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- PDB-3tlz: Microcin C7 self immunity protein MccF mutant W186F in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3tlz
TitleMicrocin C7 self immunity protein MccF mutant W186F in complex with Adenosine Monophosphate
ComponentsMccF
KeywordsHYDROLASE / serine protease
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
ADENOSINE MONOPHOSPHATE / MccF / Microcin C7 self-immunity protein MccF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 30, 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 1.3Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MccF
B: MccF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,45410
Polymers83,3872
Non-polymers1,0678
Water17,745985
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint5 kcal/mol
Surface area24260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.553, 90.189, 73.322
Angle α, β, γ (deg.)90.00, 101.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MccF


Mass: 41693.551 Da / Num. of mol.: 2 / Mutation: W186F
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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 985 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 282 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES pH 7.5, 10% PEG 8000, 8% Ethylene Glycol, vapor diffusion, temperature 282K, VAPOR DIFFUSION

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.47→71.8 Å / Num. obs: 115009 / % possible obs: 97.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.067 / Rsym value: 0.065 / Net I/σ(I): 38.094
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 5.593 / Rsym value: 0.236 / % possible all: 95

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TLA

3tla


Resolution: 1.5→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.135 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19272 5452 5 %RANDOM
Rwork0.17307 ---
obs0.17405 103446 98.02 %-
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 mean: 18.818 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å2-0.46 Å2
2--1.57 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5246 0 70 985 6301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225458
X-RAY DIFFRACTIONr_bond_other_d0.0010.026
X-RAY DIFFRACTIONr_angle_refined_deg1.0151.9867391
X-RAY DIFFRACTIONr_angle_other_deg0.426310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2395676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98923.75224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.80315937
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.651530
X-RAY DIFFRACTIONr_chiral_restr0.0680.2833
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214052
X-RAY DIFFRACTIONr_gen_planes_other00.024
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_it0.3021.53338
X-RAY DIFFRACTIONr_mcbond_other0.0651.54
X-RAY DIFFRACTIONr_mcangle_it0.60925407
X-RAY DIFFRACTIONr_scbond_it1.00632120
X-RAY DIFFRACTIONr_scangle_it1.7184.51980
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 387 -
Rwork0.199 7513 -
obs--96.57 %

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