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- PDB-7ndk: Crystal structure of ZC3H12C PIN catalytic mutant -

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Basic information

Entry
Database: PDB / ID: 7ndk
TitleCrystal structure of ZC3H12C PIN catalytic mutant
ComponentsProbable ribonuclease ZC3H12C
KeywordsRNA BINDING PROTEIN / Endo-ribonuclease / Regnase
Function / homology
Function and homology information


RNA endonuclease activity / cytoplasmic ribonucleoprotein granule / Hydrolases; Acting on ester bonds / mRNA binding / nucleus / metal ion binding
Similarity search - Function
Rege-1, UBA-like domain / Endoribonuclease Regnase 1/ZC3H12, C-terminal domain / UBA-like domain / Endoribonuclease Regnase 1/ ZC3H12 C-terminal domain / Ribonuclease Zc3h12a-like, NYN domain / Zc3h12a-like Ribonuclease NYN domain / Zinc finger, CCCH-type / Zinc finger C3H1-type profile.
Similarity search - Domain/homology
Probable ribonuclease ZC3H12C
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsGarg, A. / Heinemann, U.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: PIN and CCCH Zn-finger domains coordinate RNA targeting in ZC3H12 family endoribonucleases.
Authors: Garg, A. / Roske, Y. / Yamada, S. / Uehata, T. / Takeuchi, O. / Heinemann, U.
History
DepositionFeb 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ribonuclease ZC3H12C
B: Probable ribonuclease ZC3H12C
C: Probable ribonuclease ZC3H12C
D: Probable ribonuclease ZC3H12C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6546
Polymers76,6084
Non-polymers462
Water1,69394
1
A: Probable ribonuclease ZC3H12C


Theoretical massNumber of molelcules
Total (without water)19,1521
Polymers19,1521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable ribonuclease ZC3H12C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1752
Polymers19,1521
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Probable ribonuclease ZC3H12C


Theoretical massNumber of molelcules
Total (without water)19,1521
Polymers19,1521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Probable ribonuclease ZC3H12C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1752
Polymers19,1521
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.753, 61.475, 111.620
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Probable ribonuclease ZC3H12C / Zinc finger CCCH domain-containing protein 12C


Mass: 19151.951 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Zc3h12c, Kiaa1726 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5DTV4, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M KSCN, 20% PEG 3350 and 0.1 M Bis-Tris propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.521
11-h,-k,l20.479
ReflectionResolution: 2.34→38.75 Å / Num. obs: 21746 / % possible obs: 97 % / Redundancy: 2.25 % / CC1/2: 0.998 / Net I/σ(I): 10.19
Reflection shellResolution: 2.34→2.39 Å / Num. unique obs: 1417 / CC1/2: 0.629

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NDI

7ndi


Resolution: 2.34→38.75 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.299 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2748 1082 5 %RANDOM
Rwork0.2292 ---
obs0.2314 20656 96.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.13 Å2 / Biso mean: 61.591 Å2 / Biso min: 27.73 Å2
Baniso -1Baniso -2Baniso -3
1-35.81 Å20 Å24.11 Å2
2--22.95 Å2-0 Å2
3----58.76 Å2
Refinement stepCycle: final / Resolution: 2.34→38.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5130 0 2 94 5226
Biso mean--41.29 54.07 -
Num. residues----623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195241
X-RAY DIFFRACTIONr_bond_other_d0.0020.024994
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9617057
X-RAY DIFFRACTIONr_angle_other_deg0.938311550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1065612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34423.258267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76115964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1141552
X-RAY DIFFRACTIONr_chiral_restr0.0690.2756
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215702
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021130
LS refinement shellResolution: 2.34→2.398 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.411 76 -
Rwork0.319 1470 -
obs--94.21 %

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