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- PDB-3iuy: Crystal structure of DDX53 DEAD-box domain -

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Basic information

Entry
Database: PDB / ID: 3iuy
TitleCrystal structure of DDX53 DEAD-box domain
ComponentsProbable ATP-dependent RNA helicase DDX53
KeywordsHYDROLASE / REC-A-like / DEAD-box / Structural Genomics / Structural Genomics Consortium / SGC / ATP-binding / Helicase / Nucleotide-binding / Nucleus / RNA-binding
Function / homology
Function and homology information


RNA helicase activity / RNA helicase / intracellular membrane-bounded organelle / mRNA binding / nucleolus / ATP hydrolysis activity / nucleoplasm / ATP binding / cytosol
Similarity search - Function
KH domain / K Homology domain, type 1 / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / Type-1 KH domain profile. / DEAD-box RNA helicase Q motif profile. / K Homology domain, type 1 superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain ...KH domain / K Homology domain, type 1 / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / Type-1 KH domain profile. / DEAD-box RNA helicase Q motif profile. / K Homology domain, type 1 superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / K Homology domain / K homology RNA-binding 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
ADENOSINE MONOPHOSPHATE / Probable ATP-dependent RNA helicase DDX53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSchutz, P. / Karlberg, T. / Collins, R. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Schutz, P. / Karlberg, T. / Collins, R. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kallas, A. / Kraulis, P. / Kotenyova, T. / Kotzsch, A. / Markova, N. / Moche, M. / Nielsen, T.K. / Nordlund, P. / Nyman, T. / Persson, C. / Roos, A.K. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Wisniewska, M. / Schuler, H.M. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2010
Title: Comparative Structural Analysis of Human DEAD-Box RNA Helicases.
Authors: Schutz, P. / Karlberg, T. / van den Berg, S. / Collins, R. / Lehtio, L. / Hogbom, M. / Holmberg-Schiavone, L. / Tempel, W. / Park, H.W. / Hammarstrom, M. / Moche, M. / Thorsell, A.G. / Schuler, H.
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Data collection / Structure summary / Category: audit_author / diffrn_radiation_wavelength / Item: _audit_author.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

Downloads & links

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX53
B: Probable ATP-dependent RNA helicase DDX53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2656
Polymers51,5002
Non-polymers7654
Water2,792155
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A: Probable ATP-dependent RNA helicase DDX53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1333
Polymers25,7501
Non-polymers3832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ATP-dependent RNA helicase DDX53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1333
Polymers25,7501
Non-polymers3832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.442, 61.251, 65.787
Angle α, β, γ (deg.)90.00, 96.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable ATP-dependent RNA helicase DDX53 / DEAD box protein 53 / DEAD box protein CAGE / Cancer-associated gene protein / Cancer/testis antigen 26 / CT26


Mass: 25750.002 Da / Num. of mol.: 2 / Fragment: UNP residues 204-430, Helicase ATP-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX53, CAGE / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE
References: UniProt: Q86TM3, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 27% PEG6000, 0.1M MES pH 6, 0.2M AmmoniumChloride, 15% Glycerol, 0.2M NaCl , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→65.382 Å / Num. obs: 17649 / % possible obs: 100 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.187 / Rsym value: 0.187 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.539.50.5781.22440925710.578100
2.53-2.689.50.4521.52312424370.452100
2.68-2.879.50.3222.12134922560.322100
2.87-3.19.50.2422.92005821140.242100
3.1-3.399.50.17341853919500.173100
3.39-3.798.90.1733.51587017880.173100
3.79-4.389.30.12751470715790.127100
4.38-5.379.30.0995.61226613170.099100
5.37-7.599.10.1095.7957010490.109100
7.59-45.138.60.1184.150565880.11899.6

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMAC5.5.0035refinement
PDB_EXTRACT3.005data extraction
DNAdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.13 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.882 / Occupancy max: 1 / Occupancy min: 0 / SU B: 8.703 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.515 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 926 5.3 %RANDOM
Rwork0.201 ---
obs0.204 17613 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.43 Å2 / Biso mean: 23.168 Å2 / Biso min: 4.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 48 155 3387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223299
X-RAY DIFFRACTIONr_angle_refined_deg1.1572.0154496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3135413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89124.464112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41715560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3281515
X-RAY DIFFRACTIONr_chiral_restr0.070.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212369
X-RAY DIFFRACTIONr_mcbond_it0.3861.52095
X-RAY DIFFRACTIONr_mcangle_it0.72523407
X-RAY DIFFRACTIONr_scbond_it0.87631204
X-RAY DIFFRACTIONr_scangle_it1.4984.51089
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 64 -
Rwork0.232 1259 -
all-1323 -
obs--100 %

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