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- PDB-7r4w: Single stranded DNA binding protein SSB M5 from Fervidobacterium ... -

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Basic information

Entry
Database: PDB / ID: 7r4w
TitleSingle stranded DNA binding protein SSB M5 from Fervidobacterium gondwanense
ComponentsSingle-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / single stranded DNA binding
Function / homology
Function and homology information


single-stranded DNA binding / 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, OB-fold
Similarity search - Domain/homology
ACETIC ACID / PHOSPHATE ION / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesFervidobacterium gondwanense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHakansson, M. / Svensson, L.A. / Werbowy, O. / Al-Karadaghi, S. / Kaczorowski, T. / Kaczorowska, A.K. / Dorawa, S.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)685778European Union
CitationJournal: To Be Published
Title: Molecular characterization of a single stranded DNA binding protein from Fervidobacterium gondwanense
Authors: Werbowy, O. / Hakansson, M. / Svensson, L.A. / Al-Karadaghi, S. / Kaczorowski, T. / Kaczarowska, A.K. / Dorawa, S.
History
DepositionFeb 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)17,0024
Polymers16,7871
Non-polymers2153
Water1629
1
A: Single-stranded DNA-binding protein
hetero molecules

A: Single-stranded DNA-binding protein
hetero molecules

A: Single-stranded DNA-binding protein
hetero molecules

A: Single-stranded DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,00716
Polymers67,1474
Non-polymers86012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area7260 Å2
ΔGint-65 kcal/mol
Surface area21690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.390, 62.390, 172.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Single-stranded DNA-binding protein / SSB


Mass: 16786.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fervidobacterium gondwanense (bacteria)
Gene: SAMN02745226_00543 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1M7S684
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 1 M Diammonium phosphate, 0.1 M sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→43.13 Å / Num. obs: 7947 / % possible obs: 99.4 % / Redundancy: 25.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.027 / Rrim(I) all: 0.134 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.3827.15.5206697620.5211.0615.603199.5
8.91-43.121.10.035361617110.0080.03661.898.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vW9

2vw9


Resolution: 2.3→43.13 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.926 / SU B: 18.225 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 391 4.9 %RANDOM
Rwork0.187 ---
obs0.1902 7538 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 193.92 Å2 / Biso mean: 90.814 Å2 / Biso min: 49.56 Å2
Baniso -1Baniso -2Baniso -3
1-2.53 Å20 Å20 Å2
2--2.53 Å20 Å2
3----5.06 Å2
Refinement stepCycle: final / Resolution: 2.3→43.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms804 0 13 9 826
Biso mean--99.66 75 -
Num. residues----100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.013825
X-RAY DIFFRACTIONr_bond_other_d0.0010.017800
X-RAY DIFFRACTIONr_angle_refined_deg2.0911.6451112
X-RAY DIFFRACTIONr_angle_other_deg1.3921.5951836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.385598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.34220.81649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.80715149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.169159
X-RAY DIFFRACTIONr_chiral_restr0.080.2107
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02908
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02183
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 27 -
Rwork0.378 542 -
all-569 -
obs--99.3 %
Refinement TLS params.Method: refined / Origin x: 0.434 Å / Origin y: -10.673 Å / Origin z: 13.17 Å
111213212223313233
T0.2007 Å20.038 Å20.0079 Å2-0.0417 Å20.0385 Å2--0.064 Å2
L3.9611 °20.7129 °2-0.2405 °2-6.023 °2-0.7214 °2--6.0155 °2
S-0.0555 Å °-0.2702 Å °-0.464 Å °0.5929 Å °0.0313 Å °-0.0079 Å °0.6817 Å °0.0419 Å °0.0242 Å °

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