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- PDB-4udn: structure of metal-free periplasmic metal binding protein from ca... -

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Basic information

Entry
Database: PDB / ID: 4udn
Titlestructure of metal-free periplasmic metal binding protein from candidatus liberibacter asiaticus
ComponentsPERIPLASMIC SOLUTE BINDING PROTEIN
KeywordsMETAL BINDING PROTEIN / METAL ION TRANSPORTER / PERIPLASMIC
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 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsSharma, N. / Selvakumar, P. / Kumar, P. / Sharma, A.K.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Crystal Structure of a Periplasmic Solute Binding Protein in Metal-Free, Intermediate and Metal-Bound States from Candidatus Liberibacter Asiaticus.
Authors: Sharma, N. / Selvakumar, P. / Bhose, S. / Ghosh, D.K. / Kumar, P. / Sharma, A.K.
History
DepositionDec 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: PERIPLASMIC SOLUTE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,80511
Polymers30,8971
Non-polymers90810
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.530, 94.530, 94.360
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: 30897.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDATUS LIBERIBACTER ASIATICUS (bacteria)
Plasmid: PET28C / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: C6XF58
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 4.06 Å3/Da / Density % sol: 69.7 % / Description: NONE
Crystal growpH: 4.6
Details: 0.1M SODIUM ACETATE TRIHYDRATE PH 4.6, 2M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 30, 2014 / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→47.18 Å / Num. obs: 23857 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.4 / % possible all: 85.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CL2

4cl2


Resolution: 2.21→42.3 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.741 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22386 1209 5.1 %RANDOM
Rwork0.18392 ---
obs0.18594 22523 95.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.427 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.18 Å20 Å2
2--0.18 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.21→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 53 171 2329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192189
X-RAY DIFFRACTIONr_bond_other_d0.0010.022094
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.9862960
X-RAY DIFFRACTIONr_angle_other_deg0.76334837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7435263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37424.83591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12115387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.311159
X-RAY DIFFRACTIONr_chiral_restr0.0760.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212377
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02462
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_it3.7212.8421062
X-RAY DIFFRACTIONr_mcbond_other3.7182.8351060
X-RAY DIFFRACTIONr_mcangle_it5.3384.2321321
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7233.3961127
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.214→2.272 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 74 -
Rwork0.298 1320 -
obs--75.93 %

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