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- PDB-4d1a: STRUCTURE OF MHP1, A NUCLEOBASE-CATION-SYMPORT-1 FAMILY TRANSPORT... -

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Basic information

Entry
Database: PDB / ID: 4d1a
TitleSTRUCTURE OF MHP1, A NUCLEOBASE-CATION-SYMPORT-1 FAMILY TRANSPORTER, IN A CLOSED CONFORMATION WITH INDOLYLMETHYL-HYDANTOIN
ComponentsHYDANTOIN TRANSPORT PROTEIN
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN TRANSPORTER / SUBSTRATE-BOUND / OCCLUDED STATE
Function / homology
Function and homology information


nucleobase transmembrane transporter activity / metal ion binding / plasma membrane
Similarity search - Function
Uracil/uridine/allantoin permease / Hydantoin permease / Hydantoin permease / Purine-cytosine permease / Permease for cytosine/purines, uracil, thiamine, allantoin / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-I5H / Hydantoin permease
Similarity search - Component
Biological speciesMICROBACTERIUM LIQUEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsWeyand, S. / Brueckner, F. / Geng, T. / Drew, D. / Iwata, S. / Henderson, P.J.F. / Cameron, A.D.
CitationJournal: Embo J. / Year: 2014
Title: Molecular Mechanism of Ligand Recognition by Membrane Transport Protein, Mhp1.
Authors: Simmons, K.J. / Jackson, S.M. / Brueckner, F. / Patching, S.G. / Beckstein, O. / Ivanova, E. / Geng, T. / Weyand, S. / Drew, D. / Lanigan, J. / Sharples, D.J. / Sansom, M.S. / Iwata, S. / ...Authors: Simmons, K.J. / Jackson, S.M. / Brueckner, F. / Patching, S.G. / Beckstein, O. / Ivanova, E. / Geng, T. / Weyand, S. / Drew, D. / Lanigan, J. / Sharples, D.J. / Sansom, M.S. / Iwata, S. / Fishwick, C.W. / Johnson, A.P. / Cameron, A.D. / Henderson, P.J.
History
DepositionMay 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYDANTOIN TRANSPORT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2693
Polymers54,0171
Non-polymers2522
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.430, 106.360, 100.550
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 HYDANTOIN TRANSPORT PROTEIN / MHP1


Mass: 54017.148 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-487
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MICROBACTERIUM LIQUEFACIENS (bacteria) / Strain: AJ3912 / Plasmid: PWALDOGFPE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): LEMO21 / References: UniProt: D6R8X8
#2: Chemical ChemComp-I5H / (5S)-5-(1H-indol-3-ylmethyl)imidazolidine-2,4-dione


Mass: 229.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11N3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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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: 4.3 Å3/Da / Density % sol: 72 %
Description: COORDINATES WERE RESTRAINED TO 2JLN DURING REFINEMENT
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED IN 27-33 % PEG 300, 0.1M NACL AND 0.1M NA-PHOSPHATE (PH 7.0). INDOLYLMETHYL-HYDANTOIN WAS ADDED TO THE DROP AS A SATURATED SOLUTION.

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 23, 2011
RadiationMonochromator: SI(III) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→36.5 Å / Num. obs: 12215 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 133.24 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.2
Reflection shellResolution: 3.4→3.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.2 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JLN

2jln


Resolution: 3.4→36.534 Å / SU ML: 0.34 / σ(F): 1.33 / Phase error: 42.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2826 610 5 %
Rwork0.2475 --
obs0.2494 12166 90.82 %
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 191 Å2
Refinement stepCycle: LAST / Resolution: 3.4→36.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3513 0 18 0 3531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073634
X-RAY DIFFRACTIONf_angle_d1.2024963
X-RAY DIFFRACTIONf_dihedral_angle_d15.3411228
X-RAY DIFFRACTIONf_chiral_restr0.053586
X-RAY DIFFRACTIONf_plane_restr0.006604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4002-3.74210.37981300.34932825X-RAY DIFFRACTION90
3.7421-4.28280.34491590.292846X-RAY DIFFRACTION91
4.2828-5.39310.25311640.23882894X-RAY DIFFRACTION92
5.3931-36.53570.26471570.22332991X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 5.3534 Å / Origin y: 16.1417 Å / Origin z: 29.9783 Å
111213212223313233
T1.1639 Å20.0917 Å2-0.3028 Å2-0.8945 Å2-0.1844 Å2--1.0849 Å2
L5.1912 °20.8208 °20.3511 °2-9.9722 °2-1.0223 °2--2.5762 °2
S0.2599 Å °-0.1839 Å °0.0873 Å °0.27 Å °-0.2097 Å °0.1071 Å °0.0207 Å °0.0264 Å °-0.0413 Å °
Refinement TLS groupSelection details: ALL

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