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- PDB-3r26: Perrhenate Binding to Molybdate Binding Protein -

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Basic information

Entry
Database: PDB / ID: 3r26
TitlePerrhenate Binding to Molybdate Binding Protein
ComponentsMolybdate-binding periplasmic protein
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


response to chromate / tungstate ion transport / ABC-type molybdate transporter activity / tungstate binding / molybdate ion binding / molybdate ion transport / molybdenum ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Molybdate ABC transporter, substrate-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
PERRHENATE / Molybdate-binding protein ModA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAryal, B.P. / Brugarolas, P. / He, C.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2012
Title: Binding of ReO(4) (-) with an engineered MoO (4) (2-)-binding protein: towards a new approach in radiopharmaceutical applications.
Authors: Aryal, B.P. / Brugarolas, P. / He, C.
History
DepositionMar 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 21, 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

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Assembly

Deposited unit
A: Molybdate-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6122
Polymers25,3621
Non-polymers2501
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.589, 81.589, 80.624
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Molybdate-binding periplasmic protein


Mass: 25361.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: modA, b0763, JW0746 / Production host: Escherichia coli (E. coli) / References: UniProt: P37329
#2: Chemical ChemComp-REO / PERRHENATE


Mass: 250.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O4Re
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 27.5% PEG8000, 0.1M sodium acetate, 2.5M sodium perrhenate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 32457 / % possible obs: 84.4 % / Redundancy: 11.1 % / Net I/σ(I): 24.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 6.6 / Num. unique all: 1002 / % possible all: 84.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.88 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: (1) DATA WAS COLLECTED TO THE HIGHER RESOLUTION OF 1.59 A. HOWEVER, DATA BELOW 1.7 A HAD LOW COMPLETENESS (LESS THAN 55%), AND THE SIGNAL-TO-NOISE RATIO I/SIGMA(I) WAS SIGNIFICANTLY LOW ...Details: (1) DATA WAS COLLECTED TO THE HIGHER RESOLUTION OF 1.59 A. HOWEVER, DATA BELOW 1.7 A HAD LOW COMPLETENESS (LESS THAN 55%), AND THE SIGNAL-TO-NOISE RATIO I/SIGMA(I) WAS SIGNIFICANTLY LOW (LESS THAN 1.5). THEREFORE THE DATA WAS SCALED TO 1.7 A. (2) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20535 1677 5.1 %RANDOM
Rwork0.17136 ---
obs0.17316 31184 95.09 %-
all-34562 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.138 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0.15 Å20 Å2
2---0.31 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 5 113 1861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0221807
X-RAY DIFFRACTIONr_angle_refined_deg2.031.9612459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1355237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.1962570
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04515300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.933156
X-RAY DIFFRACTIONr_chiral_restr0.1910.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211351
X-RAY DIFFRACTIONr_mcbond_it2.2271.51165
X-RAY DIFFRACTIONr_mcangle_it3.18721870
X-RAY DIFFRACTIONr_scbond_it4.6223642
X-RAY DIFFRACTIONr_scangle_it6.3774.5587
X-RAY DIFFRACTIONr_rigid_bond_restr2.94331807
X-RAY DIFFRACTIONr_sphericity_free13.6343113
X-RAY DIFFRACTIONr_sphericity_bonded8.71331770
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 79 -
Rwork0.264 1539 -
obs--64.8 %

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