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- PDB-3axf: Perrhenate binding to A11C/R153C ModA mutant -

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Basic information

Entry
Database: PDB / ID: 3axf
TitlePerrhenate binding to A11C/R153C ModA mutant
ComponentsMolybdate-binding periplasmic protein
KeywordsMETAL BINDING PROTEIN / molybdate binding protein
Function / homology
Function and homology information


response to chromate / tungstate ion transport / ABC-type molybdate transporter activity / molybdate ion binding / tungstate 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: 2 Å
AuthorsHe, C. / Aryal, B.P. / Brugarolas, P.
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
DepositionApr 4, 2011Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Molybdate-binding periplasmic protein
B: Molybdate-binding periplasmic protein
C: Molybdate-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7706
Polymers76,0193
Non-polymers7513
Water2,630146
1
A: Molybdate-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5902
Polymers25,3401
Non-polymers2501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Molybdate-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5902
Polymers25,3401
Non-polymers2501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Molybdate-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5902
Polymers25,3401
Non-polymers2501
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.751, 77.458, 163.033
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A3 - 233
2114B3 - 233
3114C3 - 233

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Components

#1: Protein Molybdate-binding periplasmic protein


Mass: 25339.750 Da / Num. of mol.: 3 / Mutation: A11C, R153C / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P37329
#2: Chemical ChemComp-REO / PERRHENATE / Perrhenate


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


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 26% PEG8000, 0.1 M sodium acetate, 2.5 mM sodium perrhenate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 27, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 43585 / % possible obs: 56.4 % / Redundancy: 13.4 % / Net I/σ(I): 39.6
Reflection shellResolution: 2→2.24 Å / Mean I/σ(I) obs: 8.9 / % possible all: 56.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.675 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: (1) DATA WAS COLLECTED TO THE HIGHER RESOLUTION OF 1.5 A. HOWEVER, DATA BELOW 2.0 A HAD LOW COMPLETENESS (LESS THAN 55%), AND THE SIGNAL-TO-NOISE RATIO I/SIGMA(I) WAS SIGNIFICANTLY LOW (LESS ...Details: (1) DATA WAS COLLECTED TO THE HIGHER RESOLUTION OF 1.5 A. HOWEVER, DATA BELOW 2.0 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 2.0 A. (2) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25788 2322 5 %RANDOM
Rwork0.20395 ---
obs0.2066 43585 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.779 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5217 0 15 146 5378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0225465
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9161.9627447
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64225.286210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.03915912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7331515
X-RAY DIFFRACTIONr_chiral_restr0.1630.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214103
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0021.53528
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61225679
X-RAY DIFFRACTIONr_scbond_it2.69631937
X-RAY DIFFRACTIONr_scangle_it3.9744.51763
X-RAY DIFFRACTIONr_rigid_bond_restr2.06235465
X-RAY DIFFRACTIONr_sphericity_free9.9993146
X-RAY DIFFRACTIONr_sphericity_bonded2.85935346
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1652 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.490.5
Bmedium positional0.520.5
Cmedium positional0.580.5
Amedium thermal1.532
Bmedium thermal1.922
Cmedium thermal1.622
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 161 -
Rwork0.268 3173 -
obs--100 %
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)
11.57810.532-0.50640.5825-0.57512.729-0.04340.44690.2119-0.03980.23690.01670.0272-0.4661-0.19350.0623-0.0344-0.02780.20290.11440.1178-35.9576-22.659814.2365
20.6979-0.01770.14441.22950.10140.9101-0.0329-0.02070.0202-0.05710.0682-0.0112-0.05930.0814-0.03530.0505-0.0073-0.00260.03-0.00280.0643-13.6241-18.249535.2858
32.79420.3516-2.44580.7975-0.75432.9074-0.44580.5692-0.0235-0.43540.2856-0.07540.711-0.47770.16020.6555-0.13380.06110.5464-0.17010.2912-32.8358-55.961713.9107
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 233
2X-RAY DIFFRACTION2B3 - 233
3X-RAY DIFFRACTION3C3 - 233

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