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- PDB-3cka: The crystal structure of OspA mutant -

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Basic information

Entry
Database: PDB / ID: 3cka
TitleThe crystal structure of OspA mutant
ComponentsOuter surface protein A
KeywordsMEMBRANE PROTEIN / beta-sheet
Function / homologyOuter surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / cell surface / Outer Surface Protein A / Outer surface protein A / Outer surface protein A
Function and homology information
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMakabe, K. / Biancalana, M. / Terechko, V. / Koide, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Minimalist design of water-soluble cross-{beta} architecture.
Authors: Biancalana, M. / Makabe, K. / Koide, S.
History
DepositionMar 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 16, 2014Group: Structure summary
Revision 1.3Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_mutation / _struct_ref_seq_dif.align_id ..._entity.pdbx_mutation / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Outer surface protein A
B: Outer surface protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0539
Polymers69,3852
Non-polymers1,6687
Water9,314517
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-22.8 kcal/mol
Surface area31830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.293, 83.647, 106.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Outer surface protein A


Mass: 34692.629 Da / Num. of mol.: 2
Mutation: ...Mutation: E37S,E45S,K46S,K48A,K60A,K64S,K83A,E104S,K107S,E123Y,K125L,V132L,E134F,I136Y,K308S,E309S,K323S,E37S,E45S,K46S,K48A,K60A,K64S,K83A,E104S,K107S,E123Y,K125L,V132L,E134F,I136Y,K308S,E309S,K323S,E37S,E45S,K46S,K48A,K60A,K64S,K83A,E104S,K107S,E123Y,K125L,V132L,E134F,I136Y,K308S,E309S,K323S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Gene: ospA / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D2Y4L7, UniProt: Q45040, UniProt: D0VWU8*PLUS
#2: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS AN INSERTION BETWEEN SEQUENCE DATABASE REFERENCE RESIDUES 141 AND 142. THE SEQUENCE OF THE ...THERE IS AN INSERTION BETWEEN SEQUENCE DATABASE REFERENCE RESIDUES 141 AND 142. THE SEQUENCE OF THE INSERTION IS KSSTYELFNEKGELSFKYITRADKSSTYELFNEKGELSFKYITRADKSSTYELFNE KGELSFKYITRADKSSTYELFNEKGELSFKYITRAD

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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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 30% PEG400, 0.1M Tris-HCl, 10mg/ml protein with 4mM Thioflavin-T, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.95373 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 82033 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 22.2
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.5 / Num. unique all: 8124 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OY7

2oy7


Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.799 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24033 4100 5 %RANDOM
Rwork0.20214 ---
all0.20407 77805 --
obs0.20407 77805 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.523 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2---0.63 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4807 0 80 517 5404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224990
X-RAY DIFFRACTIONr_bond_other_d0.0010.023378
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.9916703
X-RAY DIFFRACTIONr_angle_other_deg0.97138378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1185651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32226.374182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91215964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7521510
X-RAY DIFFRACTIONr_chiral_restr0.1260.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025476
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02908
X-RAY DIFFRACTIONr_nbd_refined0.2240.2821
X-RAY DIFFRACTIONr_nbd_other0.2060.23311
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22430
X-RAY DIFFRACTIONr_nbtor_other0.090.22811
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2369
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5571.53429
X-RAY DIFFRACTIONr_mcbond_other0.3881.51317
X-RAY DIFFRACTIONr_mcangle_it2.10425105
X-RAY DIFFRACTIONr_scbond_it3.52432005
X-RAY DIFFRACTIONr_scangle_it4.8014.51589
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.678 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 224 -
Rwork0.226 4631 -
obs--80.08 %

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