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- PDB-4d1c: STRUCTURE OF MHP1, A NUCLEOBASE-CATION-SYMPORT-1 FAMILY TRANSPORT... -

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Basic information

Entry
Database: PDB / ID: 4d1c
TitleSTRUCTURE OF MHP1, A NUCLEOBASE-CATION-SYMPORT-1 FAMILY TRANSPORTER, IN A CLOSED CONFORMATION WITH bromovinylhydantoin bound.
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-B5H / Hydantoin permease
Similarity search - Component
Biological speciesMICROBACTERIUM LIQUEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 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)54,3073
Polymers54,0171
Non-polymers2902
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)90.012, 107.323, 109.255
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-B5H / (5Z)-5-[(3-bromophenyl)methylidene]imidazolidine-2,4-dione


Mass: 267.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7BrN2O2
#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: 4.9 Å3/Da / Density % sol: 75 % / Description: NONE
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 27-33 % PEG 300, 0.1M NACL AND 0.1M NA-PHOSPHATE (PH 7.0). BROMOVINYLHYDANTOIN 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: I03 / Wavelength: 0.9191
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 18, 2010
RadiationMonochromator: SI(III) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9191 Å / Relative weight: 1
ReflectionResolution: 3.7→30 Å / Num. obs: 11569 / % possible obs: 98 % / Observed criterion σ(I): -1 / Redundancy: 4.6 % / Biso Wilson estimate: 124.12 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15
Reflection shellResolution: 3.7→3.76 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D1A

4d1a


Resolution: 3.7→28.896 Å / SU ML: 0.53 / σ(F): 1.11 / Phase error: 32.56 / Stereochemistry target values: ML
Details: COORDINATES RESTRAINED TO 2JLN DURING REFINEMENT. THE DEPOSITED COORDINATES CONTAIN TM10 IN THE SAME CONFORMATION AS SEEN FOR 4D1A. THERE IS, HOWEVER, SOME DENSITY WITH THIS HELIX MORE SIMILAR TO 2JLN.
RfactorNum. reflection% reflection
Rfree0.2875 2044 9.9 %
Rwork0.2571 --
obs0.2599 11466 95.4 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 183 Å2
Refinement stepCycle: LAST / Resolution: 3.7→28.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3513 0 16 0 3529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053631
X-RAY DIFFRACTIONf_angle_d1.1124958
X-RAY DIFFRACTIONf_dihedral_angle_d15.0371228
X-RAY DIFFRACTIONf_chiral_restr0.043585
X-RAY DIFFRACTIONf_plane_restr0.006604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.78590.39441080.41281215X-RAY DIFFRACTION93
3.7859-3.88040.41751620.37651215X-RAY DIFFRACTION94
3.8804-3.9850.33121310.34291199X-RAY DIFFRACTION94
3.985-4.1020.37291350.34131243X-RAY DIFFRACTION94
4.102-4.2340.30551220.30641243X-RAY DIFFRACTION94
4.234-4.38480.26141360.2551245X-RAY DIFFRACTION95
4.3848-4.55970.28191340.23921238X-RAY DIFFRACTION95
4.5597-4.76640.25971210.22721268X-RAY DIFFRACTION96
4.7664-5.01640.23151700.22031254X-RAY DIFFRACTION98
5.0164-5.32890.31221370.22651253X-RAY DIFFRACTION97
5.3289-5.73740.3291280.24921295X-RAY DIFFRACTION98
5.7374-6.30930.32591490.25721280X-RAY DIFFRACTION99
6.3093-7.20990.26571410.26411296X-RAY DIFFRACTION99
7.2099-9.03730.25761430.21251282X-RAY DIFFRACTION98
9.0373-28.89690.25991270.24031191X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 5.0543 Å / Origin y: 16.6692 Å / Origin z: -22.1615 Å
111213212223313233
T1.4167 Å20.1823 Å2-0.2263 Å2-1.0328 Å2-0.2722 Å2--1.365 Å2
L3.4214 °2-0.021 °20.7322 °2-16.8801 °2-0.886 °2--2.9113 °2
S0.0658 Å °-0.1709 Å °0.1037 Å °0.875 Å °-0.0584 Å °-0.6714 Å °0.1584 Å °0.1375 Å °-0.1219 Å °
Refinement TLS groupSelection details: ALL

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