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- PDB-7y57: Crystal structure of NS1 nuclease domain in P21 space group -

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Basic information

Entry
Database: PDB / ID: 7y57
TitleCrystal structure of NS1 nuclease domain in P21 space group
ComponentsNS1 protein
KeywordsDNA BINDING PROTEIN / NS1 / nuclease domain
Function / homology
Function and homology information


viral genome replication
Similarity search - Function
Rep protein catalytic-like / Rep protein catalytic domain like / Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHATE ION / NS1 protein
Similarity search - Component
Biological speciesHuman parvovirus B19
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.183 Å
AuthorsZhang, X.Y. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Comput Struct Biotechnol J / Year: 2022
Title: Structures and implications of the nuclease domain of human parvovirus B19 NS1 protein.
Authors: Zhang, Y. / Shao, Z. / Gao, Y. / Fan, B. / Yang, J. / Chen, X. / Zhao, X. / Shao, Q. / Zhang, W. / Cao, C. / Liu, H. / Gan, J.
History
DepositionJun 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS1 protein
B: NS1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0903
Polymers39,9952
Non-polymers951
Water73941
1
A: NS1 protein


Theoretical massNumber of molelcules
Total (without water)19,9971
Polymers19,9971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NS1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0922
Polymers19,9971
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.538, 71.716, 56.960
Angle α, β, γ (deg.)90.000, 93.570, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 41 or resid 43 through 172))
21(chain B and (resid 2 through 41 or resid 43 through 172))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUASNASN(chain A and (resid 2 through 41 or resid 43 through 172))AA2 - 413 - 42
12LEULEUGLYGLY(chain A and (resid 2 through 41 or resid 43 through 172))AA43 - 17244 - 173
21GLUGLUASNASN(chain B and (resid 2 through 41 or resid 43 through 172))BB2 - 413 - 42
22LEULEUGLYGLY(chain B and (resid 2 through 41 or resid 43 through 172))BB43 - 17244 - 173

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Components

#1: Protein NS1 protein


Mass: 19997.445 Da / Num. of mol.: 2 / Fragment: nuclease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parvovirus B19 / Gene: NS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q75U85
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulfate (dibasic) and HEPES/Sodium hydroxide pH 7.5 buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 34825 / % possible obs: 98.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 31.24 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.068 / Rrim(I) all: 0.126 / Χ2: 0.642 / Net I/σ(I): 3.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.242.30.38214570.8840.2650.4670.46884
2.24-2.282.30.38716240.810.280.480.44989.5
2.28-2.322.50.32516390.9090.2270.3980.45594.1
2.32-2.372.80.42917360.3160.2910.5210.52697.7
2.37-2.4230.3318020.9110.2150.3950.44399.2
2.42-2.483.20.30117450.9230.1940.3590.44199.4
2.48-2.543.30.26317650.9380.1680.3130.45599.7
2.54-2.613.30.25817740.9510.1630.3060.46399.6
2.61-2.693.40.25317620.9370.1620.3010.45199.8
2.69-2.773.20.2217780.9630.1460.2650.4899.7
2.77-2.873.30.20117870.9550.1310.2410.54599.7
2.87-2.993.60.18217600.9590.1120.2140.50599.8
2.99-3.123.60.13517840.980.0830.1580.51399.8
3.12-3.293.60.12117360.9790.0750.1420.568100
3.29-3.493.50.09917790.9770.0630.1170.61599.9
3.49-3.763.30.07917840.9880.0520.0940.563100
3.76-4.143.60.0717900.9930.0430.0820.651100
4.14-4.743.60.06417680.9830.040.0760.97100
4.74-5.973.40.06217740.9870.040.0730.896100
5.97-503.50.07217810.9450.0470.0861.93299.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Y56

7y56


Resolution: 2.183→43.454 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 30.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 855 4.75 %
Rwork0.223 17155 -
obs0.2248 18010 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.06 Å2 / Biso mean: 37.8615 Å2 / Biso min: 17.69 Å2
Refinement stepCycle: final / Resolution: 2.183→43.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2716 0 5 41 2762
Biso mean--67.22 34.01 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032806
X-RAY DIFFRACTIONf_angle_d0.7023816
X-RAY DIFFRACTIONf_chiral_restr0.044424
X-RAY DIFFRACTIONf_plane_restr0.004484
X-RAY DIFFRACTIONf_dihedral_angle_d8.4342236
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1488X-RAY DIFFRACTION10.007TORSIONAL
12B1488X-RAY DIFFRACTION10.007TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.31930.34951340.2935264792
2.3193-2.49840.31031310.26852877100
2.4984-2.74980.29231420.25812902100
2.7498-3.14760.28361310.24272907100
3.1476-3.96520.2451560.21162897100
3.9652-300.22131610.18732925100
Refinement TLS params.Method: refined / Origin x: 50.9496 Å / Origin y: -52.3411 Å / Origin z: 14.7626 Å
111213212223313233
T0.2222 Å2-0.0073 Å20.0015 Å2-0.2095 Å20.0002 Å2--0.1978 Å2
L0.3618 °2-0.1269 °2-0.0639 °2-0.9021 °20.286 °2--0.4965 °2
S-0.0008 Å °-0.0161 Å °0.0283 Å °-0.0987 Å °0.0292 Å °-0.0768 Å °-0.0167 Å °0.0196 Å °-0.0304 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 172
2X-RAY DIFFRACTION1allB2 - 172
3X-RAY DIFFRACTION1allS1 - 42
4X-RAY DIFFRACTION1allC1

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