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- PDB-4n58: Crystal Structure of Pectocin M2 at 1.86 Angstroms -

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Basic information

Entry
Database: PDB / ID: 4n58
TitleCrystal Structure of Pectocin M2 at 1.86 Angstroms
ComponentsPectocin M2
KeywordsHYDROLASE / Plant-Like ferredoxin / Colicin M-like cytotoxic domain / Lipid-II hydrolase / Bacteriocin / Protein Antibiotc
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 PBR1692 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsGrinter, R. / Roszak, A.W. / Zeth, K. / Cogdell, C.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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Pectocin M2
B: Pectocin M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,32868
Polymers61,8072
Non-polymers6,52166
Water7,891438
1
A: Pectocin M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,97432
Polymers30,9031
Non-polymers3,07031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pectocin M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,35436
Polymers30,9031
Non-polymers3,45135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Pectocin M2
hetero molecules

A: Pectocin M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,94764
Polymers61,8072
Non-polymers6,14062
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area14890 Å2
ΔGint-380 kcal/mol
Surface area26640 Å2
MethodPISA
4
B: Pectocin M2
hetero molecules

B: Pectocin M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,70972
Polymers61,8072
Non-polymers6,90270
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area17860 Å2
ΔGint-417 kcal/mol
Surface area26220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.450, 117.450, 128.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-630-

HOH

21B-451-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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 PBR1692 (bacteria)
Strain: PBR1692 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A0A067XG75*PLUS

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Non-polymers , 6 types, 504 molecules

#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.: 18 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 438 / 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: 4.14 Å3/Da / Density % sol: 70.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.8 M Ammonium Sulphate, 3% MPD, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2012
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.86→64.22 Å / Num. all: 86224 / Num. obs: 86224 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 20 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 47
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 20.8 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 5.5 / Num. unique all: 6313 / % possible all: 99.8

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIXmodel building
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→58.79 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.72 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19714 4306 5 %RANDOM
Rwork0.16787 ---
all0.1693 81712 --
obs0.1693 81736 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.237 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.73 Å20 Å2
2--0.73 Å20 Å2
3----2.38 Å2
Refinement stepCycle: LAST / Resolution: 1.86→58.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4113 0 389 438 4940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.024583
X-RAY DIFFRACTIONr_bond_other_d0.0020.024266
X-RAY DIFFRACTIONr_angle_refined_deg2.5462.036168
X-RAY DIFFRACTIONr_angle_other_deg1.02139844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7135546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33325.243206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.79515718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2571521
X-RAY DIFFRACTIONr_chiral_restr0.1430.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024941
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02952
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_it2.72.4452151
X-RAY DIFFRACTIONr_mcbond_other2.6862.4442150
X-RAY DIFFRACTIONr_mcangle_it3.4183.6452690
X-RAY DIFFRACTIONr_mcangle_other3.4183.6472691
X-RAY DIFFRACTIONr_scbond_it5.7313.4042432
X-RAY DIFFRACTIONr_scbond_other5.7313.4062433
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2494.8083469
X-RAY DIFFRACTIONr_long_range_B_refined11.09423.3655286
X-RAY DIFFRACTIONr_long_range_B_other11.09122.465136
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.861→1.909 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 353 -
Rwork0.243 5949 -
obs--99.89 %
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)
11.895-0.79310.00952.3005-0.21162.6172-0.11430.06080.43860.17380.1028-0.2401-0.25490.00280.01150.1194-0.0225-0.05120.1510.04540.201865.854655.512215.8314
210.9125-9.77962.44218.9578-1.13696.28370.04790.50950.7956-0.0418-0.4441-0.667-0.0280.1330.39620.01990.02790.0240.22060.09430.215745.759564.0245.3587
31.4173-0.6047-0.43230.54020.2060.1453-0.0916-0.22090.09030.11260.1049-0.10770.07270.0861-0.01330.18150.07260.00740.2474-0.01640.088218.518965.253213.0418
45.28571.40560.64313.04190.42364.4849-0.18080.2828-0.7863-0.37960.2046-0.40040.69150.1308-0.02380.38410.04620.12710.1682-0.01040.2189123.959145.6333.6924
56.95663.9111.861112.1171-1.96216.74870.24960.2805-0.57690.19020.0877-0.01710.07840.5079-0.33730.0452-0.00510.00030.0865-0.02520.0982104.722436.442316.0555
61.55860.80210.34020.42130.17130.4536-0.07740.2889-0.074-0.07280.1385-0.0490.08240.045-0.06110.1945-0.0327-0.00560.2249-0.00260.088377.903335.45678.2923
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 96
2X-RAY DIFFRACTION2A97 - 110
3X-RAY DIFFRACTION3A116 - 272
4X-RAY DIFFRACTION4B3 - 96
5X-RAY DIFFRACTION5B97 - 110
6X-RAY DIFFRACTION6B116 - 273

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