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- PDB-4cl2: structure of periplasmic metal binding protein from candidatus li... -

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Basic information

Entry
Database: PDB / ID: 4cl2
Titlestructure of periplasmic metal binding protein from candidatus liberibacter asiaticus
ComponentsPERIPLASMIC SOLUTE BINDING PROTEIN
KeywordsTRANSPORT 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 speciesCANDIDATUS LIBERIBACTER ASIATICUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsSharma, N. / Selvakumar, P. / Bhose, S. / Ghosh, D.K. / 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
DepositionJan 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3May 30, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Dec 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: PERIPLASMIC SOLUTE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,83112
Polymers30,8971
Non-polymers93411
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.060, 94.060, 94.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2079-

HOH

21A-2238-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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)
Strain: PSY62 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: C6XF58

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Non-polymers , 5 types, 273 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 68.49 % / 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: BRUKER / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 7, 2013 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→30.85 Å / Num. obs: 57802 / % possible obs: 95.7 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.5
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.1 / % possible all: 92.1

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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 3HH8

3hh8


Resolution: 1.63→29.29 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.691 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.19419 2927 5.1 %RANDOM
Rwork0.16694 ---
obs0.1683 54875 95.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.332 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.09 Å20 Å2
2--0.09 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.63→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 51 262 2402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192238
X-RAY DIFFRACTIONr_bond_other_d0.0030.022131
X-RAY DIFFRACTIONr_angle_refined_deg1.7971.9863044
X-RAY DIFFRACTIONr_angle_other_deg0.89634934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7365279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31424.83591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82715399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.17159
X-RAY DIFFRACTIONr_chiral_restr0.120.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212480
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02475
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_it2.751.3971094
X-RAY DIFFRACTIONr_mcbond_other2.5531.3871091
X-RAY DIFFRACTIONr_mcangle_it3.5932.0581373
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7261.8971143
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: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 233 -
Rwork0.343 3821 -
obs--91.51 %
Refinement TLS params.Method: refined / Origin x: 29.405 Å / Origin y: -27.262 Å / Origin z: 20.984 Å
111213212223313233
T0.033 Å2-0.005 Å2-0.0051 Å2-0.0418 Å20.0068 Å2--0.0192 Å2
L1.0229 °2-0.3397 °2-0.3789 °2-1.5124 °20.4086 °2--1.1618 °2
S0.0058 Å °0.0881 Å °0.0794 Å °-0.0446 Å °-0.0274 Å °0.032 Å °-0.1462 Å °-0.0099 Å °0.0215 Å °

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