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- PDB-4a1f: Crystal structure of C-terminal domain of Helicobacter pylori Dna... -

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Basic information

Entry
Database: PDB / ID: 4a1f
TitleCrystal structure of C-terminal domain of Helicobacter pylori DnaB Helicase
ComponentsREPLICATIVE DNA HELICASE
KeywordsHYDROLASE / DNA REPLICATION / ATPASE
Function / homology
Function and homology information


primosome complex / DNA 5'-3' helicase / DNA replication, synthesis of primer / DNA helicase activity / isomerase activity / 5'-3' DNA helicase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity ...primosome complex / DNA 5'-3' helicase / DNA replication, synthesis of primer / DNA helicase activity / isomerase activity / 5'-3' DNA helicase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA replication / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...DNA helicase, DnaB type / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Replicative DNA helicase DnaB
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsStelter, M. / Kapp, U. / Timmins, J. / Terradot, L.
CitationJournal: Structure / Year: 2012
Title: Architecture of a Dodecameric Bacterial Replicative Helicase.
Authors: Stelter, M. / Gutsche, I. / Kapp, U. / Bazin, A. / Bajic, G. / Goret, G. / Jamin, M. / Timmins, J. / Terradot, L.
History
DepositionSep 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REPLICATIVE DNA HELICASE
B: REPLICATIVE DNA HELICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9535
Polymers77,3862
Non-polymers5673
Water1,892105
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-5.9 kcal/mol
Surface area30030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.859, 102.164, 85.141
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein REPLICATIVE DNA HELICASE / DNAB HELICASE


Mass: 38692.938 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 152-488
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O25916, DNA helicase
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.83 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growDetails: 0.1 M CITRIC ACID PH 5.0, 2-10% W/V POLYETHYLENE GLYCOL 6000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→45.6 Å / Num. obs: 30696 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Biso Wilson estimate: 57.44 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.5→40.178 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 1547 5 %
Rwork0.2173 --
obs0.219 30672 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.801 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.8841 Å20 Å20 Å2
2--2.9322 Å20 Å2
3---2.9519 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4916 0 39 105 5060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055031
X-RAY DIFFRACTIONf_angle_d0.8756777
X-RAY DIFFRACTIONf_dihedral_angle_d18.4831923
X-RAY DIFFRACTIONf_chiral_restr0.058765
X-RAY DIFFRACTIONf_plane_restr0.004885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.58950.33431500.30182898X-RAY DIFFRACTION100
2.5895-2.69320.30071430.27672903X-RAY DIFFRACTION99
2.6932-2.81570.31541430.27182900X-RAY DIFFRACTION100
2.8157-2.96410.33611660.25222901X-RAY DIFFRACTION99
2.9641-3.14980.22831430.22752923X-RAY DIFFRACTION99
3.1498-3.39290.25531430.21622900X-RAY DIFFRACTION99
3.3929-3.73410.22891790.1942884X-RAY DIFFRACTION99
3.7341-4.27390.21881690.18542903X-RAY DIFFRACTION98
4.2739-5.38260.21051690.17792924X-RAY DIFFRACTION98
5.3826-40.18270.27441420.21862989X-RAY DIFFRACTION95
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)
10.9155-0.1062-0.13682.17930.2056-0.3030.29630.14530.241-0.0172-0.2737-0.2661-0.20210.07530.00010.47450.08750.01760.3810.01110.364-69.220128.5359-15.2679
20.45740.2065-0.00451.4677-0.63561.13590.1033-0.15490.2730.1169-0.16080.1804-0.06340.06810.12630.225-0.0231-0.00670.1439-0.00950.2523-39.087417.9141-3.7702
32.35981.03631.30252.4199-0.36560.6512-0.1270.17280.34720.0235-0.0564-0.233-0.06270.12840.16590.3812-0.0734-0.0390.32060.02830.4246-25.45622.78565.8335
44.32821.5733-0.0870.3133-1.17352.61790.2231-0.49540.12640.5149-0.3244-0.01320.2452-0.12740.06940.3467-0.12860.01090.1996-0.03220.1376-35.52117.168211.2353
52.8038-1.8354-0.61972.36212.00073.29521.2513-0.0063-0.35540.42920.2753-1.2110.89090.1757-1.33941.04340.0028-0.24270.769-0.09971.1389-32.2585-8.28272.6701
61.84261.2826-0.9879-0.3283-0.55591.92760.1462-0.0247-0.5626-0.0671-0.1727-0.13090.2931-0.0007-0.00180.2444-0.0157-0.03560.1307-0.05290.2665-39.00013.2478-4.2579
71.01671.08630.18210.9245-0.81012.6334-0.08270.3383-0.4661-0.099-0.3321-0.28370.41650.77880.20210.25720.15560.04620.51540.06830.2765-22.04616.5267-17.2679
80.05150.09420.24850.82530.35182.56160.24131.32180.6507-0.2157-0.4928-0.6148-0.20142.35160.01910.44210.01770.05321.40320.32030.7465-10.052216.7243-21.9083
93.31320.06760.3114-0.34520.28280.8782-0.28350.48740.6428-0.4978-0.0110.0894-0.07230.18010.290.3414-0.0192-0.02110.30830.15330.3107-32.742820.3034-13.3863
100.5021-0.40330.61770.7978-0.08661.5216-0.3173-1.28511.17192.46090.62180.32880.22031.2146-0.16570.1506-0.34470.3340.84030.29210.41017.897822.3532-28.497
110.1276-0.2379-0.24440.5887-0.42890.32220.6916-0.04410.8536-0.1196-0.936-0.6370.24881.19260.2690.51580.10320.1851.77880.16240.7018-17.807417.9882-35.6196
120.3342-0.91990.24972.2966-0.97891.4103-0.21870.11860.4405-0.0338-0.0378-0.2830.23890.40280.09410.45720.18240.00661.1956-0.02920.4655-31.283920.1296-44.4954
132.60990.8671.60182.7107-1.27382.75890.22990.44790.2027-0.76060.0156-0.12530.35030.068-0.07310.26150.17810.11660.72470.18380.1231-30.952923.9023-52.7328
141.0058-1.44910.952.80441.01911.5340.2240.4403-0.341-0.2224-0.55730.3030.87920.97570.08840.46540.37410.0681.2162-0.12060.1536-27.22266.6178-43.9338
150.4042-0.0749-0.28221.06931.40121.09880.49450.7169-0.1933-0.3396-0.37810.02530.30120.2170.07840.42910.27930.01440.9345-0.11950.4336-30.71463.6778-33.1009
162.59740.3806-1.57460.2258-0.82611.2928-0.04350.9939-0.1172-0.28730.0304-0.12080.4086-0.4148-0.12380.39740.10470.03180.5460.01170.3234-48.994813.0897-23.5569
171.52150.37870.78930.6222-1.43792.1102-0.06530.420.25550.230.0010.1255-0.32120.22450.11070.2913-0.00660.00650.27090.0850.2461-45.883918.0997-22.0625
181.3023-0.53360.3191.3444-1.13971.54650.50791.4096-0.06620.1001-0.64180.34510.03441.20060.51770.6010.03030.03821.03020.2310.6342-31.963522.6811-30.3021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 151:175)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 176:221)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 222:263)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 264:317)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 318:330)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 331:378)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 379:415)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 416:430)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 431:474)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 151:175)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 176:196)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 197:251)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 252:304)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 305:362)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 363:390)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 391:405)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 406:449)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 450:467)

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