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- PDB-3bgw: The Structure Of A DnaB-Like Replicative Helicase And Its Interac... -

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Basic information

Entry
Database: PDB / ID: 3bgw
TitleThe Structure Of A DnaB-Like Replicative Helicase And Its Interactions With Primase
ComponentsDNAB-Like Replicative Helicase
KeywordsREPLICATION / ATPase
Function / homology
Function and homology information


double-stranded DNA helicase activity / DNA 5'-3' helicase / DNA replication, synthesis of primer / DNA replication / hydrolase activity / DNA binding / ATP binding / identical protein binding
Similarity search - Function
DNAb Helicase; Chain A / DNAb Helicase; Chain A / 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. ...DNAb Helicase; Chain A / DNAb Helicase; Chain A / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus phage SPP1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.91 Å
AuthorsWang, G. / Klein, M.G. / Tokonzaba, E. / Zhang, Y. / Holden, L.G. / Chen, X.S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: The structure of a DnaB-family replicative helicase and its interactions with primase.
Authors: Wang, G. / Klein, M.G. / Tokonzaba, E. / Zhang, Y. / Holden, L.G. / Chen, X.S.
History
DepositionNov 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNAB-Like Replicative Helicase
B: DNAB-Like Replicative Helicase
C: DNAB-Like Replicative Helicase
D: DNAB-Like Replicative Helicase
E: DNAB-Like Replicative Helicase
F: DNAB-Like Replicative Helicase


Theoretical massNumber of molelcules
Total (without water)300,0866
Polymers300,0866
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29730 Å2
MethodPISA
2
D: DNAB-Like Replicative Helicase
E: DNAB-Like Replicative Helicase
F: DNAB-Like Replicative Helicase


Theoretical massNumber of molelcules
Total (without water)150,0433
Polymers150,0433
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
MethodPISA
3
A: DNAB-Like Replicative Helicase
B: DNAB-Like Replicative Helicase
C: DNAB-Like Replicative Helicase


Theoretical massNumber of molelcules
Total (without water)150,0433
Polymers150,0433
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.634, 184.411, 184.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22C
32E
13B
23D
33F
14A
24B
34C
44D
54E
64F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNALAALA4AA12 - 9214 - 94
21ASNASNALAALA4BB12 - 9214 - 94
31ASNASNALAALA4CC12 - 9214 - 94
41ASNASNALAALA4DD12 - 9214 - 94
51ASNASNALAALA4EE12 - 9214 - 94
61ASNASNALAALA4FF12 - 9214 - 94
12SERSERGLUGLU4AA93 - 14695 - 148
22SERSERGLUGLU4CC93 - 14695 - 148
32SERSERGLUGLU4EE93 - 14695 - 148
13SERSERGLUGLU4BB93 - 14695 - 148
23SERSERGLUGLU4DD93 - 14695 - 148
33SERSERGLUGLU4FF93 - 14695 - 148
14GLYGLYLEULEU1AA173 - 435175 - 437
24GLYGLYLEULEU1BB173 - 435175 - 437
34GLYGLYLEULEU1CC173 - 435175 - 437
44GLYGLYLEULEU1DD173 - 435175 - 437
54GLYGLYLEULEU1EE173 - 435175 - 437
64GLYGLYLEULEU1FF173 - 435175 - 437

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
DNAB-Like Replicative Helicase


Mass: 50014.270 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage SPP1 (virus) / Genus: Lambda-like viruses / Gene: G40P / Production host: Escherichia coli (E. coli) / References: UniProt: Q38152
Has protein modificationY

