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- PDB-3pgz: Crystal structure of a single strand binding protein (SSB) from b... -

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Basic information

Entry
Database: PDB / ID: 3pgz
TitleCrystal structure of a single strand binding protein (SSB) from bartonella henselae
ComponentsSingle-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / SSGCID / BARTONELLA HENSELAE / SINGLE-STRAND BINDING PROTEIN / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


single-stranded DNA binding / DNA recombination / DNA replication
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a single strand binding protein (SSB) from bartonella henselae
Authors: Seattle Structural Genomics Center for Infectious Disease / Abendroth, J. / Edwards, T.E. / Staker, B.
History
DepositionNov 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)43,2508
Polymers43,2502
Non-polymers06
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint0 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.760, 93.760, 63.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Single-stranded DNA-binding protein


Mass: 21624.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Strain: HOUSTON-1 / Gene: BH10130, ssb4 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6G302, UniProt: A0A0H3LX24*PLUS
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 6 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.86 Å3/Da / Density % sol: 33.99 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 25 % PEG 3350, 200 MM NACL, 100 MM TRIS HCL, PROTEIN AT 4.5 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 19153 / Num. obs: 18898 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 35.73 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 22.67
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 5 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1386 / % possible all: 96

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3lGJ

3lgj


Resolution: 2.1→46.88 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / SU B: 10.621 / SU ML: 0.124 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.256 972 5.2 %RANDOM
Rwork0.21 ---
all0.212 18898 --
obs0.212 18828 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 0 6 134 1944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221871
X-RAY DIFFRACTIONr_bond_other_d0.0010.021296
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.9422531
X-RAY DIFFRACTIONr_angle_other_deg0.85933149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1645232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64924.563103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71615357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1531519
X-RAY DIFFRACTIONr_chiral_restr0.1030.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022093
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02376
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_it0.8381.51116
X-RAY DIFFRACTIONr_mcbond_other0.1761.5464
X-RAY DIFFRACTIONr_mcangle_it1.63921799
X-RAY DIFFRACTIONr_scbond_it2.5783755
X-RAY DIFFRACTIONr_scangle_it4.3874.5726
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 61 -
Rwork0.316 1265 -
obs--95.6 %
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)
13.02770.5248-0.42351.29940.09770.7544-0.0450.0793-0.1692-0.12560.0558-0.1509-0.0030.0356-0.01080.064-0.02770.02290.1098-0.02240.0643-9.279944.571112.9969
226.40613.77815.692510.64798.24069.2594-0.22630.8256-0.1643-0.3992-0.05690.1564-0.4816-0.51960.28320.2645-0.1179-0.15190.3066-0.11520.3527-28.297730.95483.1081
32.31490.4005-0.55140.7509-0.47541.1501-0.04340.0991-0.0854-0.06590.0503-0.07450.01440.0136-0.00690.065-0.0210.01820.1078-0.03880.0731-10.28644.67310.3882
42.22280.6192-0.83211.3594-0.64922.08850.03810.0277-0.02170.0726-0.019-0.1538-0.19030.1344-0.01920.047-0.0062-0.00590.1038-0.02570.067-12.623347.380714.5618
52.37550.60910.44970.9670.50041.2228-0.22410.40930.2075-0.11680.08590.1476-0.1303-0.13340.13830.0584-0.0509-0.03230.20450.04230.0871-33.07250.58764.8916
619.96346.38667.33222.67322.17242.74390.0478-0.10380.12860.0427-0.06270.1066-0.0026-0.00590.01490.1591-0.10160.0170.2356-0.03790.0863-10.152663.59819.0348
72.62150.3522-0.39691.68240.98421.5225-0.14260.44850.1457-0.18750.00350.2243-0.1206-0.10510.13910.0574-0.0091-0.05010.1790.05310.0674-30.395250.62464.1446
83.2332-0.388-0.79421.59791.2292.1997-0.10290.43610.0405-0.1054-0.05490.2526-0.0245-0.25050.15780.0153-0.018-0.03140.13750.00230.094-31.145346.66897.3503
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 36
2X-RAY DIFFRACTION2A37 - 52
3X-RAY DIFFRACTION3A53 - 96
4X-RAY DIFFRACTION4A97 - 115
5X-RAY DIFFRACTION5B2 - 35
6X-RAY DIFFRACTION6B36 - 51
7X-RAY DIFFRACTION7B52 - 96
8X-RAY DIFFRACTION8B97 - 115

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