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- PDB-6iwv: Crystal structure of a single strand DNA binding protein -

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Basic information

Entry
Database: PDB / ID: 6iwv
TitleCrystal structure of a single strand DNA binding protein
ComponentsSingle-stranded DNA-binding protein 2
KeywordsDNA BINDING PROTEIN / a single strand DNA binding protein
Function / homology
Function and homology information


single-stranded DNA binding / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Single-stranded DNA binding protein, SSDP / Sequence-specific single-strand DNA-binding protein / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif
Similarity search - Domain/homology
Single-stranded DNA-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsWang, H.Y. / Yan, X.X.
CitationJournal: Protein Sci. / Year: 2019
Title: Crystal structure of the LUFS domain of human single-stranded DNA binding Protein 2 (SSBP2).
Authors: Wang, H. / Wang, Z. / Tang, Q. / Yan, X.X. / Xu, W.
History
DepositionDec 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Single-stranded DNA-binding protein 2
B: Single-stranded DNA-binding protein 2


Theoretical massNumber of molelcules
Total (without water)15,7102
Polymers15,7102
Non-polymers00
Water2,180121
1
A: Single-stranded DNA-binding protein 2
B: Single-stranded DNA-binding protein 2

A: Single-stranded DNA-binding protein 2
B: Single-stranded DNA-binding protein 2


Theoretical massNumber of molelcules
Total (without water)31,4194
Polymers31,4194
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_556x,x-y,-z+3/21
Buried area7730 Å2
ΔGint-78 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.906, 116.906, 42.355
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-102-

HOH

21A-120-

HOH

31A-151-

HOH

41A-158-

HOH

51B-153-

HOH

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Components

#1: Protein Single-stranded DNA-binding protein 2 / Sequence-specific single-stranded-DNA-binding protein 2


Mass: 7854.858 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SSBP2, SSDP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P81877
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 0.1 M Bis-Tris pH 6.3, 1.9 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→20 Å / Num. obs: 26784 / % possible obs: 99.09 % / Redundancy: 22.8 % / CC1/2: 1 / Rpim(I) all: 0.015 / Net I/σ(I): 94.73
Reflection shellResolution: 1.52→1.55 Å / Num. unique obs: 1288 / CC1/2: 0.626 / Rpim(I) all: 0.728

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data collection
HKL-3000data scaling
AutoSolphasing
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.52→20 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.476 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.061 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18055 1293 4.9 %RANDOM
Rwork0.14568 ---
obs0.14733 25214 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.964 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.19 Å20 Å2
2--0.37 Å20 Å2
3----1.22 Å2
Refinement stepCycle: 1 / Resolution: 1.52→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 0 121 1177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191135
X-RAY DIFFRACTIONr_bond_other_d0.0020.021015
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.921559
X-RAY DIFFRACTIONr_angle_other_deg0.92732348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6895138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65123.51954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00215170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.679154
X-RAY DIFFRACTIONr_chiral_restr0.0920.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211286
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02288
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_it3.0383.495528
X-RAY DIFFRACTIONr_mcbond_other3.0243.491527
X-RAY DIFFRACTIONr_mcangle_it3.6455.236662
X-RAY DIFFRACTIONr_mcangle_other3.6495.239663
X-RAY DIFFRACTIONr_scbond_it4.1993.798607
X-RAY DIFFRACTIONr_scbond_other4.1883.796607
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7015.568893
X-RAY DIFFRACTIONr_long_range_B_refined5.33929.3281481
X-RAY DIFFRACTIONr_long_range_B_other5.08228.8731448
X-RAY DIFFRACTIONr_rigid_bond_restr3.4132147
X-RAY DIFFRACTIONr_sphericity_free29.018549
X-RAY DIFFRACTIONr_sphericity_bonded13.65552170
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 93 -
Rwork0.258 1818 -
obs--99.95 %
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)
11.8824.21542.2169.21854.92742.5877-1.35060.7019-1.653-0.89260.33890.23731.9508-1.3131.12761.0894-0.1940.23210.6597-0.10860.779437.8343.701736.8054
22.56260.2348-0.28413.4293-1.5134.12190.0630.06830.08320.1005-0.0743-0.25780.02620.211-0.01480.23350.0263-0.00140.24340.00790.264839.455136.737516.7188
32.65662.7737-0.10833.2132-1.21753.2838-0.41520.0506-0.120.29980.3794-1.00830.22770.40480.04980.3310.03910.01990.32890.0010.35345.850338.307218.0265
42.8296-0.0941-0.77782.8007-1.88053.7527-0.02360.0583-0.3625-0.41960.14060.30370.8084-0.36690.05720.4273-0.0136-0.03470.3490.0480.350235.319620.762224.9178
54.07660.4413-0.84932.6955-0.72076.9316-0.04430.2163-0.3165-0.35020.03120.1070.7054-0.35170.00270.2953-0.016-0.02470.28010.00630.277829.59730.769516.1567
64.36330.6216-1.74512.7253-0.00272.0554-0.29310.3573-0.4449-0.078-0.30120.61830.6066-0.87190.210.36760.0247-0.03410.4148-0.05080.412224.020330.561115.9036
74.5289-1.81960.13392.4369-1.39382.0711-0.0955-0.33080.36620.31440.0744-0.0976-0.15370.13070.15030.33460.0279-0.02040.28820.03060.336737.647129.991931.4799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 15 )A11 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 45 )A16 - 45
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 59 )A46 - 59
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 76 )A60 - 76
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 45 )B12 - 45
6X-RAY DIFFRACTION6chain 'B' and (resid 46 through 59 )B46 - 59
7X-RAY DIFFRACTION7chain 'B' and (resid 60 through 73 )B60 - 73

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