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- PDB-1wrb: Crystal structure of the N-terminal RecA-like domain of DjVLGB, a... -

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Basic information

Entry
Database: PDB / ID: 1wrb
TitleCrystal structure of the N-terminal RecA-like domain of DjVLGB, a pranarian Vasa-like RNA helicase
ComponentsDjVLGB
KeywordsHYDROLASE / RNA HELICASE / DEAD BOX / VASA / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


gamete generation / P granule / RNA helicase activity / cell differentiation / hydrolase activity / RNA helicase / RNA binding / ATP binding / nucleus
Similarity search - Function
Ded1/Dbp1, DEAD-box helicase domain / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. ...Ded1/Dbp1, DEAD-box helicase domain / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesDugesia japonica (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKurimoto, K. / Muto, Y. / Obayashi, N. / Terada, T. / Shirouzu, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Kigawa, T. ...Kurimoto, K. / Muto, Y. / Obayashi, N. / Terada, T. / Shirouzu, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Kigawa, T. / Okumura, H. / Tanaka, A. / Shibata, N. / Kashikawa, M. / Agata, K. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Struct.Biol. / Year: 2005
Title: Crystal structure of the N-terminal RecA-like domain of a DEAD-box RNA helicase, the Dugesia japonica vasa-like gene B protein
Authors: Kurimoto, K. / Muto, Y. / Obayashi, N. / Terada, T. / Shirouzu, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Kigawa, T. / Okumura, H. / Tanaka, A. / Shibata, N. / Kashikawa, M. / ...Authors: Kurimoto, K. / Muto, Y. / Obayashi, N. / Terada, T. / Shirouzu, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Kigawa, T. / Okumura, H. / Tanaka, A. / Shibata, N. / Kashikawa, M. / Agata, K. / Yokoyama, S.
History
DepositionOct 14, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: DjVLGB
B: DjVLGB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1644
Polymers56,9722
Non-polymers1922
Water4,179232
1
A: DjVLGB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5822
Polymers28,4861
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: DjVLGB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5822
Polymers28,4861
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: DjVLGB
hetero molecules

B: DjVLGB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1644
Polymers56,9722
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_664-x+1,-y+1,z-1/21
Buried area3970 Å2
ΔGint-52 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.242, 138.242, 47.508
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 DjVLGB


Mass: 28485.807 Da / Num. of mol.: 2 / Fragment: N-terminal RecA-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dugesia japonica (invertebrata) / Description: E.coli cell free system / References: UniProt: O97032
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 1.99 Å3/Da / Density % sol: 38.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 1, 2002
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 18468 / Num. obs: 18468 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.44 Å / % possible all: 94.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / σ(F): 0
RfactorNum. reflection
Rfree0.2815 888
Rwork0.241 -
all-18409
obs-18409
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 10 232 3888
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007097
X-RAY DIFFRACTIONc_angle_d1.3583
X-RAY DIFFRACTIONc_dihedral_angle_d23.82215
X-RAY DIFFRACTIONc_improper_angle_d1.09288
LS refinement shellResolution: 2.4→2.5 Å
RfactorNum. reflection
Rfree0.3453 86
Rwork0.2539 -
obs-1931

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