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- PDB-4aps: Crystal structure of a POT family peptide transporter in an inwar... -

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Basic information

Entry
Database: PDB / ID: 4aps
TitleCrystal structure of a POT family peptide transporter in an inward open conformation.
ComponentsDI-OR TRIPEPTIDE H+ SYMPORTER
KeywordsTRANSPORT PROTEIN / PEPTIDE TRANSPORT / MAJOR FACILITATOR SUPERFAMILY / TRANSPORTER / MFS
Function / homology
Function and homology information


oligopeptide transport / peptide transmembrane transporter activity / identical protein binding / 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 symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; ...Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Di-or tripeptide:H+ symporter
Similarity search - Component
Biological speciesSTREPTOCOCCUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.3 Å
AuthorsSolcan, N. / Kwok, J. / Fowler, P.W. / Cameron, A.D. / Drew, D. / Iwata, S. / Newstead, S.
CitationJournal: Embo J. / Year: 2012
Title: Alternating Access Mechanism in the Pot Family of Oligopeptide Transporters.
Authors: Solcan, N. / Kwok, J. / Fowler, P.W. / Cameron, A.D. / Drew, D. / Iwata, S. / Newstead, S.
History
DepositionApr 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Oct 31, 2012Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DI-OR TRIPEPTIDE H+ SYMPORTER
B: DI-OR TRIPEPTIDE H+ SYMPORTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5553
Polymers107,4422
Non-polymers1121
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-28.7 kcal/mol
Surface area42190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.390, 112.990, 215.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.802, -0.023, 0.597), (-0.022, -1, -0.009), (0.597, -0.006, -0.802)
Vector: -21.16, 190.88, 71.15)

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Components

#1: Protein DI-OR TRIPEPTIDE H+ SYMPORTER


Mass: 53721.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS THERMOPHILUS (bacteria) / Strain: LMG 18311 / Plasmid: PWALDO-GFPD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q5M4H8
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
Nonpolymer detailsCADMIUM ION (CD): IDENTITY OF CD ION CONFIRMED USING SAD DATA AT 7.1 KEV.

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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: 5.4 Å3/Da / Density % sol: 77 % / Description: NONE
Crystal growpH: 6.5
Details: 26 % PEG 400, 0.1 M MES PH 6.50, 0.03 M MGCL2 0.001 M CDCL2

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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: Jul 5, 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: 3.3→82 Å / Num. obs: 33300 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 127.67 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.1
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1.1 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
Aimlessdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 3.3→22.62 Å / Cor.coef. Fo:Fc: 0.7832 / Cor.coef. Fo:Fc free: 0.7858 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.361 / SU Rfree Blow DPI: 0.488
Details: RESIDUES 1-10, 270-281, 350-352, 472-491 ARE DISORDERED IN THE CRYSTAL AND WERE NOT BUILT INTO THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.2895 1421 5.09 %RANDOM
Rwork0.2722 ---
obs0.2731 27943 83.45 %-
Displacement parametersBiso mean: 140.73 Å2
Baniso -1Baniso -2Baniso -3
1--9.5188 Å20 Å20 Å2
2---17.3228 Å20 Å2
3---26.8416 Å2
Refine analyzeLuzzati coordinate error obs: 1.21 Å
Refinement stepCycle: LAST / Resolution: 3.3→22.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6890 0 1 0 6891
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114106HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9825538HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2956SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes70HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1970HARMONIC5
X-RAY DIFFRACTIONt_it14106HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion18.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion928SEMIHARMONIC5
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_contact15863SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.42 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2826 16 4.1 %
Rwork0.2415 374 -
all0.2431 390 -
obs--83.45 %
Refinement TLS params.

T22: -0.6079 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°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)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.6045-0.0532-0.2250.233-0.46546.1522-0.33190.2324-0.3511-1.0885-0.1221-1.08850.36810.57140.4539-0.09260.0080.304-0.04590.607959.358393.376536.1986
24.0418-0.2875-0.651400.19885.51310.0093-0.4802-0.06631.08850.04610.056-0.97130.181-0.05530.60790.0064-0.3040.02220.572145.921895.920876.9797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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