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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: 3.25 Å3/Da / Density % sol: 62.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes (pH 7.5), 1 1.25 M MgAc, and 0.02 0.04% n-octylglucoside, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.9→40 Å / Num. all: 35965 / Num. obs: 35317 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.084 / Rsym value: 0.095 / Net I/σ(I): 23
Reflection shellResolution: 3.9→4.04 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.0508 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3242 / Rsym value: 0.082 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.91→38.81 Å / Cor.coef. Fo:Fc: 0.825 / Cor.coef. Fo:Fc free: 0.811 / SU B: 159.178 / SU ML: 0.983 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 1.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Hydrogens have been added in the riding positions.The bad geometry on ASN174 in chains A and F is due to low resolution. The structure is the best authors can do at this resolution with the ...Details: Hydrogens have been added in the riding positions.The bad geometry on ASN174 in chains A and F is due to low resolution. The structure is the best authors can do at this resolution with the currently available crystallography program.
RfactorNum. reflection% reflectionSelection details
Rfree0.34889 1750 5 %RANDOM
Rwork0.33801 ---
obs0.33858 33329 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 119.949 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.91→38.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19724 0 0 0 19724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02220017
X-RAY DIFFRACTIONr_angle_refined_deg0.611.96326976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.22452491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.53925.133974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.164153743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.41115132
X-RAY DIFFRACTIONr_chiral_restr0.0440.23027
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0215018
X-RAY DIFFRACTIONr_nbd_refined0.2560.38943
X-RAY DIFFRACTIONr_nbtor_refined0.3290.513825
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.5973
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3430.376
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3670.52
X-RAY DIFFRACTIONr_mcbond_it0.463212794
X-RAY DIFFRACTIONr_mcangle_it0.83320071
X-RAY DIFFRACTIONr_scbond_it0.18227988
X-RAY DIFFRACTIONr_scangle_it0.32236905
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
41A2093tight positional0.120.05
42B2093tight positional0.080.05
43C2093tight positional0.090.05
44D2093tight positional0.080.05
45E2093tight positional0.090.05
46F2093tight positional0.130.05
11A626medium positional0.160.5
12B626medium positional0.130.5
13C626medium positional0.10.5
14D626medium positional0.10.5
15E626medium positional0.10.5
16F626medium positional0.090.5
21A381medium positional0.210.5
22C381medium positional0.290.5
23E381medium positional0.30.5
31B381medium positional0.170.5
32D381medium positional0.320.5
33F381medium positional0.30.5
41A2093tight thermal0.040.5
42B2093tight thermal0.030.5
43C2093tight thermal0.020.5
44D2093tight thermal0.020.5
45E2093tight thermal0.020.5
46F2093tight thermal0.030.5
11A626medium thermal0.12
12B626medium thermal0.062
13C626medium thermal0.042
14D626medium thermal0.042
15E626medium thermal0.042
16F626medium thermal0.042
21A381medium thermal0.082
22C381medium thermal0.052
23E381medium thermal0.052
31B381medium thermal0.052
32D381medium thermal0.072
33F381medium thermal0.052
LS refinement shellResolution: 3.91→4.013 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 93 -
Rwork0.392 2142 -
obs--85.24 %
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)
14.6847-1.29282.43681.0569-0.6211.79640.0699-0.38550.1535-0.02930.08210.15420.0682-0.2326-0.152-0.8431-0.02010.075-0.4955-0.1284-0.918329.111-35.3388.245
23.3027-1.33612.57391.7474-0.97833.0151-0.0646-0.27790.53010.2399-0.0905-0.152-0.51620.20110.1551-0.5379-0.1027-0.0521-0.171-0.3448-0.564347.614-23.20532.949
31.1420.36440.54264.2287-0.78711.0529-0.2056-0.561-0.19190.79460.1539-0.3215-0.15960.43290.05170.307-0.0191-0.23490.5692-0.1853-0.178944.467-21.24965.143
43.11423.22610.81737.54531.08490.268-0.1848-0.63820.16830.95260.18210.3160.5954-0.15020.00270.4958-0.0020.31780.67780.0147-0.243915.324-36.26973.647
52.5519-2.8824-2.14124.68183.45483.4608-0.2996-0.5149-0.52470.7119-0.15720.66550.643-0.15410.45680.1328-0.4072-0.0750.61690.1981-0.0628-9.965-46.5155.512
62.7866-1.208-1.61614.08861.69085.22660.3031-0.4718-0.26810.8022-0.17290.2029-0.2914-0.4339-0.1302-0.5187-0.3393-0.0857-0.16950.0028-0.71962.784-47.18824.886
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 43614 - 438
2X-RAY DIFFRACTION2BB12 - 43614 - 438
3X-RAY DIFFRACTION3CC12 - 43614 - 438
4X-RAY DIFFRACTION4DD12 - 43614 - 438
5X-RAY DIFFRACTION5EE12 - 43614 - 438
6X-RAY DIFFRACTION6FF12 - 43614 - 438

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