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- PDB-1x3g: Crystal structure of the single-stranded DNA-binding protein from... -

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Basic information

Entry
Database: PDB / ID: 1x3g
TitleCrystal structure of the single-stranded DNA-binding protein from Mycobacterium SMEGMATIS
ComponentsSingle-strand binding protein
KeywordsDNA BINDING PROTEIN / Oligonucleotide binding fold / DNA-binding protein
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 proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSaikrishnan, K. / Manjunath, G.P. / Singh, P. / Jeyakanthan, J. / Dauter, Z. / Sekar, K. / Muniyappa, K. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologus SSBs: biological implications of structural plasticity and variability in ...Title: Structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologus SSBs: biological implications of structural plasticity and variability in quaternary association.
Authors: Saikrishnan, K. / Manjunath, G.P. / Singh, P. / Jeyakanthan, J. / Dauter, Z. / Sekar, K. / Muniyappa, K. / Vijayan, M.
#1: 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.
#2: 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 5, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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)34,9553
Polymers34,8422
Non-polymers1121
Water1,36976
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)69,9096
Polymers69,6844
Non-polymers2252
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)79.886, 79.886, 81.288
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 / SSB / Helix-destabilizing protein


Mass: 17421.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Plasmid: PET17B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AFI5
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.1 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1M sodium acetate, 500mM sodium chloride, 50mM cadmium acetate, 20mM Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 6324 / Num. obs: 6048 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.114
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.481 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.885 / SU B: 16.665 / SU ML: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25807 587 9.7 %RANDOM
Rwork0.20399 ---
all0.20941 5455 --
obs0.20941 5455 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.172 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0.34 Å20 Å2
2---0.69 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 0 1 76 1724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211665
X-RAY DIFFRACTIONr_bond_other_d0.0010.021569
X-RAY DIFFRACTIONr_angle_refined_deg1.8791.9392266
X-RAY DIFFRACTIONr_angle_other_deg1.96433597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8585225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021905
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02348
X-RAY DIFFRACTIONr_nbd_refined0.2570.2341
X-RAY DIFFRACTIONr_nbd_other0.2710.21745
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0920.21115
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1520.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4380.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3510.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined1.4130.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7661.51129
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.37121791
X-RAY DIFFRACTIONr_scbond_it3.7953536
X-RAY DIFFRACTIONr_scangle_it7.034.5475
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.476 -
Rwork0.31 416

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