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- PDB-4ovj: Extracellular solute-binding protein family 1 from Alicyclobacill... -

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Basic information

Entry
Database: PDB / ID: 4ovj
TitleExtracellular solute-binding protein family 1 from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
ComponentsExtracellular solute-binding protein family 1
KeywordsTRANSPORT PROTEIN / Solute binding protein / MCSG / PSI-biology / Midwest center for structural genomics
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / Extracellular solute-binding protein family 1
Function and homology information
Biological speciesAlicyclobacillus acidocaldarius subsp. acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsChang, C. / Clancy, S. / Li, H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: to be published
Title: extracellular solute-binding protein family 1 from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
Authors: Chang, C. / Clancy, S. / Li, H. / Joachimiak, A.
History
DepositionOct 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references / Other
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Experimental preparation / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / exptl_crystal / pdbx_database_status / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / software / struct_keywords / symmetry
Item: _citation.journal_id_CSD / _entity_src_gen.gene_src_common_name ..._citation.journal_id_CSD / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_alt_source_flag / _entity_src_gen.pdbx_gene_src_scientific_name / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.type / _software.version / _struct_keywords.text / _symmetry.Int_Tables_number
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extracellular solute-binding protein family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9312
Polymers45,8351
Non-polymers961
Water7,584421
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-15 kcal/mol
Surface area17290 Å2
Unit cell
Length a, b, c (Å)59.716, 38.819, 82.456
Angle α, β, γ (deg.)90.000, 92.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Extracellular solute-binding protein family 1


Mass: 45834.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius subsp. acidocaldarius (strain ATCC 27009 / DSM 446 / JCM 5260 / NBRC 15652 / NCIMB 11725 / NRRL B-14509 / 104-1A) (bacteria)
Strain: ATCC 27009 / DSM 446 / JCM 5260 / NBRC 15652 / NCIMB 11725 / NRRL B-14509 / 104-1A
Gene: Aaci_2460 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C8WSI1
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.08 Å3/Da / Density % sol: 40.97 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Li Sulfate, 0.1 M HEPES , 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2013
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 45947 / Num. obs: 45731 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 23.8
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.23 / % possible all: 94.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
HKL-30003.11phasing
HKL-30003.11data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.65→34.54 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.127 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.084
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1629 2155 5 %RANDOM
Rwork0.1191 40723 --
obs0.1212 42878 93.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.46 Å2 / Biso mean: 16.7321 Å2 / Biso min: 6.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0 Å20.14 Å2
2---0.25 Å2-0 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.65→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3086 0 5 421 3512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193362
X-RAY DIFFRACTIONr_bond_other_d0.0010.023127
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9584601
X-RAY DIFFRACTIONr_angle_other_deg0.73637241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9595435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64926.013153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64715534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.805156
X-RAY DIFFRACTIONr_chiral_restr0.0690.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213983
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02771
X-RAY DIFFRACTIONr_rigid_bond_restr1.97136489
X-RAY DIFFRACTIONr_sphericity_free28.122596
X-RAY DIFFRACTIONr_sphericity_bonded7.29156716
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 83 -
Rwork0.124 1661 -
all-1744 -
obs--51.28 %

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