2
3---8.4222 Å2
Refinement stepCycle: LAST / Resolution: 2.85→29.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3569 0 2 0 3571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013673
X-RAY DIFFRACTIONf_angle_d1.485013
X-RAY DIFFRACTIONf_dihedral_angle_d19.711240
X-RAY DIFFRACTIONf_chiral_restr0.09592
X-RAY DIFFRACTIONf_plane_restr0614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.92120.41171020.3541983X-RAY DIFFRACTION66
2.9212-3.00010.34751510.32992202X-RAY DIFFRACTION73
3.0001-3.08830.41291170.30632336X-RAY DIFFRACTION77
3.0883-3.18790.36951070.30332565X-RAY DIFFRACTION83
3.1879-3.30170.28311350.26962776X-RAY DIFFRACTION91
3.3017-3.43370.29431520.2472805X-RAY DIFFRACTION93
3.4337-3.58970.28431310.22792834X-RAY DIFFRACTION93
3.5897-3.77850.25731270.20462849X-RAY DIFFRACTION92
3.7785-4.01470.21911730.18912791X-RAY DIFFRACTION93
4.0147-4.32380.2081490.17222841X-RAY DIFFRACTION93
4.3238-4.75720.24111640.16562816X-RAY DIFFRACTION93
4.7572-5.44160.28251480.18022868X-RAY DIFFRACTION94
5.4416-6.8410.27231790.21942836X-RAY DIFFRACTION94
6.841-29.0150.26931460.24922863X-RAY DIFFRACTION94

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