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- PDB-6dd5: Crystal Structure of the Cas6 Domain of Marinomonas mediterranea ... -

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Basic information

Entry
Database: PDB / ID: 6dd5
TitleCrystal Structure of the Cas6 Domain of Marinomonas mediterranea MMB-1 Cas6-RT-Cas1 Fusion Protein
ComponentsMMB-1 Cas6 Fused to Maltose Binding Protein,CRISPR-associated endonuclease Cas1
KeywordsHYDROLASE / Crispr Cas Protein / Endoribonuclease
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / RNA-directed DNA polymerase activity / outer membrane-bounded periplasmic space / endonuclease activity / defense response to virus ...maintenance of CRISPR repeat elements / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / RNA-directed DNA polymerase activity / outer membrane-bounded periplasmic space / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function
RNA-directed DNA polymerase (reverse transcriptase), msDNA / CRISPR-associated endonuclease Cas1, N-terminal domain / : / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein ...RNA-directed DNA polymerase (reverse transcriptase), msDNA / CRISPR-associated endonuclease Cas1, N-terminal domain / : / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
alpha-maltose / CRISPR-associated endonuclease Cas1 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Marinomonas mediterranea MMB-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.85 Å
AuthorsStamos, J.L. / Mohr, G. / Silas, S. / Makarova, K.S. / Markham, L.M. / Yao, J. / Lucas-Elio, P. / Sanchez-Amat, A. / Fire, A.Z. / Koonin, E.V. / Lambowitz, A.M.
CitationJournal: Mol. Cell / Year: 2018
Title: A Reverse Transcriptase-Cas1 Fusion Protein Contains a Cas6 Domain Required for Both CRISPR RNA Biogenesis and RNA Spacer Acquisition.
Authors: Mohr, G. / Silas, S. / Stamos, J.L. / Makarova, K.S. / Markham, L.M. / Yao, J. / Lucas-Elio, P. / Sanchez-Amat, A. / Fire, A.Z. / Koonin, E.V. / Lambowitz, A.M.
History
DepositionMay 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MMB-1 Cas6 Fused to Maltose Binding Protein,CRISPR-associated endonuclease Cas1
B: MMB-1 Cas6 Fused to Maltose Binding Protein,CRISPR-associated endonuclease Cas1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,06823
Polymers150,5662
Non-polymers2,50221
Water00
1
A: MMB-1 Cas6 Fused to Maltose Binding Protein,CRISPR-associated endonuclease Cas1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,58212
Polymers75,2831
Non-polymers1,29911
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MMB-1 Cas6 Fused to Maltose Binding Protein,CRISPR-associated endonuclease Cas1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,48611
Polymers75,2831
Non-polymers1,20310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.278, 110.760, 192.906
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 or (resid 4 through 5...
21(chain B and (resid 3 through 1236 or resid 1244 through 1294))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEILEILE(chain A and (resid 3 or (resid 4 through 5...AA33
12GLUGLUGLUGLU(chain A and (resid 3 or (resid 4 through 5...AA4 - 54 - 5
13LYSLYSALAALA(chain A and (resid 3 or (resid 4 through 5...AA2 - 12942 - 666
14LYSLYSALAALA(chain A and (resid 3 or (resid 4 through 5...AA2 - 12942 - 666
15LYSLYSALAALA(chain A and (resid 3 or (resid 4 through 5...AA2 - 12942 - 666
16LYSLYSALAALA(chain A and (resid 3 or (resid 4 through 5...AA2 - 12942 - 666
21ILEILETYRTYR(chain B and (resid 3 through 1236 or resid 1244 through 1294))BB3 - 12363 - 608
22VALVALALAALA(chain B and (resid 3 through 1236 or resid 1244 through 1294))BB1244 - 1294616 - 666

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Components

#1: Protein MMB-1 Cas6 Fused to Maltose Binding Protein,CRISPR-associated endonuclease Cas1 / MBP / MMBP / Maltodextrin-binding protein


Mass: 75283.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Marinomonas mediterranea MMB-1 (bacteria)
Gene: malE, Z5632, ECs5017, cas1, Marme_0669 / Strain: ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEY0, UniProt: F2K1V9, Hydrolases; Acting on ester bonds
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4

