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- PDB-5zha: Structure of Y68F mutant Mn-Bound periplasmic metal binding prote... -

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Basic information

Entry
Database: PDB / ID: 5zha
TitleStructure of Y68F mutant Mn-Bound periplasmic metal binding protein from candidatus liberibacter asiaticus
ComponentsPeriplasmic solute binding protein
KeywordsMETAL BINDING PROTEIN / ABC transporter / Periplasmic metal binding protein
Function / homology
Function and homology information


metal ion transport / cell envelope / cell adhesion / metal ion binding
Similarity search - Function
Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Periplasmic solute binding protein
Similarity search - Component
Biological speciesCandidatus Liberibacter asiaticus str. psy62 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsSaini, G. / Sharma, N. / Dalal, V. / Kumar, P. / Sharma, A.K.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: The analysis of subtle internal communications through mutation studies in periplasmic metal uptake protein CLas-ZnuA2
Authors: Saini, G. / Sharma, N. / Dalal, V. / Warghane, A. / Ghosh, D.K. / Kumar, P. / Sharma, A.K.
History
DepositionMar 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic solute binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,59525
Polymers30,8811
Non-polymers1,71424
Water6,684371
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-13 kcal/mol
Surface area12680 Å2
2
A: Periplasmic solute binding protein
hetero molecules

A: Periplasmic solute binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,19150
Polymers61,7622
Non-polymers3,42948
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area5650 Å2
ΔGint-34 kcal/mol
Surface area22700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.952, 93.952, 94.567
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Periplasmic solute binding protein


Mass: 30881.055 Da / Num. of mol.: 1 / Fragment: UNP residues 20-294 / Mutation: Y68F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Liberibacter asiaticus str. psy62 (bacteria)
Strain: psy62 / Gene: CLIBASIA_02120 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: C6XF58

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Non-polymers , 5 types, 395 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 3.9 Å3/Da / Density % sol: 68.47 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 4.6
Details: 0.1M SODIUM ACETATE TRIHYDRATE pH 4.6, 2M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 31, 2015
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→40.8 Å / Num. obs: 45940 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 25.3 Å2 / Net I/σ(I): 23.5
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UDN

4udn


Resolution: 1.84→40.8 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.515 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18905 2040 4.8 %RANDOM
Rwork0.14009 ---
obs0.14248 40046 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.228 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.84→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2082 0 110 371 2563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192299
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.9973095
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3795277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72924.62493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83215398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3751510
X-RAY DIFFRACTIONr_chiral_restr0.1320.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211706
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_it3.7472.7771108
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.0674.0571375
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.4493.431188
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.30742.4993801
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.54532296
X-RAY DIFFRACTIONr_sphericity_free34.1365227
X-RAY DIFFRACTIONr_sphericity_bonded18.11952425
LS refinement shellResolution: 1.84→1.887 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 130 -
Rwork0.298 2943 -
obs--99.64 %

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