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- PDB-5vj4: Crystal structure of a putative surface protein encoded by BTA121 -

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Basic information

Entry
Database: PDB / ID: 5vj4
TitleCrystal structure of a putative surface protein encoded by BTA121
ComponentsUncharacterized protein
KeywordsLIPID BINDING PROTEIN / Relapsing fever
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / Uncharacterized protein
Function and homology information
Biological speciesBorrelia turicatae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsLuo, Z. / Asojo, O.
CitationJournal: Sci Rep / Year: 2017
Title: Crystal Structure of Borrelia turicatae protein, BTA121, a differentially regulated gene in the tick-mammalian transmission cycle of relapsing fever spirochetes.
Authors: Luo, Z. / Kelleher, A.J. / Darwiche, R. / Hudspeth, E.M. / Shittu, O.K. / Krishnavajhala, A. / Schneiter, R. / Lopez, J.E. / Asojo, O.A.
History
DepositionApr 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,64115
Polymers81,3922
Non-polymers1,24913
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-196 kcal/mol
Surface area25330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.055, 102.055, 183.211
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Uncharacterized protein


Mass: 40695.973 Da / Num. of mol.: 2 / Fragment: residues 71-445
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia turicatae (bacteria) / Strain: 91E135 / Gene: BTA121 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R9P931
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.4 Å3/Da / Density % sol: 63.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.8M lithium sulfate, 50mM sodium HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 26628 / % possible obs: 100 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 20.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2665 / CC1/2: 0.738 / Rpim(I) all: 0.037 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→39.8 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 12.405 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.266
RfactorNum. reflection% reflectionSelection details
Rfree0.22401 1293 4.9 %RANDOM
Rwork0.19598 ---
obs0.19732 25264 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 82.974 Å2
Baniso -1Baniso -2Baniso -3
1--2.16 Å2-1.08 Å2-0 Å2
2---2.16 Å20 Å2
3---7 Å2
Refinement stepCycle: 1 / Resolution: 2.8→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4324 0 65 7 4396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194453
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.9766026
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8365546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77823.857210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89615739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1321532
X-RAY DIFFRACTIONr_chiral_restr0.1080.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023331
X-RAY DIFFRACTIONr_gen_planes_other
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_it13.79716.2662190
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it17.98430.3672734
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it18.2316.9922263
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined23.17670.30718902
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: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 94 -
Rwork0.365 1843 -
obs--99.44 %

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