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- PDB-4kw3: Crystal structure of the non-structural protein 1 N-terminal orig... -

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Basic information

Entry
Database: PDB / ID: 4kw3
TitleCrystal structure of the non-structural protein 1 N-terminal origin-recognition/nickase domain from the emerging human bocavirus
ComponentsNS1
KeywordsVIRAL PROTEIN / Nuclease domain / Human bocavirus 1 NS1 N-terminal domain origin of replication binding protein with endonuclease activity / DNA binding
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / viral DNA genome replication / DNA helicase activity / endonuclease activity / DNA helicase / DNA replication / host cell nucleus / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Initiator protein NS1 / Initiator protein NS1
Similarity search - Component
Biological speciesHuman bocavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Single isomorphous replacement (SIR) / Resolution: 2.7 Å
AuthorsTewary, S.K. / Zhao, H. / Tang, L.
CitationJournal: J.Virol. / Year: 2013
Title: Structure of the NS1 Protein N-Terminal Origin Recognition/Nickase Domain from the Emerging Human Bocavirus.
Authors: Tewary, S.K. / Zhao, H. / Shen, W. / Qiu, J. / Tang, L.
History
DepositionMay 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 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: NS1
B: NS1


Theoretical massNumber of molelcules
Total (without water)62,3202
Polymers62,3202
Non-polymers00
Water45025
1
A: NS1


Theoretical massNumber of molelcules
Total (without water)31,1601
Polymers31,1601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NS1


Theoretical massNumber of molelcules
Total (without water)31,1601
Polymers31,1601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)199.804, 199.804, 56.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NS1 / NS1 protein / NS1-70 / NS1-70K / NS2


Mass: 31159.818 Da / Num. of mol.: 2 / Fragment: N-terminal Domain, UNP residues 1-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human bocavirus / Gene: NS1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q3YPH6, UniProt: D0EZM8*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 4.52 Å3/Da / Density % sol: 72.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% MPD [(+/-)-2-Methyl-2,4-pentanediol], pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.97945
SYNCHROTRONAPS 23-ID-B20.99712
Detector
TypeIDDetectorDateDetails
PSI PILATUS 6M1PIXELMar 30, 2012mirrors
MAR scanner 300 mm plate2IMAGE PLATEJul 19, 2012mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degsSINGLE WAVELENGTHMx-ray1
2Double crystal cryo-cooled Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979451
20.997121
ReflectionResolution: 2.7→37.41 Å / Num. all: 32126 / Num. obs: 32126 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.7 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 27.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Blu-Iceicedata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Single isomorphous replacement (SIR)
Resolution: 2.7→37.41 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 19.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2067 1600 5 %
Rwork0.1714 --
obs0.1732 32001 99.83 %
all-32001 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→37.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4302 0 0 25 4327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094416
X-RAY DIFFRACTIONf_angle_d1.1715980
X-RAY DIFFRACTIONf_dihedral_angle_d13.8951654
X-RAY DIFFRACTIONf_chiral_restr0.08642
X-RAY DIFFRACTIONf_plane_restr0.006772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.78640.26811410.20832669X-RAY DIFFRACTION100
2.7864-2.88590.28371430.20992722X-RAY DIFFRACTION100
2.8859-3.00140.23471440.19832731X-RAY DIFFRACTION100
3.0014-3.13790.1941430.18372741X-RAY DIFFRACTION100
3.1379-3.30330.25751430.19112720X-RAY DIFFRACTION100
3.3033-3.51010.22421450.18332751X-RAY DIFFRACTION100
3.5101-3.78090.19451440.16752748X-RAY DIFFRACTION100
3.7809-4.16090.18821450.15232758X-RAY DIFFRACTION100
4.1609-4.7620.16741470.14742793X-RAY DIFFRACTION100
4.762-5.99560.22191480.18082803X-RAY DIFFRACTION100
5.9956-37.41370.19461570.1652965X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 67.6809 Å / Origin y: 44.9855 Å / Origin z: 13.8958 Å
111213212223313233
T0.4482 Å20.0717 Å20.0235 Å2-0.3338 Å20.0143 Å2--0.3217 Å2
L1.5172 °21.0301 °2-0.3252 °2-2.1043 °2-0.1518 °2--0.7447 °2
S0.1015 Å °-0.0726 Å °-0.0312 Å °0.3653 Å °-0.0542 Å °0.0831 Å °0.2411 Å °0.1255 Å °-0.0469 Å °
Refinement TLS groupSelection details: all

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