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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: 3.28 Å3/Da / Density % sol: 62.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: 0.1 M Sodium Acetate, 2.5 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.85→48.23 Å / Num. obs: 47006 / % possible obs: 100 % / Redundancy: 14.8 % / Biso Wilson estimate: 53.99 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.052 / Rrim(I) all: 0.202 / Net I/σ(I): 17.3 / Num. measured all: 696144
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.85-2.9515.11.46345310.7660.3891.514100
11.04-48.2313.10.02791510.0080.02899.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å48.23 Å
Translation3 Å48.23 Å

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Processing

Software
NameVersionClassification
XDSJun 17, 2015data reduction
Aimless0.5.17data scaling
PHASER2.6.0phasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B3W

5b3w


Resolution: 2.85→48.226 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.03
RfactorNum. reflection% reflection
Rfree0.2252 2277 4.85 %
Rwork0.1869 --
obs0.1888 46930 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.24 Å2 / Biso mean: 55.15 Å2 / Biso min: 20.48 Å2
Refinement stepCycle: final / Resolution: 2.85→48.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10125 0 143 0 10268
Biso mean--78.77 --
Num. residues----1297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610488
X-RAY DIFFRACTIONf_angle_d0.77214257
X-RAY DIFFRACTIONf_chiral_restr0.0491564
X-RAY DIFFRACTIONf_plane_restr0.0051834
X-RAY DIFFRACTIONf_dihedral_angle_d10.0836187
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6097X-RAY DIFFRACTION4.832TORSIONAL
12B6097X-RAY DIFFRACTION4.832TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.85-2.9120.39871180.315227802898
2.912-2.97970.39421430.282627432886
2.9797-3.05420.27071290.25927492878
3.0542-3.13680.29061320.245727772909
3.1368-3.2290.27781540.224927202874
3.229-3.33320.26141530.217627522905
3.3332-3.45230.26451470.209127632910
3.4523-3.59050.23311430.195927752918
3.5905-3.75390.23091390.184827642903
3.7539-3.95170.1921380.167627792917
3.9517-4.19920.20351650.151927762941
4.1992-4.52320.1961350.143727942929
4.5232-4.97790.16821430.136128032946
4.9779-5.69730.20861510.16328152966
5.6973-7.17420.21051380.196928743012
7.1742-48.23340.21490.183329893138
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)
13.48320.6282-0.28761.62410.26631.7704-0.11010.18130.301-0.2272-0.01830.2286-0.0636-0.18820.09960.29370.0228-0.04240.262-0.04990.274617.003730.1462213.8321
22.5961.10070.60075.11530.27991.7425-0.0442-0.15020.39780.4115-0.02810.3104-0.0938-0.11440.07640.34480.02190.02110.3077-0.01510.501627.770854.7808244.0132
32.1943-0.56921.0664.0862-1.24474.8657-0.1019-0.0723-0.02640.3408-0.1304-0.33210.01660.23050.19940.3088-0.01120.01360.24150.05520.405937.960234.7674249.1177
42.06040.82350.31282.8471.23462.55030.07410.01750.0712-0.30750.2656-0.7462-0.43090.5771-0.19470.4162-0.08130.13720.3906-0.09490.468664.787363.0626202.5902
51.2754-0.28740.51787.8079-1.63782.13590.00870.0838-0.09350.6776-0.0305-0.6163-0.01590.1057-0.05470.42040.02020.07140.3374-0.07430.509567.560834.7054237.259
61.91340.79171.01574.18291.29565.4247-0.0248-0.0620.00530.04230.01710.02130.13770.06770.00680.30080.00760.06270.2319-0.03050.392759.669555.0513244.4351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:372)A2 - 372
2X-RAY DIFFRACTION2(chain A and resid 1001:1131)A1001 - 1131
3X-RAY DIFFRACTION3(chain A and resid 1132:1294)A1132 - 1294
4X-RAY DIFFRACTION4(chain B and resid 3:372)B3 - 372
5X-RAY DIFFRACTION5(chain B and resid 1001:1131)B1001 - 1131
6X-RAY DIFFRACTION6(chain B and resid 1132:1294)B1132 - 1294

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