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- PDB-4onr: Crystal structure of Borrelia burgdorferi decorin-binding protein DbpA -

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Basic information

Entry
Database: PDB / ID: 4onr
TitleCrystal structure of Borrelia burgdorferi decorin-binding protein DbpA
ComponentsDECORIN-BINDING PROTEIN DbpA
KeywordsCELL ADHESION / GAG-BINDING PROTEIN / HELICAL BUNDLE PROTEIN / LYME DISEASE / BACTERIAL ADHESIN
Function / homology
Function and homology information


: / Decorin-binding protein / Decorin-binding protein / Decorin-binding superfamily / Decorin binding protein / A middle domain of Talin 1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / DbpA
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsTomchick, D.R. / Deka, R.K. / Blevins, J.S.
CitationJournal: Infect.Immun. / Year: 2014
Title: Identification of Lysine Residues in the Borrelia burgdorferi DbpA Adhesin Required for Murine Infection.
Authors: Fortune, D.E. / Lin, Y.P. / Deka, R.K. / Groshong, A.M. / Moore, B.P. / Hagman, K.E. / Leong, J.M. / Tomchick, D.R. / Blevins, J.S.
History
DepositionJan 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: DECORIN-BINDING PROTEIN DbpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1182
Polymers18,0601
Non-polymers591
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.524, 49.524, 57.943
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein DECORIN-BINDING PROTEIN DbpA


Mass: 18059.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Strain: Bb297 / Gene: dbpA / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q1W5I8
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 1.97 Å3/Da / Density % sol: 37.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.1 M CHES, 0.05 M NaCl, 30% PEG 3000, 10% (w/v) ethylene glycol, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97935
SYNCHROTRONAPS 19-BM20.97899, 0.97915
Detector
TypeIDDetectorDateDetails
SBC-31CCDFeb 13, 2004monochromator
SBC-32CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979351
20.978991
30.979151
ReflectionResolution: 1.6→22.8 Å / Num. all: 18358 / Num. obs: 18358 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Biso Wilson estimate: 22.59 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 33.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.6-1.643.30.6311.71,287.9
1.68-1.721,299.4
1.72-1.771,2100
1.77-1.831,2100
1.83-1.91,2100
1.9-1.971,2100
1.97-2.061,2100
2.06-2.171,2100
2.17-2.311,2100
2.31-2.491,2100
2.49-2.741,2100
2.74-3.131,2100
3.13-3.951,2100
3.95-22.81,297.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→22.77 Å / SU ML: 0.18 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 21.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.201 937 5.12 %RANDOM
Rwork0.1694 ---
obs0.1711 18318 98.87 %-
all-18318 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.96 Å2 / Biso mean: 34.7595 Å2 / Biso min: 13.73 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.6→22.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1120 0 1 171 1292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011156
X-RAY DIFFRACTIONf_angle_d1.1351551
X-RAY DIFFRACTIONf_chiral_restr0.046182
X-RAY DIFFRACTIONf_plane_restr0.007199
X-RAY DIFFRACTIONf_dihedral_angle_d14.462449
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6002-1.68450.2731300.24442319244993
1.6845-1.790.25071490.192524732622100
1.79-1.92820.24011310.18525022633100
1.9282-2.12210.21551340.171325192653100
2.1221-2.42890.22711230.149925022625100
2.4289-3.05890.18711530.171325062659100
3.0589-22.77220.17781170.1642560267799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.8025-3.0475-0.28933.79790.79212.1854-0.0725-0.1085-0.49050.1505-0.05030.21340.4019-0.01640.1270.3396-0.0203-0.01830.2111-0.01660.233222.9263-3.4388-2.9115
22.9503-0.3489-0.45662.89470.1542.1755-0.02810.1369-0.0274-0.2167-0.1825-0.05110.158-0.10390.18240.193500.00370.1451-0.01290.136320.75575.8793-2.004
33.457-0.8154-0.46053.20850.5532.4647-0.0524-0.30440.22230.09290.0169-0.2482-0.01150.21780.03120.1797-0.0045-0.00650.1735-0.00730.159526.18319.24234.7633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 75 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 129 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 175 )A0

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