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- PDB-1ue1: Crystal structure of the single-stranded dna-binding protein from... -

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Basic information

Entry
Database: PDB / ID: 1ue1
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 / 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 / MIR / Resolution: 2.5 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 8, 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 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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-strand binding protein
B: Single-strand binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8103
Polymers34,7442
Non-polymers651
Water3,819212
1
A: Single-strand binding protein
B: Single-strand binding protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)69,6196
Polymers69,4884
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Unit cell
Length a, b, c (Å)78.720, 78.720, 77.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 17372.066 Da / Num. of mol.: 2
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1M SODIUM ACETATE, 500mM SODIUN CHLORIDE, 50mM ZINC SULFATE, 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
31 Msodium acetate1reservoir
4500 mM1reservoirNaCl
550-100 mMzinc sulfate1reservoir
620 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: Apr 5, 2002
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 9456 / Num. obs: 9456 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 44.1 Å2 / Rmerge(I) obs: 0.081
Reflection shellResolution: 2.5→2.54 Å / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.5 Å / Redundancy: 4.8 %
Reflection shell
*PLUS
% possible obs: 99.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.41

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→15 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 173687.49 / 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
Rfree0.288 931 10.5 %RANDOM
Rwork0.228 ---
obs0.228 8844 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.9437 Å2 / ksol: 0.298619 e/Å3
Displacement parametersBiso mean: 67 Å2
Baniso -1Baniso -2Baniso -3
1--7.66 Å2-6.35 Å20 Å2
2---7.66 Å20 Å2
3---15.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.36 Å
Luzzati d res low-15 Å
Luzzati sigma a0.56 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 1 212 1938
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it7.211.5
X-RAY DIFFRACTIONc_mcangle_it10.142
X-RAY DIFFRACTIONc_scbond_it9.822
X-RAY DIFFRACTIONc_scangle_it12.322.5
LS refinement shellResolution: 2.5→2.54 Å / Rfactor Rfree error: 0.11 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 -11.9 %
Rwork0.449 96 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.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_deg0.92

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