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- PDB-2xtr: Structure of the P176A Colicin M mutant from E. coli -

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Basic information

Entry
Database: PDB / ID: 2xtr
TitleStructure of the P176A Colicin M mutant from E. coli
ComponentsCOLICIN-M
KeywordsANTIMICROBIAL PROTEIN / CMA / BACTERICIN
Function / homology
Function and homology information


killing of cells of another organism / defense response to bacterium
Similarity search - Function
de novo design (two linked rop proteins) - #280 / Colicin M, catalytic domain / Colicin M / Colicin M / de novo design (two linked rop proteins) / Beta-Lactamase / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Colicin-M
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsHelbig, S. / Patzer, S.I. / Braun, V. / Zeth, K.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Activation of Colicin M by the Fkpa Prolyl Cis- Trans Isomerase/Chaperone.
Authors: Helbig, S. / Patzer, S.I. / Schiene-Fischer, C. / Zeth, K. / Braun, V.
History
DepositionOct 12, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _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
B: COLICIN-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0353
Polymers58,9732
Non-polymers621
Water4,179232
1
A: COLICIN-M


Theoretical massNumber of molelcules
Total (without water)29,4861
Polymers29,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: COLICIN-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5482
Polymers29,4861
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.832, 114.772, 225.402
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 4 / Auth seq-ID: 2 - 265 / Label seq-ID: 2 - 265

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

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Components

#1: Protein COLICIN-M


Mass: 29486.479 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05820
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PRO 176 TO ALA ENGINEERED RESIDUE IN CHAIN B, PRO 176 TO ALA

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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: 2.9 Å3/Da / Density % sol: 57.54 % / Description: NONE
Crystal growpH: 6.5 / Details: 20% PEG3350 0.2 M NANO3, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→47 Å / Num. obs: 36063 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 9.2
Reflection shellResolution: 2.14→2.19 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XMX

2xmx


Resolution: 2.14→46.94 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.893 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24104 1898 5 %RANDOM
Rwork0.18804 ---
obs0.19069 36063 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.938 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.14→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4134 0 4 232 4370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224241
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0271.955768
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.525540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13724.302172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35315675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2061514
X-RAY DIFFRACTIONr_chiral_restr0.1310.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213212
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0691.52685
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.92924332
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.39831556
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2614.51436
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: 2011 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.340.5
2Bmedium positional0.340.5
1Amedium thermal1.332
2Bmedium thermal1.332
LS refinement shellResolution: 2.141→2.196 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 123 -
Rwork0.266 2343 -
obs--100 %
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)
12.6001-0.1501-0.18442.19740.76540.44590.14540.1426-0.0161-0.1078-0.0619-0.2620.08380.0085-0.08350.11150.02770.01410.05020.01360.033331.040712.51865.8407
20.591-0.26510.13620.4754-0.20040.50380.0142-0.03520.1084-0.0381-0.043-0.11330.0325-0.01870.02880.04240.0110.01810.05460.00470.072431.332316.52914.9814
32.4496-2.20760.07163.1510.02071.9611-0.0135-0.1103-0.1836-0.00980.02120.0170.05610.13-0.00770.0376-0.01510.02490.03780.00740.073720.15096.082212.8912
40.6672-0.4845-0.10310.89430.06260.0175-0.0327-0.0481-0.00090.05360.0405-0.01760.01060.0108-0.00790.06250.0148-0.00550.06390.01150.048214.867422.157416.989
50.8596-1.0223-0.86031.63111.17030.92560.00590.019-0.02810.0886-0.0167-0.04980.0536-0.03460.01070.07090.0075-0.01020.081-0.0020.03677.813637.84329.3332
60.6789-0.7523-0.54821.27421.0491.3919-0.03370.02090.0787-0.0548-0.02090.05040.0573-0.02640.05460.06780.0108-0.01740.01450.02080.07412.521327.482115.7225
70.19070.164-0.16510.31120.05962.11790.02720.110.0087-0.03310.06030.04650.0297-0.168-0.08740.03850.0185-0.02370.07590.00370.0384-8.9612-1.615710.5988
80.25040.0030.07140.1312-0.17750.3648-0.0137-0.01330.0497-0.00270.0590.03890.03790.0012-0.04530.04690.0134-0.01150.10.00950.039-9.00660.645820.2031
92.9354-0.28920.01852.3645-0.59390.1959-0.14740.24350.17270.10270.08540.0484-0.08860.03510.0620.1211-0.065-0.09050.13250.0410.07841.08668.132112.4717
100.49170.03530.77160.04790.0461.66790.0384-0.0597-0.0622-0.0206-0.00620.0230.0498-0.0388-0.03220.05510.0062-0.00240.0680.01160.045911.9683-4.173734.0501
110.5979-0.03330.89960.1137-0.03561.36280.0468-0.0069-0.0683-0.02110.03760.00940.06130.0078-0.08440.04410.0148-0.00790.07050.01310.047510.7253-7.771331.0751
122.27540.07-2.99671.3811-5.481625.0151-0.0536-0.13330.0906-0.09260.1830.00690.4058-0.5605-0.12940.0667-0.0057-0.02990.06530.00120.020713.70430.284845.5433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 29
2X-RAY DIFFRACTION2A30 - 104
3X-RAY DIFFRACTION3A105 - 121
4X-RAY DIFFRACTION4A122 - 160
5X-RAY DIFFRACTION5A161 - 218
6X-RAY DIFFRACTION6A219 - 271
7X-RAY DIFFRACTION7B2 - 29
8X-RAY DIFFRACTION8B30 - 103
9X-RAY DIFFRACTION9B104 - 121
10X-RAY DIFFRACTION10B122 - 179
11X-RAY DIFFRACTION11B180 - 259
12X-RAY DIFFRACTION12B260 - 271

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