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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 / homologySH3 type barrels. - #780 / SH3 type barrels. / Roll / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta / L(+)-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
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 2.0Dec 24, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / entity / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / software / struct_asym / struct_conf / struct_conn / struct_ncs_dom / struct_ncs_dom_lim / struct_sheet_range / symmetry
Item: _cell.volume / _entity.pdbx_number_of_molecules ..._cell.volume / _entity.pdbx_number_of_molecules / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.percent_reflns_obs / _software.version / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _symmetry.space_group_name_Hall
Description: Ligand identity / Provider: author / Type: Coordinate replacement

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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)105,7386
Polymers105,3902
Non-polymers3494
Water11,782654
1
A: 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 area22140 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 area390 Å2
ΔGint-8 kcal/mol
Surface area22370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.808, 126.836, 150.715
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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


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.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.99 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2446 2987 4.93 %
Rwork0.1996 --
obs0.2017 60586 94.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7221 0 22 654 7897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027406
X-RAY DIFFRACTIONf_angle_d0.41910015
X-RAY DIFFRACTIONf_dihedral_angle_d3.809979
X-RAY DIFFRACTIONf_chiral_restr0.041131
X-RAY DIFFRACTIONf_plane_restr0.0031272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.32031430.2642825X-RAY DIFFRACTION100
2.13-2.170.31331540.26032875X-RAY DIFFRACTION100
2.17-2.210.28461430.24222898X-RAY DIFFRACTION100
2.21-2.240.2511110.24122028X-RAY DIFFRACTION98
2.27-2.30.31291090.24042042X-RAY DIFFRACTION100
2.3-2.350.31171540.24092881X-RAY DIFFRACTION100
2.35-2.40.31381400.24662885X-RAY DIFFRACTION100
2.4-2.460.27721540.24082884X-RAY DIFFRACTION100
2.46-2.530.31841550.22962882X-RAY DIFFRACTION100
2.53-2.60.26771570.23392869X-RAY DIFFRACTION100
2.6-2.690.3241980.2322029X-RAY DIFFRACTION70
2.69-2.780.28151590.23522889X-RAY DIFFRACTION100
2.78-2.890.29541450.23262919X-RAY DIFFRACTION100
2.9-3.030.22951430.22652927X-RAY DIFFRACTION100
3.03-3.190.26461370.21462898X-RAY DIFFRACTION100
3.19-3.380.23421630.2132916X-RAY DIFFRACTION100
3.38-3.640.23391320.19042592X-RAY DIFFRACTION89
3.64-4.010.22011210.17552281X-RAY DIFFRACTION77
4.01-4.580.21041500.15332953X-RAY DIFFRACTION100
4.58-5.750.1891520.1593013X-RAY DIFFRACTION100
5.75-19.990.23141670.18033113X-RAY DIFFRACTION100
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)
12.56160.8920.29013.02831.44243.8865-0.10770.0303-0.2158-0.067-0.14790.6840.5889-0.30560.1950.2863-0.033-0.01190.2172-0.05050.374-29.70753.1501-32.4708
22.489-0.40160.33095.60431.04553.0288-0.18840.01460.4519-0.39010.00480.2489-0.5833-0.0360.15280.3271-0.0258-0.06320.2718-0.01340.3324-23.096421.1648-33.3447
31.64510.54180.39532.07890.24146.156-0.0277-0.19630.00150.3032-0.22690.60370.196-0.70710.25370.2952-0.04070.07380.3319-0.12480.5134-34.05211.1045-19.8789
47.46841.72880.20084.07191.89432.6671-0.3054-1.0831-1.43151.2642-0.20070.20251.0381-0.33340.35260.9203-0.15120.2540.47520.03990.592-28.88699.32173.5544
50.83210.6256-0.2262.8698-0.15521.4999-0.0683-0.0590.01020.01030.02260.00850.0128-0.00440.0510.19410.0018-0.00930.2722-0.03590.2223-16.670429.7145-13.3076
62.70640.4126-0.32583.49020.0643.3811-0.05440.16970.3205-0.2620.0226-0.2937-0.2980.07730.0240.21250.00950.03570.2290.03840.2808-0.4614-8.2311-32.5995
71.57991.2116-0.3247.0073-0.74321.2011-0.16230.2301-0.3763-0.38690.0045-0.39960.5598-0.0970.14160.3730.00960.12650.3357-0.05810.3653-0.9485-31.2895-34.6916
81.98660.6846-0.31362.66070.64245.66090.0954-0.2063-0.06310.3884-0.1132-0.61050.3780.45270.03390.2956-0.005-0.04370.31680.04060.45517.1808-13.8398-20.282
94.38871.61381.3892.46050.22721.52770.2707-0.51780.26970.8232-0.26940.1272-0.101-0.0753-0.0160.5671-0.0370.04660.3986-0.05860.2613-8.9973-17.0924-0.5866
101.13640.5650.10052.6840.52121.5997-0.0599-0.0478-0.06430.23860.01520.09090.2434-0.07630.04350.3163-0.01220.05870.28-0.00490.2114-11.9173-32.0588-16.2794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 159 )
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 222 )
4X-RAY DIFFRACTION4chain 'A' and (resid 223 through 248 )
5X-RAY DIFFRACTION5chain 'A' and (resid 249 through 454 )
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 102 )
7X-RAY DIFFRACTION7chain 'B' and (resid 103 through 159 )
8X-RAY DIFFRACTION8chain 'B' and (resid 160 through 222 )
9X-RAY DIFFRACTION9chain 'B' and (resid 223 through 285 )
10X-RAY DIFFRACTION10chain 'B' and (resid 286 through 454 )

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