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- PDB-4rgp: Crystal Structure of Uncharacterized CRISPR/Cas System-associated... -

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Basic information

Entry
Database: PDB / ID: 4rgp
TitleCrystal Structure of Uncharacterized CRISPR/Cas System-associated Protein Csm6 from Streptococcus mutans
ComponentsCsm6_III-A
KeywordsUNKNOWN FUNCTION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / 4 helix bundle
Function / homology: / Cas_Csm6 HEPN domain / metal ion binding / TRIETHYLENE GLYCOL / : / Csm6 HEPN domain-containing protein
Function and homology information
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.299 Å
AuthorsKim, Y. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Uncharacterized CRISPR/Cas System-associated Protein Csm6 from Streptococcus mutans
Authors: Kim, Y. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_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.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Csm6_III-A
B: Csm6_III-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,94712
Polymers61,3322
Non-polymers61510
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-68 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.511, 78.238, 92.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Csm6_III-A


Mass: 30666.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: I6U2G5, UniProt: Q8DTU7*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Calcium acetate, 0.1 M sodium cacodylate pH 6.5, 40 %(w/v) PEG300, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 26, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 24863 / Num. obs: 24863 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 40.7 Å2 / Rsym value: 0.087 / Net I/σ(I): 11.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1189 / Rsym value: 0.767 / % possible all: 99.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
PHENIXmodel building
PHENIX(phenix.refine: dev_1745)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.299→34.735 Å / SU ML: 0.21 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.89 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1939 8.01 %random
Rwork0.196 ---
all0.2 24220 --
obs0.2 24220 97.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.7 Å2
Refinement stepCycle: LAST / Resolution: 2.299→34.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4278 0 29 135 4442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024440
X-RAY DIFFRACTIONf_angle_d0.6136004
X-RAY DIFFRACTIONf_dihedral_angle_d14.31667
X-RAY DIFFRACTIONf_chiral_restr0.023663
X-RAY DIFFRACTIONf_plane_restr0.002777
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2986-2.35610.31431190.26471438155790
2.3561-2.41970.31691350.2591524165994
2.4197-2.49090.32921280.25251531165995
2.4909-2.57130.29111300.25161515164594
2.5713-2.66320.25721380.22951560169897
2.6632-2.76980.27421370.21941587172497
2.7698-2.89570.24971420.22611597173998
2.8957-3.04830.27621350.22531595173099
3.0483-3.23920.27221400.211611175199
3.2392-3.48910.22821440.20491628177299
3.4891-3.83980.25121460.179916311777100
3.8398-4.39450.20591500.157316581808100
4.3945-5.5330.21161400.165516831823100
5.533-34.73860.22671550.18471723187898
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.66920.26110.54950.53190.05430.76810.0480.39990.526-0.8422-0.07570.0704-0.1129-0.64770.06510.59070.0444-0.17530.4992-0.01950.59335.104463.827153.825
22.5833-0.77310.82593.27680.12621.49060.030.33740.3783-0.2929-0.1036-0.2184-0.0280.2830.0280.3291-0.0137-0.00020.28780.05340.2424.804560.024959.1166
33.58310.0874-0.21831.8971-0.34455.70780.17830.1451-0.6036-0.29270.1177-0.76460.7661-0.0336-0.2130.47690.08410.04640.3636-0.06870.558546.219642.277863.5099
40.8198-0.02050.65591.9397-0.00421.4896-0.1525-0.06180.01660.230.16670.01190.2001-0.1571-0.03270.31130.02220.03140.3586-0.01770.198321.903250.720469.5962
50.69320.37990.13062.14710.44920.8159-0.1398-0.8410.25660.0186-0.08930.7995-0.4434-0.08320.16970.42490.06590.03940.5952-0.12830.6048-3.004352.315964.0165
61.61160.2025-0.66321.750.70921.82430.0412-0.04590.01030.3877-0.18120.53620.1047-0.07950.14310.306-0.01990.04550.3202-0.02970.34565.167435.363457.0352
73.4333-0.58971.19743.812-1.16743.78830.3188-0.0717-0.78580.4269-0.1236-0.98220.56790.6562-0.05090.37010.0263-0.14980.35460.0610.542927.513518.623848.9576
80.62431.12070.72942.24491.59261.0457-0.1711-0.1464-0.0447-0.21310.2794-0.3716-0.28880.4461-0.07770.4254-0.03860.04110.47610.0210.242523.988142.316943.8774
90.9377-1.0061-0.89561.37140.66230.96720.03920.27620.0074-0.3421-0.24030.739-0.3339-0.23950.15140.27650.025-0.02630.4127-0.07030.42582.311139.322348.2837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 117 )
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 176 )
4X-RAY DIFFRACTION4chain 'A' and (resid 177 through 254 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 30 )
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 115 )
7X-RAY DIFFRACTION7chain 'B' and (resid 116 through 176 )
8X-RAY DIFFRACTION8chain 'B' and (resid 177 through 216 )
9X-RAY DIFFRACTION9chain 'B' and (resid 217 through 254 )

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