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- PDB-3gzg: Crystal structure of the Xanthomonas axonopodis pv. citri molybda... -

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Basic information

Entry
Database: PDB / ID: 3gzg
TitleCrystal structure of the Xanthomonas axonopodis pv. citri molybdate-binding protein (ModA) mutant (K127S)
ComponentsMolybdate-binding periplasmic protein; permease
KeywordsMETAL BINDING PROTEIN / molybdate complex / mutant K127S
Function / homology
Function and homology information


tungstate binding / 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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MOLYBDATE ION / Molybdate-binding protein ModA
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSantacruz-Perez, C. / Pegos, V.R. / Balan, A. / Barbosa, J.A.R.G.
CitationJournal: To be Published
Title: Crystal structure of the Xanthomonas axonopodis pv. citri molybdate-binding protein (ModA) mutant (K127S)
Authors: Santacruz-Perez, C. / Pegos, V.R. / Balan, A. / Barbosa, J.A.R.G.
History
DepositionApr 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Oct 13, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,3949
Polymers79,6263
Non-polymers7686
Water15,313850
1
A: Molybdate-binding periplasmic protein; permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8944
Polymers26,5421
Non-polymers3523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Molybdate-binding periplasmic protein; permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7022
Polymers26,5421
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Molybdate-binding periplasmic protein; permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7983
Polymers26,5421
Non-polymers2562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.075, 171.648, 113.861
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
11B-5391-

HOH

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Components

#1: Protein Molybdate-binding periplasmic protein; permease


Mass: 26542.066 Da / Num. of mol.: 3 / Mutation: K127S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: modA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8PHA1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE


Mass: 159.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: MoO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 850 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE IS LEU AND IS PROBABLY A REAL VARIANT PRESENT IN NATURE.

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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: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0,1M trihydrate sodium acetate, 0,2M ammonium sulfate, 30% PEG, monometil eter 2000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.421 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 16, 2008 / Details: mirror
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.421 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 94892 / Num. obs: 94892 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 13.7
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 2 / Rsym value: 0.822 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0069refinement
PDB_EXTRACT3.006data extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H5Y

2h5y


Resolution: 1.55→25.74 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.8 / SU ML: 0.065 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23485 2857 3 %RANDOM
Rwork0.20165 ---
obs0.20266 91914 99.22 %-
all-94892 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.55→25.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5135 0 30 850 6015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225255
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.9697160
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.555693
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71323200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66815803
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.111543
X-RAY DIFFRACTIONr_chiral_restr0.1330.2829
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213969
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_it0.7081.53472
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24625512
X-RAY DIFFRACTIONr_scbond_it2.02731783
X-RAY DIFFRACTIONr_scangle_it3.2614.51648
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 211 -
Rwork0.345 6744 -
obs--99.14 %

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