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- PDB-4zqw: CdiI from Escherichia coli EC869 in complex with a macrocyclic peptide -

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Basic information

Entry
Database: PDB / ID: 4zqw
TitleCdiI from Escherichia coli EC869 in complex with a macrocyclic peptide
Components
  • Immunity protein CdiI-o11
  • macrocyclic peptide
Keywordstoxin/inhibitor / Immunity / macrocycle / TOXIN / toxin-inhibitor complex
Function / homology
Function and homology information


deoxyribonuclease I activity / : / toxin activity / Hydrolases; Acting on ester bonds / metal ion binding
Similarity search - Function
CDI toxin, EC869-like / Immunity protein CdiI, Proteobacteria type / Immunity protein Cdil-like superfamily / CDI immunity protein / NMB0488-like fold / NMB0488-like / VENN motif-containing domain / Pre-toxin domain with VENN motif / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
macrocyclic peptide / Deoxyribonuclease CdiA-o11 / Immunity protein CdiI-o11
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.001 Å
AuthorsMorse, R.P. / Goulding, C.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102318 United States
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Diversification of beta-Augmentation Interactions between CDI Toxin/Immunity Proteins.
Authors: Morse, R.P. / Willett, J.L. / Johnson, P.M. / Zheng, J. / Credali, A. / Iniguez, A. / Nowick, J.S. / Hayes, C.S. / Goulding, C.W.
History
DepositionMay 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_validate_polymer_linkage
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Mar 27, 2019Group: Data collection / Polymer sequence / Category: entity_poly / Item: _entity_poly.type
Revision 2.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _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
B: Immunity protein CdiI-o11
A: macrocyclic peptide
D: Immunity protein CdiI-o11
C: macrocyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4886
Polymers43,4174
Non-polymers712
Water2,378132
1
B: Immunity protein CdiI-o11
A: macrocyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7443
Polymers21,7092
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-13 kcal/mol
Surface area8590 Å2
MethodPISA
2
D: Immunity protein CdiI-o11
C: macrocyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7443
Polymers21,7092
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-13 kcal/mol
Surface area8700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.779, 128.166, 44.953
Angle α, β, γ (deg.)90.00, 112.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Immunity protein CdiI-o11


Mass: 20238.869 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (strain EC869) (bacteria)
Strain: EC869 / Gene: cdiI4, cdiIo11, ECH7EC869_5884 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B3BM81
#2: Protein/peptide macrocyclic peptide


Type: Cyclic peptide / Class: Inhibitor / Mass: 1469.641 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: macrocyclic peptide, UniProt: B3BM80*PLUS
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M Sodium Acetate, 0.1 M bis-tris propane, pH 6.9, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 23561 / % possible obs: 96.5 % / Redundancy: 3.1 % / Net I/σ(I): 11.1
Reflection shellMean I/σ(I) obs: 3.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 2.001→34.811 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 26.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2308 2004 8.52 %
Rwork0.1838 --
obs0.1878 23526 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.001→34.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 0 2 132 2950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092874
X-RAY DIFFRACTIONf_angle_d1.2223885
X-RAY DIFFRACTIONf_dihedral_angle_d12.7111063
X-RAY DIFFRACTIONf_chiral_restr0.044435
X-RAY DIFFRACTIONf_plane_restr0.007496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0012-2.05130.31941290.25671422X-RAY DIFFRACTION88
2.0513-2.10670.28121360.23031494X-RAY DIFFRACTION96
2.1067-2.16870.30741350.22531498X-RAY DIFFRACTION93
2.1687-2.23870.29111400.22831509X-RAY DIFFRACTION96
2.2387-2.31870.26911440.21711524X-RAY DIFFRACTION95
2.3187-2.41150.26391470.20461503X-RAY DIFFRACTION96
2.4115-2.52120.26591440.21521555X-RAY DIFFRACTION96
2.5212-2.65410.29861390.20741545X-RAY DIFFRACTION97
2.6541-2.82030.23671460.22021540X-RAY DIFFRACTION98
2.8203-3.0380.29091490.20371570X-RAY DIFFRACTION98
3.038-3.34350.22891450.18781561X-RAY DIFFRACTION99
3.3435-3.82680.19681500.16981605X-RAY DIFFRACTION99
3.8268-4.81930.16591460.14621584X-RAY DIFFRACTION100
4.8193-34.8160.22811540.16171612X-RAY DIFFRACTION99
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)
14.52962.19750.62467.42291.3666.378-0.0184-0.01210.0798-0.0023-0.0224-0.08330.31550.23740.01920.19260.0223-0.0550.24110.03590.26818.959516.67833.5213
22.1131-0.2451-1.76588.7273-1.3391.8814-0.0629-0.31830.37190.07150.2174-0.53220.08410.1797-0.15570.2393-0.0236-0.14090.3391-0.00850.349321.401523.07835.4925
34.0247-0.0021.13324.9529-0.03617.17960.02620.051-0.0358-0.2943-0.0010.40860.31-0.3431-0.03360.2463-0.0394-0.08690.23480.03520.318710.830513.00051.5073
47.991.0087-5.64862.8153-0.17868.76710.2852-0.11050.620.0533-0.15050.1561-0.3420.2046-0.1210.3908-0.0061-0.13070.33390.08320.63487.08223.07182.5818
53.21311.19110.24226.52320.15034.83260.0198-0.18560.08660.14750.00680.4038-0.4106-0.3496-0.03150.20630.02710.07320.2643-0.02080.2495-2.78747.48344.9375
68.11063.39243.55777.5963-4.12946.67360.13540.1866-1.3118-0.4660.7307-0.0385-0.33140.2321-0.860.35780.00250.08390.266-0.07260.6376-0.84629.42850.0594
73.376-0.6779-1.26074.67870.97076.966-0.04090.3753-0.1019-0.6964-0.0083-0.3692-0.08790.29390.05410.2978-0.05370.10970.2938-0.05040.33356.645349.0289-3.1255
85.4434-0.0589-0.09495.175-1.4064.91410.2173-0.69710.34710.6284-0.0649-0.2866-0.73050.4667-0.1980.4671-0.12470.06940.3918-0.15240.33915.783356.412412.1278
96.29660.81073.94442.1654-0.9166.37710.0727-0.2804-0.771-0.06090.009-0.2217-0.114-0.1576-0.0660.3820.0430.16080.3312-0.04630.635710.29441.19692.5905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 47 )
2X-RAY DIFFRACTION2chain 'B' and (resid 48 through 76 )
3X-RAY DIFFRACTION3chain 'B' and (resid 77 through 168 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1 through 13 )
5X-RAY DIFFRACTION5chain 'D' and (resid 2 through 67 )
6X-RAY DIFFRACTION6chain 'D' and (resid 68 through 76 )
7X-RAY DIFFRACTION7chain 'D' and (resid 77 through 138 )
8X-RAY DIFFRACTION8chain 'D' and (resid 139 through 168 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 13 )

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