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- PDB-4wbq: Crystal structure of the exonuclease domain of QIP (QDE-2 interac... -

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Basic information

Entry
Database: PDB / ID: 4wbq
TitleCrystal structure of the exonuclease domain of QIP (QDE-2 interacting protein) solved by native-SAD phasing.
ComponentsQDE-2-interacting protein
KeywordsRNA BINDING PROTEIN
Function / homologyGfd2/YDR514C-like / : / DNA polymerase III subunit epsilon-like, C-terminal domain / Ribonuclease H superfamily / nucleic acid binding / Ribonuclease H-like superfamily / metal ion binding / nucleus / QDE-2-interacting protein
Function and homology information
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.693 Å
AuthorsBoland, A. / Weinert, T. / Weichenrieder, O. / Wang, M.
CitationJournal: Nat.Methods / Year: 2015
Title: Fast native-SAD phasing for routine macromolecular structure determination.
Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / ...Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / Bargsten, K. / Prota, A.E. / Surana, P. / Kottur, J. / Nair, D.T. / Basilico, F. / Cecatiello, V. / Pasqualato, S. / Boland, A. / Weichenrieder, O. / Wang, B.C. / Steinmetz, M.O. / Caffrey, M. / Wang, M.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3May 8, 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
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_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_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_asym_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: QDE-2-interacting protein
B: QDE-2-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7506
Polymers53,5902
Non-polymers1604
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-94 kcal/mol
Surface area15860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.040, 77.040, 112.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein QDE-2-interacting protein


Mass: 26794.941 Da / Num. of mol.: 2 / Fragment: UNP residues 326-565
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A5JQJ3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M CaCl2, 0.1M Hepes buffer, pH7, 20% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.0664 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.0664 Å / Relative weight: 1
ReflectionResolution: 2.693→43 Å / Num. obs: 20707 / % possible obs: 99.9 % / Redundancy: 154 % / Net I/σ(I): 37.1
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 16.94 / Num. unique all: 2661 / % possible all: 86.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.693→42.963 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 1032 4.99 %
Rwork0.1719 --
obs0.1748 20678 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.693→42.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2729 0 4 33 2766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022772
X-RAY DIFFRACTIONf_angle_d0.5873744
X-RAY DIFFRACTIONf_dihedral_angle_d11.036984
X-RAY DIFFRACTIONf_chiral_restr0.022432
X-RAY DIFFRACTIONf_plane_restr0.002471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6932-2.83520.31451430.22642855X-RAY DIFFRACTION99
2.8352-3.01270.23841480.21062765X-RAY DIFFRACTION100
3.0127-3.24530.32091380.19122825X-RAY DIFFRACTION100
3.2453-3.57170.21631500.17582809X-RAY DIFFRACTION100
3.5717-4.08820.23311500.15332789X-RAY DIFFRACTION100
4.0882-5.14940.18311480.14562818X-RAY DIFFRACTION100
5.1494-42.96830.21771550.17882785X-RAY DIFFRACTION100
Refinement TLS params.Method: refined
Refinement TLS groupSelection details: chain 'B' and resid ' 519 ' and name ' SD ' and altloc ' '

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