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- PDB-2xgl: The X-ray structure of the Escherichia coli colicin M immunity pr... -

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Basic information

Entry
Database: PDB / ID: 2xgl
TitleThe X-ray structure of the Escherichia coli colicin M immunity protein demonstrates the presence of a disulphide bridge, which is functionally essential
ComponentsCOLICIN-M IMMUNITY PROTEIN
KeywordsANTIBIOTIC / BACTERIAL CELL WALL / BACTERIOCIN IMMUNITY / BACTERIAL IMMUNITY
Function / homology
Function and homology information


bacteriocin immunity
Similarity search - Function
YebF/Colicin-M immunity protein / YebF/Colicin-M immunity protein / YebF/Cmi superfamily / YebF-like protein / YebF/Cmi domain profile. / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
: / Colicin-M immunity protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsGerard, F. / Brooks, M.A. / Barreteau, H. / Touze, T. / Graille, M. / Bouhss, A. / Blanot, D. / Tilbeurgh, H.v. / Mengin-Lecreulx, D.
CitationJournal: J.Bacteriol. / Year: 2011
Title: X-Ray Structure and Site-Directed Mutagenesis Analysis of the Escherichia Coli Colicin M Immunity Protein.
Authors: Gerard, F. / Brooks, M.A. / Barreteau, H. / Touze, T. / Graille, M. / Bouhss, A. / Blanot, D. / Tilbeurgh, H.V. / Mengin-Lecreulx, D.
History
DepositionJun 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _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 / _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

Downloads & links

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Assembly

Deposited unit
A: COLICIN-M IMMUNITY PROTEIN
B: COLICIN-M IMMUNITY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,08834
Polymers24,5892
Non-polymers1,49932
Water27015
1
A: COLICIN-M IMMUNITY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,23019
Polymers12,2951
Non-polymers93618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: COLICIN-M IMMUNITY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,85815
Polymers12,2951
Non-polymers56314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.000, 101.100, 43.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 1 / Auth seq-ID: 28 - 99 / Label seq-ID: 6 - 77

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.9594, 0.2821, 0.0041), (0.2821, 0.9594, 0.0019), (-0.0034, 0.003, -1)
Vector: -0.0914, -0.0004, 33.8888)

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Components

#1: Protein COLICIN-M IMMUNITY PROTEIN / MICROCIN-M IMMUNITY PROTEIN


Mass: 12294.682 Da / Num. of mol.: 2 / Fragment: PERIPLASMIC DOMAIN, RESIDUES 48-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: PLASMID PCOLBM-C1139 / Plasmid: PET2160 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS RARE / References: UniProt: P18002
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CMI OPEN READING FRAME CONTAINS FOUR PUTATIVE ATG INITIATION CODONS. OLSCHLAGER AND COWORKERS ...THE CMI OPEN READING FRAME CONTAINS FOUR PUTATIVE ATG INITIATION CODONS. OLSCHLAGER AND COWORKERS EARLIER DETERMINED AS MKVIS THE N-TERMINAL AMINO ACID SEQUENCE OF THE PROTEIN EXPRESSED IN VIVO, DESIGNATING THE THIRD ATG AS THE ACTUAL TRANSLATION START SIGNAL (OLSCHLAGER, T., A. TURBA, AND V. BRAUN. 1991. BINDING OF THE IMMUNITY PROTEIN INACTIVATES COLICIN M. MOL MICROBIOL 5,1105-1111.)

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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: 2.33 Å3/Da / Density % sol: 47.12 % / Description: NONE
Crystal growpH: 6.5
Details: 100 MM MES BUFFER, PH 6.5, AND 12% PEG 20,000, 90 MM CDSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.907
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 19, 2009 / Details: KIRKPATRICK-BAEZ (KB) MIRRORS
RadiationMonochromator: SI CHANNEL CUT MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.907 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 6651 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.15 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.7→46.24 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.871 / SU B: 15.795 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 1.532 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26788 308 4.6 %RANDOM
Rwork0.22183 ---
obs0.22395 6342 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.482 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å2-0 Å2-0 Å2
2---0.12 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1478 0 32 15 1525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221529
X-RAY DIFFRACTIONr_bond_other_d0.0020.021049
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9632046
X-RAY DIFFRACTIONr_angle_other_deg0.78832548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.825178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.32724.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97515270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8159
X-RAY DIFFRACTIONr_chiral_restr0.0650.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211679
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02308
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6751.5893
X-RAY DIFFRACTIONr_mcbond_other0.1121.5362
X-RAY DIFFRACTIONr_mcangle_it1.60421438
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9183636
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5354.5608
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1003 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional0.030.05
1Atight thermal0.050.5
2Btight thermal0.050.5
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 24 -
Rwork0.311 410 -
obs--92.34 %
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)
11.20380.8949-1.59851.2904-2.81075.9257-0.04250.0379-0.0747-0.0862-0.017-0.02140.0090.05530.05960.08160.0188-0.01350.0095-0.01850.03119.1264-15.5874.8877
20.5879-0.4606-1.03761.89011.70934.211-0.00440.041-0.00150.009-0.02820.0553-0.06380.01590.03260.0208-0.0173-0.01140.01980.01750.0303-13.3353-12.001129.0649
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 115
2X-RAY DIFFRACTION2B26 - 115

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