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- PDB-4n0l: Methanopyrus kandleri Csm3 crystal structure -

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Basic information

Entry
Database: PDB / ID: 4n0l
TitleMethanopyrus kandleri Csm3 crystal structure
ComponentsPredicted component of a thermophile-specific DNA repair system, contains a RAMP domainPrediction
KeywordsRNA BINDING PROTEIN / RRM-like fold / crRNA binding / Cas/Csm proteins
Function / homologyCRISPR-associated RAMP Csm3 / CRISPR type III-associated protein / RAMP superfamily / endonuclease activity / defense response to virus / RNA binding / metal ion binding / CRISPR system Cms endoribonuclease Csm3
Function and homology information
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Zn-SAD / Resolution: 2.37 Å
AuthorsHrle, A. / Su, A.A. / Ebert, J. / Benda, C. / Conti, E. / Randau, L.
CitationJournal: Rna Biol. / Year: 2013
Title: Structure and RNA-binding properties of the Type III-A CRISPR-associated protein Csm3.
Authors: Hrle, A. / Su, A.A. / Ebert, J. / Benda, C. / Randau, L. / Conti, E.
History
DepositionOct 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_label_asym_id / _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

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Assembly

Deposited unit
A: Predicted component of a thermophile-specific DNA repair system, contains a RAMP domain
B: Predicted component of a thermophile-specific DNA repair system, contains a RAMP domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3744
Polymers79,2442
Non-polymers1312
Water3,261181
1
A: Predicted component of a thermophile-specific DNA repair system, contains a RAMP domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6872
Polymers39,6221
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Predicted component of a thermophile-specific DNA repair system, contains a RAMP domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6872
Polymers39,6221
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.753, 101.017, 174.167
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Predicted component of a thermophile-specific DNA repair system, contains a RAMP domain / Prediction / Csm3


Mass: 39621.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Strain: AV19 / DSM 6324 / JCM 9639 / NBRC 100938 / Gene: MK1316 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TVS2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.05M MES, 50% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2012 / Details: LN2-COOLED DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.37→69.494 Å / Num. all: 66653 / Num. obs: 66282 / % possible obs: 99.44 % / Observed criterion σ(F): 1.99 / Observed criterion σ(I): 3
Reflection shellResolution: 2.37→2.3996 Å / % possible all: 99.44

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: Zn-SAD / Resolution: 2.37→69.494 Å / SU ML: 0.28 / σ(F): 1.99 / Phase error: 23.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 3310 4.99 %RANDOM
Rwork0.1939 ---
obs0.195 66282 99.44 %-
all-66319 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→69.494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5266 0 2 181 5449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035396
X-RAY DIFFRACTIONf_angle_d0.8257314
X-RAY DIFFRACTIONf_dihedral_angle_d14.242026
X-RAY DIFFRACTIONf_chiral_restr0.029747
X-RAY DIFFRACTIONf_plane_restr0.003989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.39960.35291260.31912402X-RAY DIFFRACTION89
2.3996-2.43540.31121350.29352532X-RAY DIFFRACTION99
2.4354-2.47340.31281410.27932654X-RAY DIFFRACTION100
2.4734-2.5140.24171370.26212612X-RAY DIFFRACTION100
2.514-2.55730.28481380.23712633X-RAY DIFFRACTION100
2.5573-2.60380.26861430.23542660X-RAY DIFFRACTION100
2.6038-2.65390.25911390.23132644X-RAY DIFFRACTION100
2.6539-2.70810.2791360.23612596X-RAY DIFFRACTION100
2.7081-2.7670.25851430.23492661X-RAY DIFFRACTION100
2.767-2.83130.27351370.22692636X-RAY DIFFRACTION100
2.8313-2.90220.26551440.22582683X-RAY DIFFRACTION100
2.9022-2.98060.26761360.21312603X-RAY DIFFRACTION100
2.9806-3.06830.23961350.19852619X-RAY DIFFRACTION100
3.0683-3.16740.1931410.20012678X-RAY DIFFRACTION100
3.1674-3.28060.25251350.20432617X-RAY DIFFRACTION100
3.2806-3.41190.23641440.21272641X-RAY DIFFRACTION100
3.4119-3.56720.21421400.1862613X-RAY DIFFRACTION100
3.5672-3.75530.19251360.16452632X-RAY DIFFRACTION100
3.7553-3.99050.16741410.16182659X-RAY DIFFRACTION100
3.9905-4.29860.17751400.15642619X-RAY DIFFRACTION100
4.2986-4.73110.16471330.15192653X-RAY DIFFRACTION100
4.7311-5.41540.21861370.17452645X-RAY DIFFRACTION100
5.4154-6.8220.24191340.21312641X-RAY DIFFRACTION100
6.822-69.5240.15281390.17242639X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -13.8794 Å / Origin y: 11.2338 Å / Origin z: 21.9168 Å
111213212223313233
T0.124 Å2-0.1075 Å20.0241 Å2-0.1051 Å20.0054 Å2--0.1207 Å2
L0.1448 °20.0403 °20.02 °2-0.1022 °20.0966 °2--0.0675 °2
S-0.0934 Å °-0.1033 Å °-0.0671 Å °-0.1063 Å °-0.0061 Å °0.0095 Å °-0.1191 Å °0.041 Å °-0.071 Å °
Refinement TLS groupSelection details: ALL

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