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- PDB-3afp: Crystal structure of the single-stranded DNA binding protein from... -

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Basic information

Entry
Database: PDB / ID: 3afp
TitleCrystal structure of the single-stranded DNA binding protein from Mycobacterium leprae (Form I)
ComponentsSingle-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / OB-fold / quaternary structure and stability / changes on oligomerisation / water-bridges / DNA damage / DNA repair / DNA replication / DNA-binding
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 leprae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKaushal, P.S. / Singh, P. / Sharma, A. / Muniyappa, K. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: X-ray and molecular-dynamics studies on Mycobacterium leprae single-stranded DNA-binding protein and comparison with other eubacterial SSB structures
Authors: Kaushal, P.S. / Singh, P. / Sharma, A. / Muniyappa, K. / Vijayan, M.
#1: 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 quaternary association
Authors: Saikrishnan, K. / Manjunath, G.P. / Singh, P. / Jeyakanthan, J. / Dauter, Z. / Sekar, K. / Muniyappa, K. / Vijayan, M.
#2: 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.
#3: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 A resolution
Authors: Yang, C. / Curth, U. / Urbanke, C. / Kang, C.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl ...Title: Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution
Authors: Raghunathan, S. / Ricard, C.S. / Lohman, T.M. / Waksman, G.
History
DepositionMar 10, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_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-stranded DNA-binding protein
B: Single-stranded DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6444
Polymers35,4392
Non-polymers2052
Water3,909217
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)71,2878
Polymers70,8784
Non-polymers4094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area9030 Å2
ΔGint-33 kcal/mol
Surface area23940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.957, 78.957, 80.213
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-182-

HOH

21A-211-

HOH

31B-175-

HOH

41B-210-

HOH

51B-243-

HOH

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Components

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


Mass: 17719.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium leprae (bacteria) / Strain: TN / Gene: ssb / Plasmid: pET21a, pMLSSB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P46390
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CD / CADMIUM ION


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


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1M Sodium acetate, 500mM NaCl, 30mM CdSO4, 20mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 27, 2006 / Details: mirrors
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 18540 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 48.3 Å2 / Rsym value: 0.06 / Net I/σ(I): 21.6
Reflection shellResolution: 2.05→2.12 Å / Mean I/σ(I) obs: 3.1 / Num. unique all: 1824 / Rsym value: 0.461 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X3E

1x3e


Resolution: 2.05→28.14 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.454 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Bulak solvent model user
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 948 5.1 %RANDOM
Rwork0.20387 ---
obs0.20527 17575 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.809 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0.53 Å20 Å2
2---1.05 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.05→28.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 7 217 1911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221707
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9542306
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8665218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18623.06775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.66415285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2881520
X-RAY DIFFRACTIONr_chiral_restr0.1110.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211263
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3191.51103
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.42621765
X-RAY DIFFRACTIONr_scbond_it3.2093604
X-RAY DIFFRACTIONr_scangle_it5.6164.5541
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 68 -
Rwork0.271 1262 -
obs--99.63 %
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)
10.13210.1269-0.00940.3448-0.26660.5618-0.0042-0.0242-0.00020.05390.03670.0022-0.0541-0.0472-0.03250.02940.0230.00570.02370.00020.014920.339733.190814.7336
20.2274-0.5658-0.0886.8845-4.19293.6169-0.18590.02520.06440.35630.35440.03570.0402-0.4177-0.16850.16810.0398-0.04820.1079-0.03520.149510.717946.972322.8734
32.6484-3.64770.80369.422-0.95760.24890.18360.0611-0.0932-0.3904-0.1413-0.50270.04920.017-0.04240.03810.02960.0240.03860.0030.115835.126426.55132.3087
40.23110.4786-0.47991.6765-1.66322.198-0.02220.06180.122-0.05010.10010.029-0.0732-0.0509-0.07790.0364-0.02180.01470.02760.02960.147523.68954.007-2.3451
50.2999-0.07420.33490.2684-0.06950.43860.0233-0.0269-0.04770.00680.01660.04230.0166-0.0182-0.03990.01040.00610.0030.01960.02320.040516.244215.27712.8086
60.07140.48110.42785.63784.6773.9084-0.00110.03190.00590.4401-0.14760.24940.3655-0.05720.14870.0587-0.015-0.00110.0731-0.00450.064326.2329-0.620111.9366
71.7904-0.07041.10541.24541.27232.0918-0.0971-0.2333-0.101-0.0224-0.13350.3138-0.0935-0.32080.23050.01270.03440.01850.11760.03390.1355-3.335126.45539.8865
80.10290.1408-0.28290.1939-0.3890.7809-0.2010.0768-0.0753-0.18470.0474-0.10450.3714-0.21630.15360.2306-0.1050.02660.0875-0.00840.25176.4735-2.7648-0.1973
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 21
2X-RAY DIFFRACTION1A28 - 34
3X-RAY DIFFRACTION1A53 - 85
4X-RAY DIFFRACTION1A98 - 120
5X-RAY DIFFRACTION2A22 - 27
6X-RAY DIFFRACTION3A35 - 52
7X-RAY DIFFRACTION4A86 - 97
8X-RAY DIFFRACTION5B3 - 21
9X-RAY DIFFRACTION5B28 - 34
10X-RAY DIFFRACTION5B53 - 85
11X-RAY DIFFRACTION5B98 - 120
12X-RAY DIFFRACTION6B22 - 27
13X-RAY DIFFRACTION7B35 - 52
14X-RAY DIFFRACTION8B86 - 97

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