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- PDB-4n59: The Crystal Structure of Pectocin M2 at 2.3 Angstroms -

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Basic information

Entry
Database: PDB / ID: 4n59
TitleThe Crystal Structure of Pectocin M2 at 2.3 Angstroms
ComponentsPectocin M2
KeywordsHYDROLASE / Lipid-II Hydrolase / Bacteriocin / Protein Antibiotic
Function / homology
Function and homology information


electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / defense response to bacterium / metal ion binding
Similarity search - Function
Colicin M, catalytic domain / Colicin M / Colicin M / Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / Beta-Lactamase ...Colicin M, catalytic domain / Colicin M / Colicin M / Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / Beta-Lactamase / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Pectocin M2
Similarity search - Component
Biological speciesPectobacterium carotovorum subsp. brasiliensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsZeth, K. / Grinter, R. / Roszak, A.W. / Cogdell, R.J. / Walker, D.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: Structure of the atypical bacteriocin pectocin M2 implies a novel mechanism of protein uptake.
Authors: Grinter, R. / Josts, I. / Zeth, K. / Roszak, A.W. / McCaughey, L.C. / Cogdell, R.J. / Milner, J.J. / Kelly, S.M. / Byron, O. / Walker, D.
History
DepositionOct 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Sep 20, 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 / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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: Pectocin M2
B: Pectocin M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,67410
Polymers61,8072
Non-polymers8678
Water91951
1
A: Pectocin M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3075
Polymers30,9031
Non-polymers4034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pectocin M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3675
Polymers30,9031
Non-polymers4644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-99 kcal/mol
Surface area27070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.649, 116.745, 60.790
Angle α, β, γ (deg.)90.00, 94.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pectocin M2


Mass: 30903.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium carotovorum subsp. brasiliensis (bacteria)
Strain: PBR1692 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A0A067XG75*PLUS
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15 % PEG3350, 0.2 M Ammonium sulphate, 3% MPD, 0.1M Bis-tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2012
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 55667 / Num. obs: 52652 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.41
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 1.85 / % possible all: 95.7

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
RefinementMethod to determine structure: SAD
Starting model: pdb entry 4N58

4n58


Resolution: 2.3→44.52 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.908 / SU B: 13.992 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27369 1384 5 %RANDOM
Rwork0.20634 ---
obs0.20964 26116 99.49 %-
all-26250 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.992 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0.59 Å2
2---1.4 Å2-0 Å2
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4079 0 34 51 4164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194200
X-RAY DIFFRACTIONr_bond_other_d0.0010.023836
X-RAY DIFFRACTIONr_angle_refined_deg1.71.9735689
X-RAY DIFFRACTIONr_angle_other_deg0.86638890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7525529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.07125.4200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.14115707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3981517
X-RAY DIFFRACTIONr_chiral_restr0.1010.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024796
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02915
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_it2.4612.042104
X-RAY DIFFRACTIONr_mcbond_other2.4572.0342103
X-RAY DIFFRACTIONr_mcangle_it4.123.0322625
X-RAY DIFFRACTIONr_mcangle_other4.3745.0772666
X-RAY DIFFRACTIONr_scbond_it3.0532.4262096
X-RAY DIFFRACTIONr_scbond_other2.9443.7892120
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6875.5533093
X-RAY DIFFRACTIONr_long_range_B_refined8.26326.9484760
X-RAY DIFFRACTIONr_long_range_B_other8.25426.9344751
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.299→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 95 -
Rwork0.283 1897 -
obs--96.75 %
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)
11.07530.04540.56271.5892-1.49022.79420.19460.5015-0.1922-0.0635-0.05010.1433-0.0604-0.0029-0.14450.41150.14840.00020.5883-0.01820.362622.08082.375335.0853
21.38031.20040.60053.49610.46090.28810.06860.0017-0.11310.296-0.1322-0.10250.02890.05370.06350.4748-0.0219-0.00180.44760.05780.460835.26213.836965.3263
33.56841.304-3.87023.3688-4.96758.77-0.8863-0.22560.04581.33650.4673-0.5803-1.3575-0.39170.41911.35980.2279-0.15540.4877-0.12870.354719.864232.151288.2455
42.117-1.9605-0.69663.17350.83050.31440.13850.10180.0332-0.0169-0.26350.0411-0.02860.06320.12510.42960.026-0.02180.44680.04360.474734.278725.181555.2414
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 111
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2A112 - 271
4X-RAY DIFFRACTION3B2 - 111
5X-RAY DIFFRACTION3B301
6X-RAY DIFFRACTION4B112 - 271

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