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- PDB-5z2j: structure of S38A mutant metal-free periplasmic metal binding pro... -

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Basic information

Entry
Database: PDB / ID: 5z2j
Titlestructure of S38A mutant metal-free periplasmic metal binding protein from candidatus liberibacter asiaticus
ComponentsPeriplasmic solute binding protein
KeywordsMETAL BINDING PROTEIN / ABC transporter Periplasmic solute binding protein
Function / homology
Function and homology information


metal ion transport / 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 speciesLiberibacter asiaticus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 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
DepositionJan 2, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic solute binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,28619
Polymers30,8811
Non-polymers1,40518
Water5,837324
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-40 kcal/mol
Surface area12890 Å2
2
A: Periplasmic solute binding protein
hetero molecules

A: Periplasmic solute binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,57338
Polymers61,7622
Non-polymers2,81036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area5890 Å2
ΔGint-56 kcal/mol
Surface area22880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.070, 94.070, 94.680
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 Periplasmic solute binding protein


Mass: 30881.055 Da / Num. of mol.: 1 / Mutation: S38A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Liberibacter asiaticus (strain psy62) (bacteria)
Strain: psy62 / Gene: CLIBASIA_02120 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: C6XF58
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 3.98 Å3/Da / Density % sol: 69.06 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / 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: Oct 12, 2015
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→81.48 Å / Num. obs: 40167 / % possible obs: 97.9 % / Redundancy: 5.8 % / Net I/σ(I): 10.2
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.3 / % possible all: 85.6

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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: 1.87→81.47 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.398 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.097 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19151 1885 4.7 %RANDOM
Rwork0.15797 ---
obs0.15953 38248 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 30.143 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å2-0 Å2
3----0.22 Å2
Refinement stepCycle: 1 / Resolution: 1.87→81.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 89 324 2546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192384
X-RAY DIFFRACTIONr_bond_other_d0.0020.022245
X-RAY DIFFRACTIONr_angle_refined_deg1.9041.9983229
X-RAY DIFFRACTIONr_angle_other_deg1.06635233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9865297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48924.53697
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35215418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1641512
X-RAY DIFFRACTIONr_chiral_restr0.1250.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212591
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02449
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_it3.1511.5011146
X-RAY DIFFRACTIONr_mcbond_other2.6861.4611137
X-RAY DIFFRACTIONr_mcangle_it4.2062.191435
X-RAY DIFFRACTIONr_mcangle_other4.2252.1941436
X-RAY DIFFRACTIONr_scbond_it4.8652.0511237
X-RAY DIFFRACTIONr_scbond_other4.8642.0561238
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9632.8691789
X-RAY DIFFRACTIONr_long_range_B_refined10.34721.242891
X-RAY DIFFRACTIONr_long_range_B_other10.34621.272892
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.872→1.921 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 137 -
Rwork0.307 2625 -
obs--93.95 %
Refinement TLS params.Method: refined / Origin x: -38.079 Å / Origin y: -11.704 Å / Origin z: 5.015 Å
111213212223313233
T0.0694 Å20.0019 Å20.0118 Å2-0.044 Å20.0027 Å2--0.0187 Å2
L2.057 °2-0.2056 °20.6323 °2-1.0064 °20.0234 °2--1.259 °2
S-0.0281 Å °0.0922 Å °0.0045 Å °-0.0867 Å °-0.0009 Å °-0.1139 Å °0.0776 Å °0.167 Å °0.029 Å °

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