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- PDB-1ue7: Crystal structure of the single-stranded dna-binding protein from... -

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Basic information

Entry
Database: PDB / ID: 1ue7
TitleCrystal structure of the single-stranded dna-binding protein from mycobacterium tuberculosis
ComponentsSingle-strand binding protein
KeywordsDNA BINDING PROTEIN / OLIGONUCLEOTIDE BINDING FOLD / DNA-BINDING PROTEIN / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
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 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 speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSaikrishnan, K. / Jeyakanthan, J. / Venkatesh, J. / Acharya, N. / Sekar, K. / Varshney, U. / Vijayan, M. / TB Structural Genomics Consortium (TBSGC)
Citation
Journal: J.MOL.BIOL. / Year: 2003
Title: Structure of Mycobacterium tuberculosis single-stranded DNA-binding protein. Variability in quaternary structure and its implications
Authors: Saikrishnan, K. / Jeyakanthan, J. / Venkatesh, J. / Acharya, N. / Sekar, K. / Varshney, U. / Vijayan, M.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2002
Title: Crystallization and preliminary X-ray studies of the single-stranded DNA-binding protein from Mycobacterium tuberculosis.
Authors: Saikrishnan, K. / Jeyakanthan, J. / Venkatesh, J. / Acharya, N. / Purnapatre, K. / Sekar, K. / Varshney, U. / Vijayan, M.
History
DepositionMay 9, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Single-strand binding protein
B: Single-strand binding protein
C: Single-strand binding protein
D: Single-strand binding protein


Theoretical massNumber of molelcules
Total (without water)69,4884
Polymers69,4884
Non-polymers00
Water3,297183
1
A: Single-strand binding protein
B: Single-strand binding protein

A: Single-strand binding protein
B: Single-strand binding protein


Theoretical massNumber of molelcules
Total (without water)69,4884
Polymers69,4884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-x+1/2,y,-z1
2
C: Single-strand binding protein
D: Single-strand binding protein

C: Single-strand binding protein
D: Single-strand binding protein


Theoretical massNumber of molelcules
Total (without water)69,4884
Polymers69,4884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+3/2,z1
Unit cell
Length a, b, c (Å)60.223, 116.720, 177.885
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein
Single-strand binding protein / Single-stranded dna-binding protein


Mass: 17372.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: PET11d / Production host: Escherichia coli (E. coli) / References: UniProt: P0A610, UniProt: P9WGD5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3.68 Å3/Da / Density % sol: 66.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 2M MAGNESIUM CHLORIDE, 500mM SODIUM CHLORIDE, 20mM TRIS-HCL, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Saikrishnan, K., (2002) Acta Cryst., D58, 327.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15-10 mg/mlprotein1drop
220 mMTris-HCl1droppH7.4
32 M1reservoirMgCl2
41 Msodium acetate1reservoir
5500 mM1reservoirNaCl
650-100 mMzinc sulfate1reservoir
720 mMTris-HCl1reservoirpH7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 48456 / Num. obs: 10610 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.101
Reflection shellResolution: 3.2→3.31 Å / % possible all: 96.9
Reflection
*PLUS
Highest resolution: 3.2 Å / Redundancy: 4.6 %
Reflection shell
*PLUS
% possible obs: 96.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.461

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UE6

1ue6


Resolution: 3.2→15 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 165044.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: A LARGE NUMBER OF THE ISOLATED WATER MOLECULES REPRESENT THE DISCREET AND ISOLATED ELECTRON DENSITIES, WHICH MAY CORRESPOND TO THE UNDEFINED REGIONS OF THE POLYPEPTIDE CHAIN PRIMARILY AT THE ...Details: A LARGE NUMBER OF THE ISOLATED WATER MOLECULES REPRESENT THE DISCREET AND ISOLATED ELECTRON DENSITIES, WHICH MAY CORRESPOND TO THE UNDEFINED REGIONS OF THE POLYPEPTIDE CHAIN PRIMARILY AT THE C-TERMINUS AND THE LOOPS
RfactorNum. reflection% reflectionSelection details
Rfree0.313 1035 10.3 %RANDOM
Rwork0.235 ---
obs0.235 10019 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.3625 Å2 / ksol: 0.298682 e/Å3
Displacement parametersBiso mean: 60 Å2
Baniso -1Baniso -2Baniso -3
1-7.7 Å20 Å20 Å2
2--3.23 Å20 Å2
3----10.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.41 Å
Luzzati d res low-10 Å
Luzzati sigma a0.37 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 0 183 3036
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it10.991.5
X-RAY DIFFRACTIONc_mcangle_it17.122
X-RAY DIFFRACTIONc_scbond_it14.542
X-RAY DIFFRACTIONc_scangle_it19.862.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 -10.9 %
Rwork0.283 1338 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99

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