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- PDB-1hv8: CRYSTAL STRUCTURE OF A DEAD BOX PROTEIN FROM THE HYPERTHERMOPHILE... -

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Basic information

Entry
Database: PDB / ID: 1hv8
TitleCRYSTAL STRUCTURE OF A DEAD BOX PROTEIN FROM THE HYPERTHERMOPHILE METHANOCOCCUS JANNASCHII
ComponentsPUTATIVE ATP-DEPENDENT RNA HELICASE MJ0669
KeywordsRNA BINDING PROTEIN / Helicase / RNA-binding Protein / ATPase
Function / homology
Function and homology information


catalytic activity, acting on DNA / DNA conformation change / RNA helicase activity / RNA helicase / ATP hydrolysis activity / RNA binding / ATP binding
Similarity search - Function
: / 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. ...: / 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
Probable ATP-dependent RNA helicase MJ0669
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsStory, R.M. / Li, H. / Abelson, J.N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Crystal structure of a DEAD box protein from the hyperthermophile Methanococcus jannaschii.
Authors: Story, R.M. / Li, H. / Abelson, J.N.
History
DepositionJan 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: PUTATIVE ATP-DEPENDENT RNA HELICASE MJ0669
B: PUTATIVE ATP-DEPENDENT RNA HELICASE MJ0669
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5828
Polymers85,0062
Non-polymers5766
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-95 kcal/mol
Surface area33920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.132, 131.450, 131.829
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PUTATIVE ATP-DEPENDENT RNA HELICASE MJ0669 / DEAD BOX HELICASE


Mass: 42503.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: Q58083
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 6
Details: ammonium sulfate, acetate,tris, DTT, EDTA, NaN3, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 303K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlprotein1drop
220 mMTris1drop
30.02 %(w/v)1dropNaN3
4500 mMammonium sulfate1drop
5100 mM1dropNaCl
61 mMEDTA1drop
75 mMdithiothreitol1drop
857-62 %satammonium sulfate1reservoir
9100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9795, 0.9793, 0.9611
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 1999
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97931
30.96111
ReflectionResolution: 2.95→25 Å / Num. all: 20100 / Num. obs: 20100 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 16.1 % / Biso Wilson estimate: 86.2 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.9
Reflection shellResolution: 2.95→3 Å / Redundancy: 2 % / Rmerge(I) obs: 0.419 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 % / Num. measured all: 322686
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVE+ DMphasing
CNSrefinement
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 3→20 Å / σ(F): 0 / Stereochemistry target values: Engh and Huber
Details: Residues 299-306 and 330-337 lie in very weak electron density and their structures are tentative
RfactorNum. reflectionSelection details
Rfree0.316 1888 random
Rwork0.27 --
all-19253 -
obs-19086 -
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5822 0 30 0 5852
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.009
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.27 / Rfactor Rwork: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4

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