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- PDB-3r9g: Crystal structure of Microcin C7 self immunity acetyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 3r9g
TitleCrystal structure of Microcin C7 self immunity acetyltransferase MccE in complex with Coenzyme A and processed Microcin C7 antibiotic
ComponentsMccE protein
KeywordsTransferase/transferase inhibitor / Microcin C7 / Acetyltransferase / Self immunity / resistance / Acetyl coenzyme A / Transferase-transferase inhibitor complex
Function / homology
Function and homology information


diaminopimelate decarboxylase activity / lysine biosynthetic process via diaminopimelate / acyltransferase activity, transferring groups other than amino-acyl groups / nucleotide binding
Similarity search - Function
Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase ...Orn/DAP/Arg decarboxylase 2, N-terminal / Pyridoxal-dependent decarboxylase, pyridoxal binding domain / Alanine racemase/group IV decarboxylase, C-terminal / PLP-binding barrel / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7MC / COENZYME A / MccE protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsNair, S.K. / Agarwal, V.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Basis for Microcin C7 Inactivation by the MccE Acetyltransferase.
Authors: Agarwal, V. / Metlitskaya, A. / Severinov, K. / Nair, S.K.
History
DepositionMar 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: MccE protein
B: MccE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7536
Polymers42,0972
Non-polymers2,6564
Water9,314517
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A: MccE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3763
Polymers21,0481
Non-polymers1,3282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MccE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3763
Polymers21,0481
Non-polymers1,3282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.976, 95.075, 53.159
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein MccE protein


Mass: 21048.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mccE / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q47510
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-7MC / 5'-O-[(R)-[(N-acetyl-L-alpha-aspartyl)amino](3-aminopropoxy)phosphoryl]adenosine


Mass: 560.455 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H29N8O10P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 282 K / Method: hanging drop / pH: 7
Details: PEG550MME, MgCl2, pH 7.0, hanging drop, temperature 282K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 87162

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.5.0056refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.685 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 4351 5 %RANDOM
Rwork0.1874 ---
obs0.1888 86851 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.53 Å2 / Biso mean: 17.6371 Å2 / Biso min: 9.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20 Å2
2---0.29 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.35→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 172 517 3476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223014
X-RAY DIFFRACTIONr_angle_refined_deg1.4992.0194094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0335351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88426.098123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.89515523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.749154
X-RAY DIFFRACTIONr_chiral_restr0.0820.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022160
X-RAY DIFFRACTIONr_mcbond_it0.7381.51758
X-RAY DIFFRACTIONr_mcangle_it1.30822847
X-RAY DIFFRACTIONr_scbond_it1.9131256
X-RAY DIFFRACTIONr_scangle_it2.924.51247
X-RAY DIFFRACTIONr_rigid_bond_restr1.01533014
X-RAY DIFFRACTIONr_sphericity_bonded1.88332959
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 315 -
Rwork0.319 5774 -
all-6089 -
obs--95.92 %

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