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- PDB-5dk5: Crystal structure of CRN-4-MES complex -

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Basic information

Entry
Database: PDB / ID: 5dk5
TitleCrystal structure of CRN-4-MES complex
ComponentsCell death-related nuclease 4
KeywordsHYDROLASE / DEDDh exonuclease / Inhibitor / Complex structure / DNase / RNase
Function / homology
Function and homology information


DNA nuclease activity / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / apoptotic DNA fragmentation / DNA catabolic process / RNA catabolic process / RNA nuclease activity / 3'-5' exonuclease activity / DNA endonuclease activity / single-stranded DNA binding / 3'-5'-RNA exonuclease activity ...DNA nuclease activity / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / apoptotic DNA fragmentation / DNA catabolic process / RNA catabolic process / RNA nuclease activity / 3'-5' exonuclease activity / DNA endonuclease activity / single-stranded DNA binding / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / metal ion binding / cytoplasm
Similarity search - Function
: / : / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / 3'-5' exonuclease crn-4
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHsiao, Y.-Y. / Yuan, H.S.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and TechnologyMOST 103-2311-B-009 -001 -MY3 Taiwan
CitationJournal: J.Med.Chem. / Year: 2016
Title: Identification of Inhibitors for the DEDDh Family of Exonucleases and a Unique Inhibition Mechanism by Crystal Structure Analysis of CRN-4 Bound with 2-Morpholin-4-ylethanesulfonate (MES)
Authors: Huang, K.-W. / Hsu, K.-C. / Chu, L.-Y. / Yang, J.-M. / Yuan, H.S. / Hsiao, Y.-Y.
History
DepositionSep 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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 / _pdbx_struct_oper_list.symmetry_operation / _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: Cell death-related nuclease 4
B: Cell death-related nuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,17615
Polymers71,1852
Non-polymers99113
Water8,143452
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint15 kcal/mol
Surface area26520 Å2
Unit cell
Length a, b, c (Å)66.259, 67.624, 178.002
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cell death-related nuclease 4


Mass: 35592.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: crn-4 / Plasmid: pGEX4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q10905, Hydrolases; Acting on ester bonds

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Non-polymers , 5 types, 465 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / 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

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.66 % / Description: Rectangular columns
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM MES monohydrate, 20mM Magnesium chloride hexahydrate, 15%(v/v) 2-Propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 47266 / % possible obs: 99.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.33
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.12 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOLREPphasing
HKL-2000data processing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CG7

3cg7


Resolution: 2.1→29.751 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 20.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2166 3662 7.77 %
Rwork0.1788 --
obs0.1818 47139 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→29.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4801 0 54 452 5307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034964
X-RAY DIFFRACTIONf_angle_d0.6966719
X-RAY DIFFRACTIONf_dihedral_angle_d12.5861838
X-RAY DIFFRACTIONf_chiral_restr0.028725
X-RAY DIFFRACTIONf_plane_restr0.002864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12770.31371380.27821627X-RAY DIFFRACTION99
2.1277-2.15680.32041340.2881643X-RAY DIFFRACTION99
2.1568-2.18760.28681390.27171661X-RAY DIFFRACTION99
2.1876-2.22020.30351290.26141641X-RAY DIFFRACTION98
2.2202-2.25490.30321500.25731631X-RAY DIFFRACTION99
2.2549-2.29190.25951290.23891656X-RAY DIFFRACTION99
2.2919-2.33140.24821470.22761651X-RAY DIFFRACTION99
2.3314-2.37380.24611430.22041644X-RAY DIFFRACTION99
2.3738-2.41940.26561370.20481640X-RAY DIFFRACTION99
2.4194-2.46880.24411500.20771644X-RAY DIFFRACTION99
2.4688-2.52240.23661580.19631625X-RAY DIFFRACTION99
2.5224-2.58110.24771390.19381653X-RAY DIFFRACTION99
2.5811-2.64560.24371490.18821654X-RAY DIFFRACTION99
2.6456-2.7170.23931270.181660X-RAY DIFFRACTION99
2.717-2.79690.21761380.17971671X-RAY DIFFRACTION99
2.7969-2.88710.22691480.17761660X-RAY DIFFRACTION99
2.8871-2.99020.22621370.17291666X-RAY DIFFRACTION100
2.9902-3.10980.221370.18131671X-RAY DIFFRACTION100
3.1098-3.25120.21731430.1681686X-RAY DIFFRACTION99
3.2512-3.42240.19451410.15991685X-RAY DIFFRACTION99
3.4224-3.63650.1991430.16211691X-RAY DIFFRACTION99
3.6365-3.91670.17721490.14561681X-RAY DIFFRACTION99
3.9167-4.30980.18581380.13141720X-RAY DIFFRACTION100
4.3098-4.93090.15811330.13361718X-RAY DIFFRACTION99
4.9309-6.20320.1781380.16251747X-RAY DIFFRACTION99
6.2032-29.7540.18421480.16241851X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -12.5884 Å / Origin y: -4.7919 Å / Origin z: 18.6382 Å
111213212223313233
T0.1749 Å2-0.0404 Å2-0.0013 Å2-0.1716 Å2-0.0146 Å2--0.2032 Å2
L0.7105 °2-0.1412 °2-0.6563 °2-0.752 °20.038 °2--1.3294 °2
S0.092 Å °-0.0654 Å °0.0831 Å °0.1989 Å °-0.024 Å °0.0234 Å °-0.175 Å °0.0761 Å °-0.0724 Å °
Refinement TLS groupSelection details: all

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