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- PDB-2gxs: HERA N-terminal domain in complex with AMP, crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 2gxs
TitleHERA N-terminal domain in complex with AMP, crystal form 2
Componentsheat resistant RNA dependent ATPase
KeywordsHYDROLASE / RNA helicase / atomic resolution / AMP complex / ribosome biogenesis / thermophilic
Function / homology
Function and homology information


nucleic acid binding / RNA helicase activity / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
: / RNA helicase Hera, dimerization 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 / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain ...: / RNA helicase Hera, dimerization 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 / DEAD/DEAH box helicase domain / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Heat resistant RNA dependent ATPase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsRudolph, M.G. / Klostermeier, D.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure and Nucleotide Binding of the Thermus thermophilus RNA Helicase Hera N-terminal Domain.
Authors: Rudolph, M.G. / Heissmann, R. / Wittmann, J.G. / Klostermeier, D.
History
DepositionMay 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS STATE THE BIOLOGICAL UNIT IS EITHER A MONOMER OR A DIMER AS SHOWN IN REMARK 350.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,67310
Polymers44,6862
Non-polymers9878
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-69 kcal/mol
Surface area17000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.564, 42.838, 68.645
Angle α, β, γ (deg.)90.00, 100.06, 90.00
Int Tables number5
Space group name H-MC121
DetailsBiological assembly could be a dimer, see publication for details

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Components

#1: Protein heat resistant RNA dependent ATPase


Mass: 22342.953 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Species: Thermus thermophilus / Strain: HB-27 / Gene: HERA / Plasmid: pET27b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: O07897
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 14% PEG6000, 0.3M CaCl2, 0.1M Tris/HCl pH9.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5419 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 14, 2006 / Details: osmic mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. all: 45511 / Num. obs: 45511 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 27.6 Å2 / Rsym value: 0.048 / Net I/σ(I): 27.5
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 3976 / Rsym value: 0.5 / % possible all: 85.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
HKL-2000data scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.56 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23942 2302 5.1 %RANDOM
Rwork0.18919 ---
obs0.19172 43198 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.853 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å2-0.39 Å2
2---0.16 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 1.66→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3132 0 57 406 3595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223419
X-RAY DIFFRACTIONr_bond_other_d0.0020.022389
X-RAY DIFFRACTIONr_angle_refined_deg1.712.0324691
X-RAY DIFFRACTIONr_angle_other_deg1.05835881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2695463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43323.182132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65715612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2861533
X-RAY DIFFRACTIONr_chiral_restr0.0940.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023769
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02652
X-RAY DIFFRACTIONr_nbd_refined0.2320.2752
X-RAY DIFFRACTIONr_nbd_other0.2160.22668
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21661
X-RAY DIFFRACTIONr_nbtor_other0.0820.21872
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2285
X-RAY DIFFRACTIONr_metal_ion_refined0.1950.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2920.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.233
X-RAY DIFFRACTIONr_mcbond_it1.1191.52213
X-RAY DIFFRACTIONr_mcbond_other0.2521.5852
X-RAY DIFFRACTIONr_mcangle_it1.63223481
X-RAY DIFFRACTIONr_scbond_it2.51131348
X-RAY DIFFRACTIONr_scangle_it3.8654.51183
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.522 137 -
Rwork0.407 2736 -
obs--83.32 %

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