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- PDB-1q0u: Crystal Structure of the BstDEAD N-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 1q0u
TitleCrystal Structure of the BstDEAD N-terminal Domain
ComponentsBstDEAD
KeywordsRNA BINDING PROTEIN / DEAD PROTEIN
Function / homology
Function and homology information


RNA strand annealing activity / response to cold / RNA helicase activity / hydrolase activity / ribosome / ATP binding / cytosol
Similarity search - Function
: / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...: / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / 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 speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsCarmel, A.B. / Matthews, B.W.
CitationJournal: RNA / Year: 2004
Title: Crystal structure of the BstDEAD N-terminal domain: a novel DEAD protein from Bacillus stearothermophilus
Authors: Carmel, A.B. / Matthews, B.W.
History
DepositionJul 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BstDEAD
B: BstDEAD


Theoretical massNumber of molelcules
Total (without water)50,9992
Polymers50,9992
Non-polymers00
Water4,270237
1
A: BstDEAD


Theoretical massNumber of molelcules
Total (without water)25,4991
Polymers25,4991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BstDEAD


Theoretical massNumber of molelcules
Total (without water)25,4991
Polymers25,4991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.463, 113.463, 65.338
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
DetailsBIOLOGICAL UNIT CONTAINED WITHIN ASYMMETRIC UNIT

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Components

#1: Protein BstDEAD


Mass: 25499.406 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)gold / References: UniProt: P83699
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: PEG 1550, CAPS, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMCAPS1reservoirpH10.5
230 %(w/v)PEG15501reservoir
357 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.9789, 0.9792, 0.9252
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2002 / Details: mirror
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97921
30.92521
ReflectionResolution: 1.85→25 Å / Num. obs: 40958 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.071 / Net I/σ(I): 6.6
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 2614 / Rsym value: 0.41 / % possible all: 98.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
TNTrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.85→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1169 -RANDOM
Rwork0.201 ---
obs0.204 40935 99.8 %-
Refinement stepCycle: LAST / Resolution: 1.85→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 0 240 3582
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg2.275
Refinement
*PLUS
Rfactor Rfree: 0.286
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.3

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