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- PDB-3lgj: Crystal structure of single-stranded binding protein (ssb) from B... -

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Basic information

Entry
Database: PDB / ID: 3lgj
TitleCrystal structure of single-stranded binding protein (ssb) from Bartonella henselae
ComponentsSingle-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / NIAID / Cat Scratch Fever / Rochalimaea / lyme disease / ALS Collaborative Crystallography / DNA replication / DNA-binding / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


single-stranded DNA binding / DNA recombination / DNA replication / metal ion binding
Similarity search - Function
Single-stranded DNA-binding protein / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Single-stranded DNA-binding protein / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of single-stranded binding protein (ssb) from Bartonella henselae
Authors: Edwards, T.E. / Abendroth, J. / Sankaran, B.
History
DepositionJan 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 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_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

Downloads & links

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Assembly

Deposited unit
A: Single-stranded DNA-binding protein
B: Single-stranded DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1413
Polymers38,1012
Non-polymers401
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-12 kcal/mol
Surface area10740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.530, 93.530, 115.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-149-

CA

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 1 - 111 / Label seq-ID: 22 - 132

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Single-stranded DNA-binding protein


Mass: 19050.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Gene: ssb2, ssb3, BH07030, BH09470 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6G3Q0, UniProt: A0A0G2Q8L7*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 1.91 Å3/Da / Density % sol: 35.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: JCSG+ condition G11, 0.1 M BisTris, 2 M ammonium sulfate, crystal tracking ID 202927g11, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→29.7 Å / Num. obs: 10787 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Biso Wilson estimate: 69.604 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 34.12
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 4.9 / Num. measured obs: 10800 / Num. unique obs: 788 / Rsym value: 0.595 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.47 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å29.67 Å
Translation3 Å29.67 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1kaw

1kaw


Resolution: 2.5→29.7 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.228 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.793 / SU B: 19.377 / SU ML: 0.197 / SU R Cruickshank DPI: 0.341 / SU Rfree: 0.26 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.341 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.267 542 5 %RANDOM
Rwork0.225 ---
obs0.228 10779 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.53 Å2 / Biso mean: 36.943 Å2 / Biso min: 20.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 1 22 1483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211508
X-RAY DIFFRACTIONr_angle_refined_deg1.511.9452049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4725190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.09924.42661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.62415234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.984152
X-RAY DIFFRACTIONr_chiral_restr0.0980.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211118
X-RAY DIFFRACTIONr_mcbond_it0.6681.5952
X-RAY DIFFRACTIONr_mcangle_it1.28321515
X-RAY DIFFRACTIONr_scbond_it2.1933556
X-RAY DIFFRACTIONr_scangle_it3.5474.5532
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 703 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.440.5
MEDIUM THERMAL0.922
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 37 -
Rwork0.356 738 -
all-775 -
obs--100 %
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)
13.6772-0.10880.27043.6995-0.04164.91550.0341-0.03270.2669-0.0861-0.0670.3718-0.4416-0.48440.03290.0610.0406-0.05080.201-0.03740.16874.4716-37.38485.8182
23.97441.0185-1.3163.3734-1.50276.3613-0.09410.17840.2727-0.1456-0.0776-0.0294-0.38680.14630.17170.1477-0.0161-0.070.08910.02110.158424.3299-29.1065-0.1463
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 113
2X-RAY DIFFRACTION1A149
3X-RAY DIFFRACTION1A150 - 158
4X-RAY DIFFRACTION2B-1 - 112
5X-RAY DIFFRACTION2B149 - 161

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