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- PDB-4d1d: STRUCTURE OF MHP1, A NUCLEOBASE-CATION-SYMPORT-1 FAMILY TRANSPORT... -

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Basic information

Entry
Database: PDB / ID: 4d1d
TitleSTRUCTURE OF MHP1, A NUCLEOBASE-CATION-SYMPORT-1 FAMILY TRANSPORTER with the inhibitor 5-(2-naphthylmethyl)-L-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
5-(2-NAPHTHYLMETHYL)-D-HYDANTOIN / 5-(2-NAPHTHYLMETHYL)-L-HYDANTOIN / 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)54,5214
Polymers54,0171
Non-polymers5043
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)87.600, 106.900, 106.800
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-5NL / 5-(2-NAPHTHYLMETHYL)-L-HYDANTOIN


Mass: 240.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12N2O2
#3: Chemical ChemComp-5ND / 5-(2-NAPHTHYLMETHYL)-D-HYDANTOIN


Mass: 240.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12N2O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
Nonpolymer details5-(2-NAPHTHYLMETHYL)-D-HYDANTOIN (5ND): HALF OCCUPANCY 5-(2-NAPHTHYLMETHYL)-L-HYDANTOIN (5NL): HALF OCCUPANCY

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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: 4.6 Å3/Da / Density % sol: 74 % / Description: NONE
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 27-33 % PEG 300, 0.1 M NACL AND 0.1M NA-PHOSPHATE (PH 7.0). NMH 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: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 19, 2011
RadiationMonochromator: SI(III) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.7→38 Å / Num. obs: 10714 / % possible obs: 97 % / Observed criterion σ(I): -1 / Redundancy: 3.3 % / Biso Wilson estimate: 129.68 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.3
Reflection shellResolution: 3.7→3.8 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2 / % possible all: 96

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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→37.777 Å / SU ML: 0.65 / σ(F): 0 / Phase error: 37.68 / Stereochemistry target values: ML
Details: COORDINATES WERE RESTRAINED TO 2JLN DURING REFINEMENT. COMPOUND WAS A MIXTURE OF D AND L FORMS OF NMH. BOTH BIND EQUALLY WELL. REFINED BOTH AT HALF OCCUPANCY.
RfactorNum. reflection% reflection
Rfree0.3077 1802 9.8 %
Rwork0.2557 --
obs0.2606 10642 88.86 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 195 Å2
Refinement stepCycle: LAST / Resolution: 3.7→37.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3513 0 37 0 3550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083655
X-RAY DIFFRACTIONf_angle_d1.2744992
X-RAY DIFFRACTIONf_dihedral_angle_d15.3471226
X-RAY DIFFRACTIONf_chiral_restr0.054587
X-RAY DIFFRACTIONf_plane_restr0.007606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.80.42021540.41371255X-RAY DIFFRACTION86
3.8-3.91170.35241120.39091156X-RAY DIFFRACTION84
3.9117-4.03780.47431250.39571218X-RAY DIFFRACTION83
4.0378-4.1820.36281220.33621255X-RAY DIFFRACTION85
4.182-4.34920.31951410.27641239X-RAY DIFFRACTION88
4.3492-4.54680.28911240.24581277X-RAY DIFFRACTION88
4.5468-4.78610.30341480.23161240X-RAY DIFFRACTION88
4.7861-5.08530.28011570.22851290X-RAY DIFFRACTION90
5.0853-5.47680.28251360.22691308X-RAY DIFFRACTION91
5.4768-6.0260.34141400.22311318X-RAY DIFFRACTION92
6.026-6.89340.30281520.26381317X-RAY DIFFRACTION93
6.8934-8.66760.24511540.24141356X-RAY DIFFRACTION95
8.6676-37.77910.3031370.22331328X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: 5.0626 Å / Origin y: 16.1843 Å / Origin z: -21.6688 Å
111213212223313233
T1.355 Å20.2057 Å2-0.0372 Å2-1.1273 Å2-0.3577 Å2--1.2732 Å2
L7.1609 °2-1.0714 °22.4955 °2-14.4465 °2-1.9955 °2--2.5954 °2
S0.3518 Å °-0.0763 Å °-0.5717 Å °0.8713 Å °-0.0225 Å °-0.2977 Å °-0.01 Å °-0.0026 Å °-0.329 Å °
Refinement TLS groupSelection details: ALL

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