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- PDB-4ja3: Partially occluded inward open conformation of the xylose transpo... -

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Basic information

Entry
Database: PDB / ID: 4ja3
TitlePartially occluded inward open conformation of the xylose transporter XylE from E. coli
ComponentsD-xylose-proton symporter
KeywordsTRANSPORT PROTEIN / MFS general substrate transporter / Xylose transporter
Function / homology
Function and homology information


D-xylose:proton symporter activity / D-xylose transmembrane transport / transmembrane transporter activity / transmembrane transport / membrane / plasma membrane
Similarity search - Function
MFS transporter, transmembrane helix TM10b / : / Sugar/inositol transporter / Sugar transport proteins signature 2. / GTP Cyclohydrolase I; Chain A, domain 1 / Sugar transport proteins signature 1. / MFS general substrate transporter like domains / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site ...MFS transporter, transmembrane helix TM10b / : / Sugar/inositol transporter / Sugar transport proteins signature 2. / GTP Cyclohydrolase I; Chain A, domain 1 / Sugar transport proteins signature 1. / MFS general substrate transporter like domains / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / D-xylose-proton symporter
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsQuistgaard, E.M. / Low, C. / Moberg, P. / Tresaugues, L. / Nordlund, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structural basis for substrate transport in the GLUT-homology family of monosaccharide transporters.
Authors: Quistgaard, E.M. / Low, C. / Moberg, P. / Tresaugues, L. / Nordlund, P.
History
DepositionFeb 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: D-xylose-proton symporter
B: D-xylose-proton symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,6647
Polymers105,8522
Non-polymers8125
Water0
1
A: D-xylose-proton symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3884
Polymers52,9261
Non-polymers4623
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D-xylose-proton symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2763
Polymers52,9261
Non-polymers3502
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)246.880, 74.380, 131.110
Angle α, β, γ (deg.)90.00, 117.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein D-xylose-proton symporter / D-xylose transporter


Mass: 52925.793 Da / Num. of mol.: 2 / Fragment: XylE
Mutation: Start methionine missing and last five residues deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: xylE, b4031, JW3991 / Plasmid: Modified pTH27 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P0AGF4
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-LU / LUTETIUM (III) ION / LU / Lutetium


Mass: 174.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Lu

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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: 5.03 Å3/Da / Density % sol: 75.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 32% PEG 400, 4% 2-methyl-2,4-pentane diol (MPD), 0.2% (w/v) octyl glucoseneopentyl glycol (OGNG), 5 mM CdCl2, 5 mM lutetium acetate, 100 mM temperature 277K, pH 6.0, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2012
RadiationMonochromator: Double crystal; Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→25.3 Å / Num. all: 40779 / Num. obs: 33439 / % possible obs: 82 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Biso Wilson estimate: 145.06 Å2 / Rsym value: 0.054
Reflection shellResolution: 3.8→3.9 Å / % possible all: 29.3

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
BUSTER2.11.4refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→25.26 Å / Cor.coef. Fo:Fc: 0.8611 / Cor.coef. Fo:Fc free: 0.7938 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3146 1342 7.75 %RANDOM
Rwork0.2852 ---
all0.2874 17321 --
obs0.2874 17321 82.34 %-
Displacement parametersBiso mean: 232 Å2
Baniso -1Baniso -2Baniso -3
1-66.6881 Å20 Å26.8954 Å2
2--4.8709 Å20 Å2
3----71.559 Å2
Refine analyzeLuzzati coordinate error obs: 1.367 Å
Refinement stepCycle: LAST / Resolution: 3.8→25.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6621 0 5 0 6626
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096785HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.059228HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2184SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes101HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1000HARMONIC5
X-RAY DIFFRACTIONt_it6785HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion24.14
X-RAY DIFFRACTIONt_chiral_improper_torsion896SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance4HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact8652SEMIHARMONIC4
LS refinement shellResolution: 3.8→4.03 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2416 95 7.49 %
Rwork0.2333 1174 -
all0.234 1269 -
obs--82.34 %
Refinement TLS params.

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)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
118.96050.56281.385513.9206-1.07152.91060.2138-0.56-0.32460.6418-0.23710.71960.0438-0.42110.0233-0.58760.4094-0.1102-0.5029-0.12570.3027261.2511121.80330.1101
219.5639-1.145-0.563510.1825-5.62526.20110.1778-0.37280.39760.4006-0.224-0.8961-0.52740.73760.0462-0.66180.3704-0.1637-0.2374-0.05150.228325.8098120.44125.5926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|8 - A|465 }A8 - 465
2X-RAY DIFFRACTION2{ B|7 - B|471 }B7 - 471

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