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- PDB-3wzh: Crystal structure of AfCsx3 -

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Basic information

Entry
Database: PDB / ID: 3wzh
TitleCrystal structure of AfCsx3
ComponentsUncharacterized protein AF_1864
KeywordsTRANSCRIPTION / endonuclease / deadenylation
Function / homologyCRISPR-associated protein Csx3 / CRISPR-associated protein (Cas_csx3) / : / Uncharacterized protein AF_1864
Function and homology information
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 3.31 Å
AuthorsYuan, Y.A. / Yan, X.
CitationJournal: Rna Biol. / Year: 2015
Title: Crystal structures of CRISPR-associated Csx3 reveal a manganese-dependent deadenylation exoribonuclease.
Authors: Yan, X. / Guo, W. / Yuan, Y.A.
History
DepositionSep 25, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Uncharacterized protein AF_1864
B: Uncharacterized protein AF_1864
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9137
Polymers25,6392
Non-polymers2755
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-41 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.726, 86.726, 112.529
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A-1 - 95
2010B-1 - 95

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Components

#1: Protein Uncharacterized protein AF_1864


Mass: 12819.334 Da / Num. of mol.: 2 / Fragment: UNP residues 2-104 / Mutation: I49Mse, L51Mse
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: AF_1864 / Production host: Escherichia coli (E. coli) / References: UniProt: O28415
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 4.76 Å3/Da / Density % sol: 74.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Citrate, Phosphate, Ammonium Sulphate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 7320 / Num. obs: 7155 / % possible obs: 97.76 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.3→3.4 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.31→22.88 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.876 / SU B: 38.38 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R: 1.168 / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25732 348 4.6 %RANDOM
Rwork0.22065 ---
all0.22242 7320 --
obs0.22242 7155 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.08 Å2-0 Å2
2--0.08 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 3.31→22.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 5 25 1623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191633
X-RAY DIFFRACTIONr_bond_other_d0.0040.021620
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.9662210
X-RAY DIFFRACTIONr_angle_other_deg1.08433738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8615196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.04923.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41415276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7111510
X-RAY DIFFRACTIONr_chiral_restr0.0910.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211764
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02358
Refine LS restraints NCS

Ens-ID: 1 / Number: 5422 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.306→3.392 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.464 21 -
Rwork0.277 518 -
obs--98.9 %
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)
13.07782.13051.35517.09311.71513.853-0.17760.1796-0.1008-0.20990.3264-0.04160.04480.0678-0.14880.149-0.03330.01860.16360.00810.01139.5784-13.74287.4804
24.71292.28911.47234.73280.54194.5820.01940.078-0.51810.14770.3122-0.04070.598-0.2419-0.33160.19830.03110.03120.06980.04410.098138.3408-19.259126.0046
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 96
2X-RAY DIFFRACTION2B-1 - 98

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