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- PDB-4rxl: Crystal structure of Molybdenum ABC transporter solute binding pr... -

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Basic information

Entry
Database: PDB / ID: 4rxl
TitleCrystal structure of Molybdenum ABC transporter solute binding protein Vc_A0726 from Vibrio Cholerae, Target EFI-510913, in complex with tungstate
ComponentsMolybdenum ABC transporter, periplasmic molybdenum-binding protein
KeywordsTRANSPORT PROTEIN / TRANSPORTER / ABC-TYPE / ENZYME FUNCTION INITIATIVE / EFI / STRUCTURAL GENOMICS
Function / homology
Function and homology information


molybdate ion binding / molybdate ion transport / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Molybdate ABC transporter, substrate-binding protein / : / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TUNGSTATE(VI)ION / Molybdenum ABC transporter, periplasmic molybdenum-binding protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsPatskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Morisco, L.L. / Wasserman, S.R. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Hillerich, B. / Siedel, R.D. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal Structure of Molybdate Transporter Vc_A0726 from Vibrio Cholerae, Target EFI-510913
Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Morisco, L.L. / Wasserman, S.R. / ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Morisco, L.L. / Wasserman, S.R. / Hillerich, B. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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 / 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 / _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: Molybdenum ABC transporter, periplasmic molybdenum-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4932
Polymers25,2451
Non-polymers2481
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.445, 56.633, 50.146
Angle α, β, γ (deg.)90.00, 90.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Molybdenum ABC transporter, periplasmic molybdenum-binding protein


Mass: 25245.482 Da / Num. of mol.: 1 / Fragment: UNP residues 23-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0726 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KLL7
#2: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: WO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PROTEIN (10 MM HEPES, PH 7.5, 5 MM DTT, 10 MM SODIUM TUNGSTATE); RESERVOIR: 0.1 M TRIS:HCL, PH 7.0, 0.2 M MAGNESIUM CHLORIDE, 10% PEG8000; CRYOPROTECTION: RESERVOIR SOLUTION PLUS 20% ...Details: PROTEIN (10 MM HEPES, PH 7.5, 5 MM DTT, 10 MM SODIUM TUNGSTATE); RESERVOIR: 0.1 M TRIS:HCL, PH 7.0, 0.2 M MAGNESIUM CHLORIDE, 10% PEG8000; CRYOPROTECTION: RESERVOIR SOLUTION PLUS 20% GLYCEROL (VOL/VOL); VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 21, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 28440 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.124 / Rsym value: 0.124 / Net I/σ(I): 18.4
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.87 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXmodel building
ARP/wARPmodel building
REFMAC5.8.0073refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.52→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.301 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20998 837 2.9 %RANDOM
Rwork0.1713 ---
obs0.17245 28440 93.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.309 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å2-0.51 Å2
2---1.11 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.52→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 5 106 1842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191787
X-RAY DIFFRACTIONr_bond_other_d0.0010.021715
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.9492444
X-RAY DIFFRACTIONr_angle_other_deg0.7633920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2295232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53524.67577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30215279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0111510
X-RAY DIFFRACTIONr_chiral_restr0.1040.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212073
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02409
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_it4.5351.929922
X-RAY DIFFRACTIONr_mcbond_other4.5241.924921
X-RAY DIFFRACTIONr_mcangle_it5.4593.2491153
X-RAY DIFFRACTIONr_mcangle_other5.4583.2551154
X-RAY DIFFRACTIONr_scbond_it10.552.812865
X-RAY DIFFRACTIONr_scbond_other10.4622.814861
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.564.3321285
X-RAY DIFFRACTIONr_long_range_B_refined12.179.8942012
X-RAY DIFFRACTIONr_long_range_B_other12.239.6691971
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 55 -
Rwork0.209 2202 -
obs--99.21 %
Refinement TLS params.Method: refined / Origin x: 25.4593 Å / Origin y: 1.5182 Å / Origin z: 20.9338 Å
111213212223313233
T0.0379 Å2-0.0065 Å20.0135 Å2-0.0191 Å2-0.0076 Å2--0.0138 Å2
L2.558 °2-0.7493 °20.4199 °2-2.2397 °2-0.3158 °2--1.7865 °2
S-0.0107 Å °0.0695 Å °0.0234 Å °-0.0442 Å °-0.08 Å °0.0309 Å °-0.0382 Å °-0.0035 Å °0.0908 Å °

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