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- PDB-6u7b: Structure of E. coli MS115-1 CdnC:HORMA-deltaN complex -

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Basic information

Entry
Database: PDB / ID: 6u7b
TitleStructure of E. coli MS115-1 CdnC:HORMA-deltaN complex
Components
  • E. coli MS115-1 CdnC
  • bacHORMA_1 domain-containing protein
KeywordsSIGNALING PROTEIN / second-messenger signaling / cGAS / CD-NTase / HORMA domain / closure motif
Function / homology
Function and homology information


2'-5'-oligoadenylate synthetase activity / diadenylate cyclase / diadenylate cyclase activity / nucleotide metabolic process / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / double-stranded RNA binding / defense response to virus / ATP binding / metal ion binding / membrane / cytosol
Similarity search - Function
Bacterial HORMA domain 1 / Bacterial HORMA domain family 1 / : / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
ACETATE ION / ADENOSINE MONOPHOSPHATE / Bacterial HORMA domain-containing protein / Cyclic AMP-AMP-AMP synthase / CD-NTase-associated protein 7
Similarity search - Component
Biological speciesEscherichia coli MS 115-1 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsYe, Q. / Corbett, K.D.
CitationJournal: Mol.Cell / Year: 2020
Title: HORMA Domain Proteins and a Trip13-like ATPase Regulate Bacterial cGAS-like Enzymes to Mediate Bacteriophage Immunity.
Authors: Ye, Q. / Lau, R.K. / Mathews, I.T. / Birkholz, E.A. / Watrous, J.D. / Azimi, C.S. / Pogliano, J. / Jain, M. / Corbett, K.D.
History
DepositionSep 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Oct 11, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E. coli MS115-1 CdnC
B: bacHORMA_1 domain-containing protein
C: E. coli MS115-1 CdnC
D: bacHORMA_1 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,49314
Polymers112,7314
Non-polymers76210
Water6,900383
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.286, 142.897, 151.157
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein E. coli MS115-1 CdnC


Mass: 36217.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli MS 115-1 (bacteria) / Gene: HMPREF9540_01758 / Production host: Escherichia coli (E. coli) / References: UniProt: D7Y2H2
#2: Protein bacHORMA_1 domain-containing protein


Mass: 20148.307 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BHS87_27760, EPS97_06770 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X1LKT4, UniProt: D7Y2H3*PLUS

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Non-polymers , 5 types, 393 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M CHES pH 9.5, 0.1 M magnesium acetate, and 17% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.09→151.16 Å / Num. obs: 67360 / % possible obs: 99.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 43.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.034 / Rrim(I) all: 0.089 / Net I/σ(I): 16.2
Reflection shellResolution: 2.09→2.14 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.305 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4202 / CC1/2: 0.566 / Rpim(I) all: 0.537 / Rrim(I) all: 1.414 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P80

6p80


Resolution: 2.09→103.84 Å / SU ML: 0.2581 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 22.6294
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233 3269 4.86 %
Rwork0.2052 63975 -
obs0.2065 67244 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.52 Å2
Refinement stepCycle: LAST / Resolution: 2.09→103.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7805 0 47 383 8235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00268030
X-RAY DIFFRACTIONf_angle_d0.628310879
X-RAY DIFFRACTIONf_chiral_restr0.03961175
X-RAY DIFFRACTIONf_plane_restr0.00381422
X-RAY DIFFRACTIONf_dihedral_angle_d12.34134786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.130.32281450.3072456X-RAY DIFFRACTION90.25
2.13-2.160.321460.28022757X-RAY DIFFRACTION99.97
2.16-2.190.26161280.26982764X-RAY DIFFRACTION99.9
2.19-2.230.31931450.2652734X-RAY DIFFRACTION99.76
2.23-2.270.29851580.25052781X-RAY DIFFRACTION99.97
2.27-2.320.29631440.24332705X-RAY DIFFRACTION99.82
2.32-2.360.26261600.23052785X-RAY DIFFRACTION100
2.36-2.420.24841320.22742764X-RAY DIFFRACTION99.9
2.42-2.470.26211400.2212738X-RAY DIFFRACTION99.72
2.47-2.530.22511410.22532779X-RAY DIFFRACTION99.79
2.53-2.60.29781650.22652759X-RAY DIFFRACTION99.97
2.6-2.680.31161310.23792751X-RAY DIFFRACTION99.9
2.68-2.760.28741540.22922811X-RAY DIFFRACTION99.93
2.76-2.860.23311360.21992767X-RAY DIFFRACTION99.93
2.86-2.980.25891410.22492788X-RAY DIFFRACTION99.97
2.98-3.110.28351400.22562790X-RAY DIFFRACTION99.93
3.11-3.280.28731490.22362807X-RAY DIFFRACTION99.73
3.28-3.480.23711130.2072840X-RAY DIFFRACTION99.93
3.48-3.750.21241270.192824X-RAY DIFFRACTION99.9
3.75-4.130.17021400.17362812X-RAY DIFFRACTION99.8
4.13-4.730.18051400.15912872X-RAY DIFFRACTION99.8
4.73-5.960.19471230.18552898X-RAY DIFFRACTION99.83
5.96-103.840.21211710.20062993X-RAY DIFFRACTION99.31
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)
13.103628972742.94665693565-1.157942628943.64145412522-1.29814407050.939331001138-0.08333050191120.121851531452-0.118959760615-0.4345572415160.07524650595630.1844982244370.150590613194-0.123814149343-0.01817304658740.4548792979410.102704191825-0.009940469971550.3873888067130.06408187672750.422677177359-47.547281897420.440613730162.930831421
22.652423392950.447147427938-1.555308033312.642409820870.3135175357063.172939820180.135629558507-0.3753437684430.2826017106970.1430710068320.1487202483040.0158325235364-0.1667180345740.456746561589-0.2000898243560.3103738128820.04906183840790.02328976152870.379985693743-0.04461082707390.264553854041-18.851678417250.179551661850.8033805261
31.78141652964-1.11080272351-0.6861564873992.533736382570.7847959745030.814578953971-0.023322380723-0.189279841342-0.129792758940.1026699006210.0716646457317-0.0836622735020.06351747019150.0817319312473-0.04849455775120.279496677712-0.0388798834534-0.01681250528930.3094692958110.04167665574230.24266863048811.929333451424.252929116113.5941561685
43.35241548261-0.331094967822-0.7316912532552.9351480662-0.1233532998752.82644503210.1036035780290.1078962551860.443752784272-0.09551076761020.119883282120.0417748578687-0.256434572433-0.149331994809-0.1692516224240.326765858241-0.008100261774930.04090298736210.3234655983280.0170766516590.331830651844-17.246385792651.44466719629.085213836
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'

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