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- PDB-6fac: CRYSTAL STRUCTURE OF THE DEAH-BOX HELICASE PRP2 IN COMPLEX WITH ADP -

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Basic information

Entry
Database: PDB / ID: 6fac
TitleCRYSTAL STRUCTURE OF THE DEAH-BOX HELICASE PRP2 IN COMPLEX WITH ADP
ComponentsPutative mRNA splicing factor
KeywordsHYDROLASE / SPLICING / ATPASE / HELICASE / G-PATCH
Function / homology
Function and homology information


catalytic step 2 spliceosome / RNA splicing / helicase activity / mRNA processing / hydrolase activity / RNA helicase / RNA binding / ATP binding / metal ion binding
Similarity search - Function
G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain ...G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / RNA-binding domain superfamily / 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 / Nucleotide-binding alpha-beta plait domain superfamily / 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-5'-DIPHOSPHATE / RNA helicase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSchmitt, A. / Hamann, F. / Neumann, P. / Ficner, R.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Crystal structure of the spliceosomal DEAH-box ATPase Prp2.
Authors: Schmitt, A. / Hamann, F. / Neumann, P. / Ficner, R.
History
DepositionDec 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative mRNA splicing factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5147
Polymers72,9211
Non-polymers5936
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-56 kcal/mol
Surface area29360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.740, 67.320, 95.620
Angle α, β, γ (deg.)90.000, 106.460, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative mRNA splicing factor / Prp2


Mass: 72920.586 Da / Num. of mol.: 1 / Fragment: residues 3- 610
Source method: isolated from a genetically manipulated source
Details: C-terminal His6-tag / Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0063660 / Plasmid: pASG-IBA25 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SEG4
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.06 M MgCl2/CaCl2, 0.1 M HEPES/MOPS pH 7.5, 20% (w/v) Etylene glycol, 10% (w/v) PEG 8000
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.05→46.41 Å / Num. obs: 46873 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.08 % / Biso Wilson estimate: 44.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.045 / Χ2: 0.996 / Net I/σ(I): 20.31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.150.7942.1961770.8340.90999.6
2.15-2.250.5293.1251480.8970.61399
2.25-2.450.3365.679650.950.38599.8
2.45-3.290.08616.83160990.9950.199.6
3.29-3.710.02639.9534380.9990.0398.9
3.71-4.130.0251.9722050.9990.02399.6
4.13-4.550.01858.0114630.9990.02199.7
4.55-140.01761.3742210.9990.0299.1
14-170.01971.08730.9990.022100
17-500.0266.61840.9980.02495.5
50-50

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FAA

6faa


Resolution: 2.05→46.41 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.8
RfactorNum. reflection% reflection
Rfree0.2441 2343 5 %
Rwork0.216 --
obs0.2174 46832 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 170.27 Å2 / Biso mean: 62.6302 Å2 / Biso min: 21.75 Å2
Refinement stepCycle: final / Resolution: 2.05→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5104 0 32 222 5358
Biso mean--61.82 58.65 -
Num. residues----653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015266
X-RAY DIFFRACTIONf_angle_d1.4767163
X-RAY DIFFRACTIONf_chiral_restr0.09821
X-RAY DIFFRACTIONf_plane_restr0.014924
X-RAY DIFFRACTIONf_dihedral_angle_d13.5995559
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.09180.37631370.35532592272999
2.0918-2.13730.37171360.343925812717100
2.1373-2.18710.36791370.34262606274399
2.1871-2.24170.33041350.32832562269799
2.2417-2.30240.3841380.318926192757100
2.3024-2.37010.31151370.300125992736100
2.3701-2.44660.31391370.288326072744100
2.4466-2.5340.31841380.272226202758100
2.534-2.63550.29221370.26526112748100
2.6355-2.75540.28431380.26072617275599
2.7554-2.90070.30061380.257726252763100
2.9007-3.08240.28421390.248626482787100
3.0824-3.32030.27611380.243226132751100
3.3203-3.65430.24341370.20552611274899
3.6543-4.18280.21871390.174526312770100
4.1828-5.26870.17551390.16012648278799
5.2687-46.4220.18371430.17322699284299
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)
10.86710.09930.83271.6017-0.62661.6917-0.07850.1717-0.0081-0.56210.0598-0.0480.50520.3361-0.02470.36390.0810.06870.3548-0.0420.26146.2201-14.84956.1968
21.7889-0.00830.2970.6882-0.61831.64130.0698-0.0944-0.203-0.00070.0299-0.29260.33040.38020.00090.34150.12680.01250.3465-0.01830.341251.0675-21.506222.4794
31.2801-0.27390.77010.67920.12022.3973-0.18080.1080.41620.34090.0261-0.242-0.52180.4614-0.00240.3954-0.1311-0.02510.50910.0390.556452.92940.093925.1204
41.1966-0.2319-0.23651.74370.24611.0326-0.17610.05140.277-0.00440.09290.4417-0.4939-0.176-0.00620.62640.1628-0.09350.357-0.02180.506129.381311.838517.6459
51.2827-0.34790.52412.9358-0.32811.6836-0.0661-0.19460.14770.2546-0.0005-0.1602-0.3259-0.0208-0.00010.36660.0518-0.03190.3988-0.04040.346239.6529-4.405827.7508
62.00720.9372-0.53911.2890.61171.17610.24-0.3731-0.3104-0.0431-0.11130.34670.4943-0.3083-0.00010.49170.0144-0.03230.4380.03350.415824.7571-27.863432.6271
73.4050.6360.29412.50340.09843.27320.4090.37960.7293-0.518-0.28930.5813-0.1594-0.67810.10810.33930.1708-0.0280.60180.01350.703212.8993-12.688421.6098
82.3805-0.34921.14691.9011-0.76912.7522-0.0858-1.0581-0.12550.7630.02230.54350.4112-0.59360.03780.42830.03610.12550.8541-0.09810.524515.9606-17.412441.047
90.97530.01360.31870.8211-0.11180.8143-0.0738-0.53620.0039-0.0267-0.16180.4518-0.1689-0.5457-0.10090.46930.11990.14120.8636-0.1610.721215.4511-13.265442.492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 268 through 405 )A268 - 405
2X-RAY DIFFRACTION2chain 'A' and (resid 406 through 451 )A406 - 451
3X-RAY DIFFRACTION3chain 'A' and (resid 452 through 488 )A452 - 488
4X-RAY DIFFRACTION4chain 'A' and (resid 489 through 536 )A489 - 536
5X-RAY DIFFRACTION5chain 'A' and (resid 537 through 698 )A537 - 698
6X-RAY DIFFRACTION6chain 'A' and (resid 699 through 749 )A699 - 749
7X-RAY DIFFRACTION7chain 'A' and (resid 750 through 826 )A750 - 826
8X-RAY DIFFRACTION8chain 'A' and (resid 827 through 880 )A827 - 880
9X-RAY DIFFRACTION9chain 'A' and (resid 881 through 920 )A881 - 920

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