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- PDB-3tlc: Microcin C7 self immunity protein MccF in complex with Microcin C... -

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Basic information

Entry
Database: PDB / ID: 3tlc
TitleMicrocin C7 self immunity protein MccF in complex with Microcin C7 antibiotic
ComponentsMccF
KeywordsHYDROLASE/ANTIBIOTIC / serine protease / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


bacteriocin immunity / hydrolase activity / identical protein binding
Similarity search - Function
Murein tetrapeptidase LD-carboxypeptidase, N-terminal domain / LD-carboxypeptidase A C-terminal domain-like / Peptidase family S66 / LD-carboxypeptidase A, C-terminal domain superfamily / Murein tetrapeptide carboxypeptidase, N-terminal / LD-carboxypeptidase, N-terminal / LD-carboxypeptidase, C-terminal / LD-carboxypeptidase N-terminal domain / LD-carboxypeptidase C-terminal domain / Glucose Oxidase; domain 1 ...Murein tetrapeptidase LD-carboxypeptidase, N-terminal domain / LD-carboxypeptidase A C-terminal domain-like / Peptidase family S66 / LD-carboxypeptidase A, C-terminal domain superfamily / Murein tetrapeptide carboxypeptidase, N-terminal / LD-carboxypeptidase, N-terminal / LD-carboxypeptidase, C-terminal / LD-carboxypeptidase N-terminal domain / LD-carboxypeptidase C-terminal domain / Glucose Oxidase; domain 1 / Class I glutamine amidotransferase-like / 3-Layer(bba) Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7MD / MccF / Microcin C7 self-immunity protein MccF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsAgarwal, V. / Nair, S.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure and function of a serine carboxypeptidase adapted for degradation of the protein synthesis antibiotic microcin C7.
Authors: Agarwal, V. / Tikhonov, A. / Metlitskaya, A. / Severinov, K. / Nair, S.K.
History
DepositionAug 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Apr 4, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MccF
B: MccF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5946
Polymers83,4332
Non-polymers1,1614
Water17,619978
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint6 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.317, 85.738, 72.962
Angle α, β, γ (deg.)90.000, 101.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MccF


Mass: 41716.586 Da / Num. of mol.: 2 / Mutation: S145A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mccF / Plasmid: pET19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2KKH9, UniProt: Q47511*PLUS
#2: Chemical ChemComp-7MD / 5'-O-[(R)-(3-aminopropoxy)(L-alpha-aspartylamino)phosphoryl]adenosine


Mass: 518.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N8O9P
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 978 / 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 Å3/Da / Density % sol: 38.37 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 8000, 8% ethylene glycol, 0.1 M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 282K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 156612 / % possible obs: 97.2 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.05 / Χ2: 1.018 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.354.10.282150270.758193.8
1.35-1.44.30.228153210.773195.2
1.4-1.464.30.184154290.782196
1.46-1.544.30.134155450.802196.7
1.54-1.644.30.103155770.824196.9
1.64-1.764.30.077156510.844197.4
1.76-1.944.30.058157900.935197.8
1.94-2.224.40.055158801.588198.7
2.22-2.84.60.045161151.569199.6
2.8-504.60.029162771.143199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0056refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TLA

3tla


Resolution: 1.3→25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 0.684 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1862 7834 5 %RANDOM
Rwork0.1741 ---
obs0.1747 156197 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 69.5 Å2 / Biso mean: 11.7927 Å2 / Biso min: 4.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.04 Å2
2--0.36 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5261 0 78 978 6317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0225479
X-RAY DIFFRACTIONr_angle_refined_deg11.9877424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3465672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.423.805226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.50915940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.431530
X-RAY DIFFRACTIONr_chiral_restr0.0670.2833
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214064
X-RAY DIFFRACTIONr_mcbond_it0.2621.53342
X-RAY DIFFRACTIONr_mcangle_it0.53725413
X-RAY DIFFRACTIONr_scbond_it0.89232137
X-RAY DIFFRACTIONr_scangle_it1.5084.52009
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 551 -
Rwork0.22 10557 -
all-11108 -
obs--94.44 %

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