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- PDB-3lr1: The crystal structure of the tungstate ABC transporter from Geoba... -

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Basic information

Entry
Database: PDB / ID: 3lr1
TitleThe crystal structure of the tungstate ABC transporter from Geobacter sulfurreducens
ComponentsTungstate ABC transporter, periplasmic tungstate-binding protein
KeywordsTRANSPORT PROTEIN / The tungstate ABC transporter / periplasmic tungstate-binding protein / structural genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology: / PBP domain / PBP superfamily domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / : / Tungstate ABC transporter, periplasmic tungstate-binding protein
Function and homology information
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsZhang, R. / Volkart, L. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the tungstate ABC transporter from Geobacter sulfurreducens
Authors: Zhang, R. / Volkart, L. / Buck, K. / Joachimiak, A.
History
DepositionFeb 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Tungstate ABC transporter, periplasmic tungstate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3964
Polymers25,9361
Non-polymers4603
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.736, 70.386, 91.161
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-359-

HOH

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Components

#1: Protein Tungstate ABC transporter, periplasmic tungstate-binding protein


Mass: 25935.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: PCA / Gene: GSU2700 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q749P2
#2: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: W
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M bis-tris, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→49.54 Å / Num. all: 20072 / Num. obs: 19739 / % possible obs: 98.34 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 23.83
Reflection shellResolution: 1.8→1.847 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 1.88 / Num. unique all: 1554 / % possible all: 96.72

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→49.54 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.939 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.155
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26527 1068 5.1 %RANDOM
Rwork0.18106 ---
obs0.18516 19739 98.34 %-
all-20072 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.97 Å20 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 8 173 1957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221814
X-RAY DIFFRACTIONr_bond_other_d0.0040.021241
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.9772447
X-RAY DIFFRACTIONr_angle_other_deg1.08533047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9165230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77524.78971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.30615322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.905157
X-RAY DIFFRACTIONr_chiral_restr0.140.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211991
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02346
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.81.51145
X-RAY DIFFRACTIONr_mcbond_other0.5561.5476
X-RAY DIFFRACTIONr_mcangle_it2.82921837
X-RAY DIFFRACTIONr_scbond_it4.7073669
X-RAY DIFFRACTIONr_scangle_it6.864.5610
X-RAY DIFFRACTIONr_rigid_bond_restr2.02833055
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 89 -
Rwork0.221 1414 -
obs-1503 96.72 %
Refinement TLS params.Method: refined / Origin x: 7.043 Å / Origin y: 15.043 Å / Origin z: 8.062 Å
111213212223313233
T0.0443 Å2-0.0033 Å20.0195 Å2-0.0717 Å20.0136 Å2--0.1069 Å2
L0.8669 °2-0.05 °2-0.244 °2-0.5024 °20.1551 °2--1.7225 °2
S-0.0144 Å °0.1101 Å °0.0268 Å °-0.0743 Å °-0.0132 Å °-0.064 Å °-0.0984 Å °-0.093 Å °0.0276 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 50
2X-RAY DIFFRACTION1A51 - 100
3X-RAY DIFFRACTION1A101 - 150
4X-RAY DIFFRACTION1A151 - 200
5X-RAY DIFFRACTION1A201 - 233

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