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- PDB-2hkd: The crystal structure of engineered OSPA -

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Basic information

Entry
Database: PDB / ID: 2hkd
TitleThe crystal structure of engineered OSPA
ComponentsOuter Surface Protein A
KeywordsDE NOVO PROTEIN / BETA SHEET / engineered protein
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
C1 set domains (antibody constant domain-like) / Outer Surface Protein A; domain 3 - #1 / Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / Outer Surface Protein A; domain 3 / Lipocalin / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Outer Surface Protein A
Similarity search - Component
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMakabe, K. / Terechko, V. / Koide, S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Atomic structures of peptide self-assembly mimics.
Authors: Makabe, K. / McElheny, D. / Tereshko, V. / Hilyard, A. / Gawlak, G. / Yan, S. / Koide, A. / Koide, S.
History
DepositionJul 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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_description / _entity_src_gen.pdbx_beg_seq_num ..._entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...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 / 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
Remark 999SEQUENCE THERE IS AN INSERTION BETWEEN SEQUENCE DATABASE REFERENCE RESIDUES 118 AND 119. THE ...SEQUENCE THERE IS AN INSERTION BETWEEN SEQUENCE DATABASE REFERENCE RESIDUES 118 AND 119. THE SEQUENCE OF THE INSERTION IS KSSTEEKFNEKGELSEKKITRADKSSTEEKFNEKGELSEKKITRADKSSTEEKFNE KGELSEKKITRAD

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer Surface Protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5762
Polymers34,3821
Non-polymers1941
Water7,638424
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.199, 76.561, 121.312
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: 34382.207 Da / Num. of mol.: 1
Mutation: E37S, E45S, K46S, K48A, K60A, K64S, K83A, E104S, K107S, K308S, K309S, K323S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Genus: Borrelia / Production host: Escherichia coli (E. coli) / References: UniProt: D0VWU8
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 31%PEG400, 100mM Tris-HCl pH9.0, 2%MPD , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9718 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 44499 / % possible obs: 96.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.157 / Rsym value: 0.157
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.12 / Rsym value: 0.71 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G8C

2g8c


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.015 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.099 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23747 2223 5 %RANDOM
Rwork0.19634 ---
all0.1984 44499 --
obs0.19841 42184 95.75 %-
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: 18.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2428 0 13 426 2867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222464
X-RAY DIFFRACTIONr_bond_other_d0.0010.022245
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9943316
X-RAY DIFFRACTIONr_angle_other_deg0.76835348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4485337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82427.71792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86615520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.999155
X-RAY DIFFRACTIONr_chiral_restr0.0850.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022700
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02396
X-RAY DIFFRACTIONr_nbd_refined0.2120.2414
X-RAY DIFFRACTIONr_nbd_other0.1960.22102
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21188
X-RAY DIFFRACTIONr_nbtor_other0.0830.21462
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2297
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3311.52094
X-RAY DIFFRACTIONr_mcbond_other0.2561.5666
X-RAY DIFFRACTIONr_mcangle_it1.43622582
X-RAY DIFFRACTIONr_scbond_it2.8483986
X-RAY DIFFRACTIONr_scangle_it3.9244.5722
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.645 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 149 -
Rwork0.265 2599 -
obs--81.93 %

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