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- PDB-1x3e: Crystal structure of the single-stranded DNA-binding protein from... -

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Basic information

Entry
Database: PDB / ID: 1x3e
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


nucleoid / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 4, 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: Advisory / 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 / 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)34,9553
Polymers34,8422
Non-polymers1121
Water4,378243
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)78.620, 78.620, 79.834
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.: 243 / 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 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1M sodium acetate, 500mM sodium chloride, 50mM cadmium sulphate, 20mM Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.15→30 Å / Num. all: 15946 / Num. obs: 15708 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.058
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.492 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.716 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23855 787 5 %RANDOM
Rwork0.20049 ---
all0.20233 14913 --
obs0.20233 14913 98.6 %-
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: 25.335 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å2-0.84 Å20 Å2
2---1.67 Å20 Å2
3---2.51 Å2
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 1 243 1941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211716
X-RAY DIFFRACTIONr_bond_other_d0.0020.021619
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.942331
X-RAY DIFFRACTIONr_angle_other_deg0.8933715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.525225
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_restr0.080.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021944
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02363
X-RAY DIFFRACTIONr_nbd_refined0.2110.2319
X-RAY DIFFRACTIONr_nbd_other0.2580.21835
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.21179
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3780.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4890.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6571.51133
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27721809
X-RAY DIFFRACTIONr_scbond_it2.1743583
X-RAY DIFFRACTIONr_scangle_it3.7484.5522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.293 -
Rwork0.267 1055
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3741.62122.38062.61451.06874.21530.09080.4579-0.1695-0.23040.0116-0.23310.05660.3611-0.10230.04610.0140.03960.1762-0.04360.051918.579234.142625.7236
2143.3532-5.227-41.42517.241.614741.22412.9922-0.84925.1775-0.3977-1.6714-1.8725-1.26693.1015-1.32090.27180.10840.21530.89270.08480.57135.35233.512317.2974
3101.9642-24.9189-24.839432.238716.229310.3398-0.5223-2.30222.79460.7675-0.04372.7057-0.1339-1.260.5660.35750.12980.02270.5282-0.14590.61084.838543.740137.5983
43.6739-1.4409-9.714731.289411.219127.20450.974-0.73491.42970.6163-0.354-3.2361-1.81441.7863-0.62010.3663-0.10570.03810.4425-0.07930.591334.561347.092640.0752
55.3941-0.54371.81823.3688-1.21634.36160.0333-0.0566-0.33130.00610.15830.18940.2253-0.1006-0.19160.0690.0194-0.0580.0894-0.05670.13725.168921.455527.3836
6101.366124.62333.2488-3.57231.13129.28921.1033-2.2757-2.84720.1208-1.0183-0.6107-0.0188-0.8051-0.0850.1201-0.027-0.08080.20440.05840.1479-13.544122.780828.0362
715.7725-15.14532.03055.1154-1.68883.92290.22860.58140.7587-1.1974-0.1943-2.1821-0.55532.4222-0.03430.56510.20650.01561.1545-0.17711.206427.477710.210429.8552
817.189125.3489.367846.77037.1695-6.80791.10980.2147-1.02971.5989-1.70670.84160.99120.75960.59691.0797-0.31010.03730.8696-0.00931.0522-4.96613.87639.8673
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 213 - 21
2X-RAY DIFFRACTION1AA28 - 3428 - 34
3X-RAY DIFFRACTION1AA53 - 8553 - 85
4X-RAY DIFFRACTION1AA98 - 12098 - 120
5X-RAY DIFFRACTION2AA22 - 2722 - 27
6X-RAY DIFFRACTION3AA35 - 5235 - 52
7X-RAY DIFFRACTION4AA86 - 9786 - 97
8X-RAY DIFFRACTION5BB3 - 213 - 21
9X-RAY DIFFRACTION5BB28 - 3428 - 34
10X-RAY DIFFRACTION5BB53 - 8553 - 85
11X-RAY DIFFRACTION5BB98 - 12098 - 120
12X-RAY DIFFRACTION6BB22 - 2722 - 27
13X-RAY DIFFRACTION7BB35 - 5235 - 52
14X-RAY DIFFRACTION8BB86 - 9786 - 97

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