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- PDB-5ipw: oligopeptide-binding protein OppA -

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Basic information

Entry
Database: PDB / ID: 5ipw
Titleoligopeptide-binding protein OppA
ComponentsOligopeptide ABC transporter, periplasmic oligopeptide-binding protein, putative
KeywordsPEPTIDE BINDING PROTEIN / oligopeptide-binding protein
Function / homologySolute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / peptide transport / peptide transmembrane transporter activity / Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein, putative
Function and homology information
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLee, H.H. / Kim, H.J. / Yoon, H.J.
CitationJournal: Extremophiles / Year: 2016
Title: Crystal structure of a putative oligopeptide-binding periplasmic protein from a hyperthermophile
Authors: Yoon, H.J. / Kim, H.J. / Mikami, B. / Yu, Y.G. / Lee, H.H.
History
DepositionMar 10, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 20, 2024Group: 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: Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein, putative


Theoretical massNumber of molelcules
Total (without water)72,9721
Polymers72,9721
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area26080 Å2
Unit cell
Length a, b, c (Å)190.494, 190.494, 133.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein, putative


Mass: 72971.508 Da / Num. of mol.: 1 / Fragment: UNP residues 31-659
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / Gene: TM_0056 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WXR2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 4.14 Å3/Da / Density % sol: 70.3 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM sodium HEPES, 1.0 M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9789 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Nov 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 37769 / % possible obs: 99.9 % / Redundancy: 13.4 % / Net I/σ(I): 39.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.49 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.244 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23928 1889 5 %RANDOM
Rwork0.20901 ---
obs0.21055 35879 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 60.952 Å2
Baniso -1Baniso -2Baniso -3
1--2.88 Å2-0 Å20 Å2
2---2.88 Å20 Å2
3---5.76 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5162 0 0 155 5317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195320
X-RAY DIFFRACTIONr_bond_other_d0.0010.024936
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.957241
X-RAY DIFFRACTIONr_angle_other_deg0.761311393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.425632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64124.335263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4915875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3261528
X-RAY DIFFRACTIONr_chiral_restr0.0660.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021237
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_it2.4656.0292531
X-RAY DIFFRACTIONr_mcbond_other2.4656.0292530
X-RAY DIFFRACTIONr_mcangle_it4.0759.0413162
X-RAY DIFFRACTIONr_mcangle_other4.0749.043163
X-RAY DIFFRACTIONr_scbond_it2.1576.212789
X-RAY DIFFRACTIONr_scbond_other2.1576.212790
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.749.2164080
X-RAY DIFFRACTIONr_long_range_B_refined6.44648.7016363
X-RAY DIFFRACTIONr_long_range_B_other6.40648.726323
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 132 -
Rwork0.328 2607 -
obs--99.71 %

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