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- PDB-3vzi: Crystal Structure of CRISPR-associated Protein -

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Basic information

Entry
Database: PDB / ID: 3vzi
TitleCrystal Structure of CRISPR-associated Protein
ComponentsCrispr-associated protein Cas5, dvulg subtype
KeywordsDNA BINDING PROTEIN / RRM / Ribonuclease / Nucleic acid
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding
Similarity search - Function
Alpha-Beta Plaits - #2660 / CRISPR pre-crRNA endoribonuclease Cas5d / CRISPR-associated protein, Cas5 / CRISPR-associated protein (Cas_Cas5) / CRISPR-associated protein Cas5, N-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
pre-crRNA processing endonuclease / Crispr-associated protein Cas5, dvulg subtype
Similarity search - Component
Biological speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsBae, E. / Koo, Y.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Conservation and Variability in the Structure and Function of the Cas5d Endoribonuclease in the CRISPR-Mediated Microbial Immune System
Authors: Koo, Y. / Ka, D. / Kim, E.J. / Suh, N. / Bae, E.
History
DepositionOct 12, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Crispr-associated protein Cas5, dvulg subtype
B: Crispr-associated protein Cas5, dvulg subtype


Theoretical massNumber of molelcules
Total (without water)50,4162
Polymers50,4162
Non-polymers00
Water93752
1
A: Crispr-associated protein Cas5, dvulg subtype


Theoretical massNumber of molelcules
Total (without water)25,2081
Polymers25,2081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Crispr-associated protein Cas5, dvulg subtype


Theoretical massNumber of molelcules
Total (without water)25,2081
Polymers25,2081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Crispr-associated protein Cas5, dvulg subtype

B: Crispr-associated protein Cas5, dvulg subtype


Theoretical massNumber of molelcules
Total (without water)50,4162
Polymers50,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1620 Å2
ΔGint-8 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.973, 54.842, 179.356
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 Crispr-associated protein Cas5, dvulg subtype


Mass: 25207.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria)
Strain: PXO99A / Gene: cas5d / Production host: Escherichia coli (E. coli) / References: UniProt: B2SNP4, UniProt: A0A0J9X178*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG3350, 0.1M DL-malic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 17, 2012
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. obs: 13585 / % possible obs: 99.8 %
Reflection shellResolution: 2.65→2.74 Å / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KG4

3kg4


Resolution: 2.66→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.873 / SU B: 30.678 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28674 673 5 %RANDOM
Rwork0.20615 ---
obs0.21014 12860 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 67.135 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å2-0 Å2-0 Å2
2--1.86 Å2-0 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.66→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3359 0 0 52 3411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193436
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9524648
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8435422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30822.195164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.15615568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0321540
X-RAY DIFFRACTIONr_chiral_restr0.10.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212652
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.66→2.729 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 44 -
Rwork0.276 743 -
obs--89.84 %
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)
13.05090.6499-1.2071.6965-1.52813.45930.1617-0.29980.08140.1664-0.0449-0.0194-0.16750.3149-0.11680.0574-0.07570.01030.2216-0.02560.0667.3706-9.9328-13.0462
212.74498.83161.04877.0282-2.64512.69870.3429-0.4910.54730.029-0.04330.42970.6966-0.9754-0.29960.3712-0.1448-0.00570.3566-0.09410.519830.585920.7758-7.2314
34.74530.9371-0.62381.9021-1.2032.99080.3487-0.1310.1454-0.0131-0.19710.0145-0.2996-0.1515-0.15160.1251-0.00860.08420.27760.04680.12733.00950.9247-37.4852
44.82784.8564-7.28476.7863-5.371118.0848-1.11020.5554-1.2377-1.4858-0.0407-1.06421.5453-0.67551.15090.6387-0.03730.20110.572-0.17210.633339.3061-32.2874-17.2939
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 69
2X-RAY DIFFRACTION1A105 - 220
3X-RAY DIFFRACTION2A76 - 104
4X-RAY DIFFRACTION3B0 - 67
5X-RAY DIFFRACTION3B105 - 220
6X-RAY DIFFRACTION4B78 - 104

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