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- PDB-8jx6: Deep-Sea Helicase 9 (DSH9) -

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Basic information

Entry
Database: PDB / ID: 8jx6
TitleDeep-Sea Helicase 9 (DSH9)
ComponentsDeep-Sea Helicase 9
KeywordsMOTOR PROTEIN / helicase / Deep-Sea / metagenome / ssDNA binding protein
Function / homologyL(+)-TARTARIC ACID
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, L. / Liu, Z. / Guo, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100994 China
CitationJournal: To Be Published
Title: Structure of Deep-Sea Helicase 9 (DSH9)
Authors: Wang, L. / Liu, Z. / Guo, F.
History
DepositionJun 30, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deep-Sea Helicase 9
B: Deep-Sea Helicase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7145
Polymers105,3902
Non-polymers3243
Water11,800655
1
A: Deep-Sea Helicase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8452
Polymers52,6951
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint0 kcal/mol
Surface area22190 Å2
MethodPISA
2
B: Deep-Sea Helicase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8693
Polymers52,6951
Non-polymers1742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-9 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.808, 126.836, 150.715
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 5 through 74 or resid 76...
d_2ens_1(chain "B" and (resid 5 through 74 or resid 76...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LEULEUVALVALAA5 - 748 - 77
d_12VALVALLYSLYSAA76 - 8279 - 85
d_13ASNASNPROPROAA84 - 17887 - 181
d_14ASPASPTHRTHRAA180 - 237183 - 240
d_15ASPASPASNASNAA239 - 270242 - 273
d_16VALVALCYSCYSAA272 - 292275 - 295
d_17LYSLYSSERSERAA294 - 306297 - 309
d_18GLYGLYILEILEAA308 - 329311 - 332
d_19PHEPHELYSLYSAA332 - 340335 - 343
d_110ASNASNASNASNAA342345
d_111LEULEUARGARGAA344 - 428347 - 431
d_112ASNASNASPASPAA430 - 454433 - 457
d_21LEULEUVALVALBB5 - 748 - 77
d_22VALVALLYSLYSBB76 - 8279 - 85
d_23ASNASNALAALABB84 - 11187 - 114
d_24VALVALPROPROBB119 - 178122 - 181
d_25ASPASPTHRTHRBB180 - 237183 - 240
d_26ASPASPASNASNBB239 - 270242 - 273
d_27VALVALCYSCYSBB272 - 292275 - 295
d_28LYSLYSSERSERBB294 - 306297 - 309
d_29GLYGLYILEILEBB308 - 329311 - 332
d_210PHEPHELYSLYSBB332 - 340335 - 343
d_211ASNASNASNASNBB342345
d_212LEULEUARGARGBB344 - 428347 - 431
d_213ASNASNASPASPBB430 - 454433 - 457

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Components

#1: Protein Deep-Sea Helicase 9


Mass: 52694.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 655 / 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: 2.58 Å3/Da / Density % sol: 52.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium Sodium tartrate tetrahydrate; 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.06→49.03 Å / Num. obs: 63166 / % possible obs: 92.5 % / Redundancy: 10.7 % / Biso Wilson estimate: 37.93 Å2 / CC1/2: 0.99 / Net I/σ(I): 23
Reflection shellResolution: 2.06→2.17 Å / Num. unique obs: 8497 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.99 Å / SU ML: 0.2353 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2467
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2408 2987 4.93 %
Rwork0.2007 57599 -
obs0.2027 60586 94.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.53 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7217 0 21 655 7893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417402
X-RAY DIFFRACTIONf_angle_d0.73110010
X-RAY DIFFRACTIONf_chiral_restr0.0461131
X-RAY DIFFRACTIONf_plane_restr0.0041271
X-RAY DIFFRACTIONf_dihedral_angle_d5.2563979
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.913918338089 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.31021430.25482825X-RAY DIFFRACTION99.66
2.13-2.170.28351540.24752875X-RAY DIFFRACTION99.97
2.17-2.210.29341430.23592898X-RAY DIFFRACTION99.93
2.21-2.240.27071110.24172028X-RAY DIFFRACTION97.67
2.27-2.30.31541090.23512042X-RAY DIFFRACTION99.95
2.3-2.350.31661540.23932881X-RAY DIFFRACTION100
2.35-2.40.29781400.24152885X-RAY DIFFRACTION99.97
2.4-2.460.27451540.23762884X-RAY DIFFRACTION100
2.46-2.530.30381550.22452882X-RAY DIFFRACTION99.97
2.53-2.60.27381570.23312869X-RAY DIFFRACTION99.97
2.6-2.690.3023980.23162029X-RAY DIFFRACTION69.94
2.69-2.780.29161590.23682889X-RAY DIFFRACTION100
2.78-2.890.30221450.23482919X-RAY DIFFRACTION99.93
2.9-3.030.23461430.22932927X-RAY DIFFRACTION99.97
3.03-3.190.2641370.22132898X-RAY DIFFRACTION100
3.19-3.380.23811630.21892916X-RAY DIFFRACTION100
3.38-3.640.23121320.19362592X-RAY DIFFRACTION88.53
3.64-4.010.20711210.17552281X-RAY DIFFRACTION77.11
4.01-4.580.1891500.15652953X-RAY DIFFRACTION99.97
4.58-5.750.18641520.15993013X-RAY DIFFRACTION100
5.75-19.990.23221670.18273113X-RAY DIFFRACTION99.73
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)
10.6242112184330.3515639625250.1772383794382.166751379840.9535623402031.39000698865-0.0408023068666-0.05987211301690.01897502659990.0281052367052-0.07289720338140.2763209979960.0703264792491-0.08695083484210.09440080766310.166607898710.00895058283690.004487863975160.246922598697-0.01061509756120.274205401445-22.906618325620.3730015289-19.6875603236
21.04247122240.478896514189-0.2784689483482.18298691218-0.2124329906181.25614618525-0.00952715051817-0.029343746840.01161633720420.164769992066-0.0258526628962-0.1400805389060.1094793802450.0002153213128710.02221988494270.2087338847220.02306457838570.007009148290150.24552488089-0.01588837904270.238193094781-5.13811354952-22.2590254409-20.2070278572
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11chain 'A'AA - B1 - 501
22chain 'B'BC - D4 - 501

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