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- PDB-2xut: Crystal structure of a proton dependent oligopeptide (POT) family... -

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Basic information

Entry
Database: PDB / ID: 2xut
TitleCrystal structure of a proton dependent oligopeptide (POT) family transporter.
ComponentsPROTON/PEPTIDE SYMPORTER FAMILY PROTEIN
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN / MAJOR FACILITATOR SUPERFAMILY TRANSPORTER / PROTON COUPLED PEPTIDE TRANSPORT
Function / homology
Function and homology information


oligopeptide transport / peptide transmembrane transporter activity / transmembrane transporter activity / transmembrane transport / membrane / plasma membrane
Similarity search - Function
Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Glutathione uptake transporter
Similarity search - Component
Biological speciesSHEWANELLA ONEIDENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.62 Å
AuthorsNewstead, S. / Drew, D. / Cameron, A.D. / Postis, V.L. / Xia, X. / Fowler, P.W. / Ingram, J.C. / Carpenter, E.P. / Sansom, M.S.P. / McPherson, M.J. ...Newstead, S. / Drew, D. / Cameron, A.D. / Postis, V.L. / Xia, X. / Fowler, P.W. / Ingram, J.C. / Carpenter, E.P. / Sansom, M.S.P. / McPherson, M.J. / Baldwin, S.A. / Iwata, S.
CitationJournal: Embo J. / Year: 2011
Title: Crystal Structure of a Prokaryotic Homologue of the Mammalian Oligopeptide-Proton Symporters, Pept1 and Pept2.
Authors: Newstead, S. / Drew, D. / Cameron, A.D. / Postis, V.L. / Xia, X. / Fowler, P.W. / Ingram, J.C. / Carpenter, E.P. / Sansom, M.S.P. / McPherson, M.J. / Baldwin, S.A. / Iwata, S.
History
DepositionOct 21, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTON/PEPTIDE SYMPORTER FAMILY PROTEIN
B: PROTON/PEPTIDE SYMPORTER FAMILY PROTEIN
C: PROTON/PEPTIDE SYMPORTER FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)173,0543
Polymers173,0543
Non-polymers00
Water00
1
A: PROTON/PEPTIDE SYMPORTER FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)57,6851
Polymers57,6851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTON/PEPTIDE SYMPORTER FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)57,6851
Polymers57,6851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PROTON/PEPTIDE SYMPORTER FAMILY PROTEIN


Theoretical massNumber of molelcules
Total (without water)57,6851
Polymers57,6851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)159.400, 159.400, 152.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.993131, -0.116976, -0.002302), (0.116992, 0.993092, 0.008936), (0.001239, -0.009144, 0.999958)-84.41685, 56.03742, -4.31474
2given(-0.984452, -0.174221, 0.022573), (-0.174583, 0.984525, -0.015228), (-0.01957, -0.018931, -0.999627)7.64841, 107.60533, 107.92352

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Components

#1: Protein PROTON/PEPTIDE SYMPORTER FAMILY PROTEIN


Mass: 57684.824 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SHEWANELLA ONEIDENSIS (bacteria) / Strain: MR-1 / Plasmid: PWALDO-GFPE / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q8EKT7
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 2 TO ASN ENGINEERED RESIDUE IN CHAIN A, THR 3 TO SER ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, THR 2 TO ASN ENGINEERED RESIDUE IN CHAIN A, THR 3 TO SER ENGINEERED RESIDUE IN CHAIN B, THR 2 TO ASN ENGINEERED RESIDUE IN CHAIN B, THR 3 TO SER ENGINEERED RESIDUE IN CHAIN C, THR 2 TO ASN ENGINEERED RESIDUE IN CHAIN C, THR 3 TO SER

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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: 6.49 Å3/Da / Density % sol: 80 %
Description: REFINEMENT WAS CARRIED OUT USING ANISOTROPIC TRUNCATION OF THE OBSERVED STRUCTURE FACTORS TO 4.3 A ALONG THE A AND B AXES, AND 3.6 ALONG C
Crystal growpH: 6.5 / Details: 30% PEG 300, 0.1M MES PH 6.50 AND 0.1M NACL

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 18, 2009
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.62→35.5 Å / Num. obs: 47021 / % possible obs: 93.8 % / Observed criterion σ(I): 1.1 / Redundancy: 2 % / Biso Wilson estimate: 105.41 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.1 / % possible all: 88.7

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 3.62→35.47 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE MODEL WAS BUILT AND REFINED USING DATA WITH ANISOTROPIC TRUNCATION OF THE OBSERVED STRUCTURE A AND B AXES, WHILST KEEPING THE C AXIS AT 3.6A.
RfactorNum. reflection% reflectionSelection details
Rfree0.2963 1688 5.84 %RANDOM
Rwork0.2765 ---
obs0.2776 28894 --
Displacement parametersBiso mean: 252.95 Å2
Baniso -1Baniso -2Baniso -3
1-5.0218 Å20 Å20 Å2
2--5.0218 Å20 Å2
3----10.0437 Å2
Refine analyzeLuzzati coordinate error obs: 1.877 Å
Refinement stepCycle: LAST / Resolution: 3.62→35.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10533 0 0 0 10533
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00910812HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1214679HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3495SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes150HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1596HARMONIC5
X-RAY DIFFRACTIONt_it10812HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.11
X-RAY DIFFRACTIONt_other_torsion24.5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1404SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12461SEMIHARMONIC4
LS refinement shellResolution: 3.62→3.76 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.4045 17 9.88 %
Rwork0.358 155 -
all0.3617 172 -
Refinement TLS params.

L33: 16.6309 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°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)
13.71073.01122.695412.50236.9731-0.45581.02180.9576-0.0101-0.3293-0.4786-0.8395-0.72290.78520.8303-0.08120.0030.22210.1687-0.448674.732264.507651.1538
29.09926.31552.130615.13187.9514-0.43940.58141.2240.01140.05540.057-1.28060.04120.38410.8566-0.12670.22740.30090.1845-0.4598-2.7194110.943247.2975
37.1683-4.33955.661914.7743-3.4524-0.1848-0.59510.96290.3871-0.38330.5092-1.43030.43110.56810.8696-0.15110.14460.3462-0.1545-0.1818-78.1858157.157257.5123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A)
2X-RAY DIFFRACTION2(CHAIN B)
3X-RAY DIFFRACTION3(CHAIN C)

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