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- PDB-7f5y: Crystal structure of the single-stranded dna-binding protein from... -

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Basic information

Entry
Database: PDB / ID: 7f5y
TitleCrystal structure of the single-stranded dna-binding protein from Mycobacterium tuberculosis- Form III
ComponentsSingle-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / DNA binding / quaternary structure / plasticity / inhibitor development
Function / homology
Function and homology information


nucleoid / enzyme activator activity / single-stranded DNA binding / DNA replication / response to antibiotic / DNA damage response / extracellular region / plasma membrane
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
FORMIC ACID / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsSrikalaivani, R. / Paul, A. / Sriram, R. / Narayanan, S. / Gopal, B. / Vijayan, M.
Funding support India, 1items
OrganizationGrant numberCountry
Office of the Principal Scientific Adviser to the Government of India India
CitationJournal: Curr.Sci. / Year: 2022
Title: Structural variability of Mycobacterium tuberculosis SSB and susceptibility to inhibition.
Authors: Srikalaivani, R. / Paul, A. / Sriram, R. / Narayanan, S. / Shee, S. / Singh, A. / Varshney, U. / Gopal, B. / Vijayan, M.
History
DepositionJun 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)35,3896
Polymers35,2052
Non-polymers1844
Water1,71195
1
A: Single-stranded DNA-binding protein
B: Single-stranded DNA-binding protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)70,77812
Polymers70,4094
Non-polymers3688
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area10830 Å2
ΔGint-55 kcal/mol
Surface area22220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.550, 59.550, 124.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

21A-341-

HOH

31B-431-

HOH

41B-450-

HOH

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Components

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


Mass: 17602.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: ssb, Rv0054, MTCY21D4.17 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGD5
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.82 Å3/Da / Density % sol: 32.31 %
Crystal growTemperature: 295 K / Method: microbatch / Details: 3.5M sodium formate, 100mM bis-tris propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→39 Å / Num. obs: 18944 / % possible obs: 96.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.9
Reflection shellResolution: 1.92→2.02 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2650 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UE1

1ue1


Resolution: 1.92→39 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.835 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22864 974 5.1 %RANDOM
Rwork0.19124 ---
obs0.19328 17963 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.592 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.92→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 12 95 1782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0141739
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171541
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.6642367
X-RAY DIFFRACTIONr_angle_other_deg0.9261.6373584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7955233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41120.79588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67315262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4731517
X-RAY DIFFRACTIONr_chiral_restr0.0630.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022037
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02311
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_it3.723.961932
X-RAY DIFFRACTIONr_mcbond_other3.7183.96933
X-RAY DIFFRACTIONr_mcangle_it5.4645.8831165
X-RAY DIFFRACTIONr_mcangle_other5.4625.8881166
X-RAY DIFFRACTIONr_scbond_it4.684.356806
X-RAY DIFFRACTIONr_scbond_other4.6464.362803
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9556.3351203
X-RAY DIFFRACTIONr_long_range_B_refined9.08345.3521708
X-RAY DIFFRACTIONr_long_range_B_other9.09845.2751696
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 91 -
Rwork0.276 1252 -
obs--93.78 %

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