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- PDB-5xut: Crystal structure of Lachnospiraceae bacterium ND2006 Cpf1 in com... -

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Basic information

Entry
Database: PDB / ID: 5xut
TitleCrystal structure of Lachnospiraceae bacterium ND2006 Cpf1 in complex with crRNA and target DNA (TCTA PAM)
Components
  • DNA (29-MER)
  • DNA (5'-D(*CP*GP*TP*CP*CP*TP*CP*TP*A)-3')
  • LbCpf1
  • crRNA
KeywordsHYDROLASE/RNA/DNA / nuclease / HYDROLASE-RNA-DNA complex
Function / homology
Function and homology information


CRISPR-associated endonuclease Cas12a / Cas12a, REC1 domain / Cas12a, RuvC nuclease domain / Cas12a, nuclease domain / Alpha helical recognition lobe domain / Nuclease domain / RuvC nuclease domain
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / Cpf1
Similarity search - Component
Biological speciesLachnospiraceae bacterium ND2006 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYamano, T. / Nishimasu, H. / Ishitani, R. / Nureki, O.
CitationJournal: Mol. Cell / Year: 2017
Title: Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1.
Authors: Yamano, T. / Zetsche, B. / Ishitani, R. / Zhang, F. / Nishimasu, H. / Nureki, O.
History
DepositionJun 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LbCpf1
B: crRNA
C: DNA (29-MER)
D: DNA (5'-D(*CP*GP*TP*CP*CP*TP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,7778
Polymers168,6064
Non-polymers1714
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16830 Å2
ΔGint-119 kcal/mol
Surface area61410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.450, 102.450, 373.885
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain DNA (29-MER) / Target DNA strand


Mass: 8888.737 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*CP*GP*TP*CP*CP*TP*CP*TP*A)-3') / Non-target DNA strand


Mass: 2666.761 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein LbCpf1


Mass: 144170.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachnospiraceae bacterium ND2006 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A182DWE3*PLUS
#2: RNA chain crRNA


