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- PDB-4arq: Structure of the pesticin S89C, S285C double mutant -

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Basic information

Entry
Database: PDB / ID: 4arq
TitleStructure of the pesticin S89C, S285C double mutant
Components(PESTICIN) x 2
KeywordsHYDROLASE / MURAMIDASE
Function / homology
Function and homology information


lysozyme activity / killing of cells of another organism / defense response to bacterium
Similarity search - Function
Pesticin, C-terminal / Pesticin, translocation and receptor binding domain / Bacterial toxin homologue of phage lysozyme, C-term / Pesticin, receptor binding domain / Lysozyme - #40 / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesYERSINIA PESTIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZeth, K. / Patzer, S.I. / Albrecht, R. / Braun, V.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure and Mechanistic Studies of Pesticin, a Bacterial Homolog of Phage Lysozymes.
Authors: Patzer, S.I. / Albrecht, R. / Braun, V. / Zeth, K.
History
DepositionApr 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Other
Revision 1.2Jul 18, 2012Group: Other
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PESTICIN
B: PESTICIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2693
Polymers80,2452
Non-polymers241
Water2,072115
1
A: PESTICIN


Theoretical massNumber of molelcules
Total (without water)40,1221
Polymers40,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PESTICIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1472
Polymers40,1231
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.964, 86.118, 122.022
Angle α, β, γ (deg.)90.00, 97.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PESTICIN


Mass: 40122.043 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: T7, PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q57159
#2: Protein PESTICIN


Mass: 40123.027 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: T7, PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q57159
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 89 TO CYS ENGINEERED RESIDUE IN CHAIN A, SER 285 TO CYS ...ENGINEERED RESIDUE IN CHAIN A, SER 89 TO CYS ENGINEERED RESIDUE IN CHAIN A, SER 285 TO CYS ENGINEERED RESIDUE IN CHAIN B, SER 89 TO CYS ENGINEERED RESIDUE IN CHAIN B, SER 285 TO CYS
Has protein modificationY

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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: 47.32 % / Description: NONE
Crystal growpH: 7 / Details: 25% PEG8000, 0.2M MGCL2, 0.1M HEPES PH 7.5

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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: 2.6→36 Å / Num. obs: 22615 / % possible obs: 97.7 % / Observed criterion σ(I): 3.3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.9
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 97.8 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.2 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AQN

4aqn


Resolution: 2.6→36.521 Å / SU ML: 0.33 / σ(F): 1.32 / Phase error: 29.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 2132 5 %
Rwork0.2267 --
obs0.2283 42460 95.11 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.444 Å2 / ksol: 0.287 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.4723 Å20 Å26.1752 Å2
2--1.2652 Å20 Å2
3----11.7375 Å2
Refinement stepCycle: LAST / Resolution: 2.6→36.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5406 0 1 115 5522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015508
X-RAY DIFFRACTIONf_angle_d1.4637431
X-RAY DIFFRACTIONf_dihedral_angle_d14.6072064
X-RAY DIFFRACTIONf_chiral_restr0.094819
X-RAY DIFFRACTIONf_plane_restr0.007972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.66050.37111380.32832668X-RAY DIFFRACTION95
2.6605-2.7270.37721400.31242687X-RAY DIFFRACTION95
2.727-2.80070.33351440.30512679X-RAY DIFFRACTION94
2.8007-2.88310.31361400.30132657X-RAY DIFFRACTION95
2.8831-2.97610.3141470.28942737X-RAY DIFFRACTION95
2.9761-3.08240.34391370.27352669X-RAY DIFFRACTION96
3.0824-3.20580.32311450.27812714X-RAY DIFFRACTION95
3.2058-3.35160.32681430.26662676X-RAY DIFFRACTION96
3.3516-3.52820.30721440.24892715X-RAY DIFFRACTION96
3.5282-3.7490.25941390.24022698X-RAY DIFFRACTION95
3.749-4.03810.22851460.19922685X-RAY DIFFRACTION95
4.0381-4.44390.21581370.18192669X-RAY DIFFRACTION94
4.4439-5.08540.22291460.172666X-RAY DIFFRACTION94
5.0854-6.40150.22951400.20292677X-RAY DIFFRACTION96
6.4015-36.5250.16411460.17712731X-RAY DIFFRACTION96
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)
10.79230.1431-0.48920.8054-0.14661.23650.12751.1545-0.0486-0.52520.16950.07210.2187-0.19640.63060.1438-0.0457-0.02360.5192-0.3809-0.750322.82676.8661-39.3171
21.85740.7266-0.4522.6457-0.08080.52850.3933-0.69950.29931.2361-0.18950.6172-0.17680.04650.16120.322-0.07060.1899-0.0736-0.07790.00455.1317-4.8461-8.8352
30.4248-0.0549-0.19070.3216-0.12171.4051-0.0657-0.4390.07780.2855-0.0930.08010.1096-0.5985-0.3780.9015-0.20020.19361.4505-0.10560.2504-19.4188.673250.1846
40.48330.0831-0.40960.47890.17721.5772-0.27630.0178-0.3019-0.0793-0.1349-0.25531.0745-0.0185-0.07780.8016-0.0210.27340.2575-0.07850.1013-1.9712-3.885720.6779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 13:164)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 165:357)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 13:152)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 153:357)

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