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- PDB-3nbf: Q28E mutant of hera helicase N-terminal domain bound to 8-oxo-ADP -

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Basic information

Entry
Database: PDB / ID: 3nbf
TitleQ28E mutant of hera helicase N-terminal domain bound to 8-oxo-ADP
ComponentsHeat resistant RNA dependent ATPase
KeywordsHYDROLASE / rna helicase / ribosome biogenesis / atp hydrolysis / base specificity / thermostability
Function / homology
Function and homology information


nucleic acid binding / RNA helicase activity / hydrolase activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
: / : / RNA helicase Hera, dimerization domain / DEAD box helicase Hera, RNA-binding domain / : / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain ...: / : / RNA helicase Hera, dimerization domain / DEAD box helicase Hera, RNA-binding domain / : / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / 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
Chem-8OD / Chem-8OP / Heat resistant RNA dependent ATPase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRudolph, M.G. / Klostermeier, D.
CitationJournal: Biol.Chem. / Year: 2011
Title: Changing nucleotide specificity of the DEAD-box helicase Hera abrogates communication between the Q-motif and the P-loop.
Authors: Strohmeier, J. / Hertel, I. / Diederichsen, U. / Rudolph, M.G. / Klostermeier, D.
History
DepositionJun 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: 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 / 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: Heat resistant RNA dependent ATPase
B: Heat resistant RNA dependent ATPase
C: Heat resistant RNA dependent ATPase
D: Heat resistant RNA dependent ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,12513
Polymers89,3764
Non-polymers3,7499
Water4,774265
1
A: Heat resistant RNA dependent ATPase
B: Heat resistant RNA dependent ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4616
Polymers44,6882
Non-polymers1,7734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-8 kcal/mol
Surface area17510 Å2
MethodPISA
2
C: Heat resistant RNA dependent ATPase
D: Heat resistant RNA dependent ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6647
Polymers44,6882
Non-polymers1,9765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-16 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.648, 60.676, 74.085
Angle α, β, γ (deg.)68.90, 77.29, 72.64
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Heat resistant RNA dependent ATPase


Mass: 22343.938 Da / Num. of mol.: 4 / Fragment: n-terminal domain / Mutation: Q28E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q72GF3
#2: Chemical
ChemComp-8OD / [(2R,3S,4R,5R)-5-(6-azanyl-8-oxo-7H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl phosphono hydrogen phosphate


Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2
#3: Chemical ChemComp-8OP / [(2R,3S,4R,5R)-5-(6-azanyl-8-oxo-7H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate


Mass: 363.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% PEG 3350, 0.2M sodium citrate, 0.1M HEPES/NaOH pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.5 Å / Num. obs: 70329 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 30.5 Å2 / Rsym value: 0.041 / Net I/σ(I): 7.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 2091 / Rsym value: 0.592 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GXS

2gxs


Resolution: 1.9→41.512 Å / SU ML: 0.27 / σ(F): 0.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 3231 4.98 %random
Rwork0.1841 ---
obs0.1861 64866 88.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.934 Å2 / ksol: 0.308 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.7702 Å2-0.9355 Å24.6631 Å2
2---4.516 Å25.7191 Å2
3---0.7458 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6232 0 240 265 6737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076619
X-RAY DIFFRACTIONf_angle_d1.0929048
X-RAY DIFFRACTIONf_dihedral_angle_d17.1032458
X-RAY DIFFRACTIONf_chiral_restr0.071083
X-RAY DIFFRACTIONf_plane_restr0.0061128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.92840.3391140.3254237779
1.9284-1.95850.32611130.3075221972
1.9585-1.99060.35821150.2862228276
1.9906-2.02490.36931270.2922229875
2.0249-2.06180.28871320.2672231578
2.0618-2.10140.34451340.2564246881
2.1014-2.14430.29971190.23255884
2.1443-2.19090.27271340.2212259685
2.1909-2.24190.25681340.2032266087
2.2419-2.2980.25511480.2017264889
2.298-2.36010.24141250.1935276490
2.3601-2.42950.26291400.1988276491
2.4295-2.50790.25811380.1991278592
2.5079-2.59760.28031400.1956282293
2.5976-2.70150.26681610.2012288395
2.7015-2.82450.25891530.2039286895
2.8245-2.97330.22431670.2144289995
2.9733-3.15960.25741400.2107287995
3.1596-3.40340.23781540.1883290695
3.4034-3.74570.21741640.1644289996
3.7457-4.28720.16351650.1329291396
4.2872-5.39960.12811610.121288695
5.3996-41.52160.18791530.1527294697
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)
11.02470.03280.12191.61420.0820.87480.0239-0.00790.03920.132-0.04350.2398-0.0564-0.16150.02660.12380.01270.00040.231-0.0120.2285-42.2026.1468-16.9869
21.21260.4683-0.08990.2691-0.36590.0818-0.2144-0.3091-0.0517-0.07970.163-0.17590.08110.01470.04030.12960.0742-0.00050.2452-0.0310.1951-8.3424-8.7851-21.4902
31.18210.45470.1572.1488-1.30591.7919-0.0080.1082-0.0659-0.0633-0.0079-0.1124-0.32340.1153-0.00020.2997-0.04180.02910.19-0.04030.1696-34.6787-27.013-41.7483
40.77630.2847-0.40351.1232-0.76111.5278-0.06020.0781-0.0093-0.0861-0.00660.01340.67310.00610.06170.5487-0.051-0.02650.22820.02860.1895-30.63686.9764-56.8436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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