Mass: 12879.634 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 49 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 3350, MIB buffer, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→49.4 Å / Num. obs: 75474 / % possible obs: 96.3 % / Redundancy: 8.9 % / Net I/σ(I): 25
Reflection shellResolution: 2.4→2.45 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XUS
Resolution: 2.4→49.404 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 3781 5.01 %
Rwork0.1929 --
obs0.1951 75435 95.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→49.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9788 1618 10 45 11461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711821
X-RAY DIFFRACTIONf_angle_d0.90416308
X-RAY DIFFRACTIONf_dihedral_angle_d17.1356843
X-RAY DIFFRACTIONf_chiral_restr0.051806
X-RAY DIFFRACTIONf_plane_restr0.0051814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.43040.38341560.30652649X-RAY DIFFRACTION97
2.4304-2.46240.32821470.28482644X-RAY DIFFRACTION97
2.4624-2.49610.3741370.27162690X-RAY DIFFRACTION97
2.4961-2.53180.30711330.25962625X-RAY DIFFRACTION97
2.5318-2.56960.32391290.26412650X-RAY DIFFRACTION97
2.5696-2.60970.32371550.26192632X-RAY DIFFRACTION97
2.6097-2.65250.35911450.26942649X-RAY DIFFRACTION97
2.6525-2.69820.35411550.27672667X-RAY DIFFRACTION97
2.6982-2.74730.29641390.26732607X-RAY DIFFRACTION96
2.7473-2.80010.34571560.24732622X-RAY DIFFRACTION96
2.8001-2.85730.30151350.25222659X-RAY DIFFRACTION96
2.8573-2.91940.36961510.25992648X-RAY DIFFRACTION96
2.9194-2.98730.35211340.24892623X-RAY DIFFRACTION96
2.9873-3.0620.2781360.24572666X-RAY DIFFRACTION96
3.062-3.14480.34111380.22742646X-RAY DIFFRACTION96
3.1448-3.23730.29111260.23382649X-RAY DIFFRACTION96
3.2373-3.34180.27441160.24212675X-RAY DIFFRACTION95
3.3418-3.46120.2681330.22772653X-RAY DIFFRACTION95
3.4612-3.59970.28611470.21592618X-RAY DIFFRACTION95
3.5997-3.76350.24581380.20862650X-RAY DIFFRACTION95
3.7635-3.96180.24441400.18592654X-RAY DIFFRACTION95
3.9618-4.20990.2171160.16772652X-RAY DIFFRACTION94
4.2099-4.53480.19671370.15122658X-RAY DIFFRACTION94
4.5348-4.99070.17581470.13982654X-RAY DIFFRACTION94
4.9907-5.7120.19751400.15722670X-RAY DIFFRACTION93
5.712-7.1930.20131410.17232659X-RAY DIFFRACTION92
7.193-49.41450.16031540.14962785X-RAY DIFFRACTION90
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.5387-0.0828-0.21410.81530.17120.8698-0.1018-0.123-0.17210.38410.1638-0.02450.1443-0.0341-0.05550.62550.10120.03170.44970.02930.5157-36.8818-60.530553.2786
21.6347-0.68290.00222.06080.1021.20570.07490.32340.1171-0.2808-0.0408-0.45870.025-0.0577-00.3922-0.0480.07510.5296-0.02540.5132-38.403-54.068915.322
31.9625-1.1741-1.96081.30671.52842.9285-0.0824-0.16750.11140.02980.01460.0967-0.1322-0.20870.09480.40080.0918-0.01440.5454-0.00470.6379-57.215-25.802942.6901
42.5016-1.89583.10534.36331.63189.79830.03210.5322-0.1651-0.1662-0.21430.2430.6439-0.67990.15230.4739-0.21070.09210.7456-0.05630.5418-59.3376-62.642618.4201
5-0.1815-0.4567-0.14331.3382-0.54260.3899-0.0311-0.1116-0.07480.35060.33150.1270.1604-0.4304-0.25430.50480.06720.12310.80380.00660.5346-43.3386-55.913843.6393
62.36130.98493.73978.4261.14175.9728-0.1527-1.18850.96540.75590.3381.19210.9383-2.0159-0.19911.0160.250.23911.3250.18910.7507-50.3017-49.82364.0276
71.64050.13961.01481.2484-0.14670.6461-0.0634-0.3317-0.00360.37680.1520.24350.105-0.3241-0.08040.61270.08630.1420.72110.01670.5104-40.9444-59.020849.0027
81.3474-1.2142-2.59371.32722.83646.1190.13740.35260.4375-0.45450.4249-0.3959-0.5693-0.0069-0.63930.5508-0.03120.12750.54920.01360.5951-27.4302-52.747328.1286
92.1832-3.6662-0.54396.7391-1.15187.2542-0.8830.5361-0.5293-0.01980.2837-1.25590.62920.74380.51730.5750.01670.26940.5794-0.13180.9872-14.2394-61.796512.5855
108.2473-4.42633.01343.5419-3.16163.1544-0.11020.1621-1.353-0.8174-0.9671-2.84082.24620.6970.98641.23930.31130.18480.9546-0.20641.3971-5.7507-76.055116.6619
113.0673-3.3172-2.64464.54371.17046.96560.44611.48920.5793-0.9538-0.775-0.9968-0.18410.75160.40130.91970.14590.13640.9305-0.22481.2444-11.52-69.65715.0833
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 558 )
2X-RAY DIFFRACTION2chain 'A' and (resid 559 through 918 )
3X-RAY DIFFRACTION3chain 'A' and (resid 919 through 1226 )
4X-RAY DIFFRACTION4chain 'B' and (resid -20 through -6 )
5X-RAY DIFFRACTION5chain 'B' and (resid -5 through 19 )
6X-RAY DIFFRACTION6chain 'C' and (resid -19 through -15 )
7X-RAY DIFFRACTION7chain 'C' and (resid -14 through -5 )
8X-RAY DIFFRACTION8chain 'C' and (resid -4 through 0 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 5 )
10X-RAY DIFFRACTION10chain 'C' and (resid 6 through 9 )
11X-RAY DIFFRACTION11chain 'D' and (resid -9 through -1 )

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