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- PDB-2iwc: Benzylpenicilloyl-acylated MecR1 extracellular antibiotic-sensor ... -

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Basic information

Entry
Database: PDB / ID: 2iwc
TitleBenzylpenicilloyl-acylated MecR1 extracellular antibiotic-sensor domain.
ComponentsMETHICILLIN RESISTANCE MECR1 PROTEIN
KeywordsANTIBIOTIC RESISTANCE / BACTERIAL ANTIBIOTIC RESISTANCE / MRSA / BETA-LACTAMASE / BENZYLPENICILLIN / METHICILLIN RESISTANCE / BETA-LACTAMIC ANTIBIOTICS / PENICILLIN-BINDING PROTEIN
Function / homology
Function and homology information


penicillin binding / response to antibiotic
Similarity search - Function
: / Peptidase M56 / BlaR1 peptidase M56 / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
OPEN FORM - PENICILLIN G / Methicillin resistance mecR1 protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMarrero, A. / Mallorqui-Fernandez, G. / Guevara, T. / Garcia-Castellanos, R. / Gomis-Ruth, F.X.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Unbound and Acylated Structures of the Mecr1 Extracellular Antibiotic-Sensor Domain Provide Insights Into the Signal-Transduction System that Triggers Methicillin Resistance.
Authors: Marrero, A. / Mallorqui-Fernandez, G. / Guevara, T. / Garcia-Castellanos, R. / Gomis-Ruth, F.X.
History
DepositionJun 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 2.0Oct 24, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_validate_close_contact / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.auth_comp_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _pdbx_struct_mod_residue.label_comp_id / _pdbx_struct_mod_residue.label_seq_id
Revision 2.1Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: METHICILLIN RESISTANCE MECR1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5652
Polymers30,2281
Non-polymers3361
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.400, 58.400, 148.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein METHICILLIN RESISTANCE MECR1 PROTEIN


Mass: 30228.447 Da / Num. of mol.: 1
Fragment: EXTRACELLULAR PENICILLIN-SENSOR DOMAIN, RESIDUES 334-585
Source method: isolated from a genetically manipulated source
Details: THE FIRST THREE RESIDUES, GLY331, HIS332 AND MET333 ARE THE RESULT OF THE CLONING STRATEGY APPLIED AND DO NOT CORRESPOND TO THE CHEMICAL SEQUENCE OF THE PROTEIN.
Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria)
Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A0B0
#2: Chemical ChemComp-PNM / OPEN FORM - PENICILLIN G


Mass: 336.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N2O4S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST THREE RESIDUES, GLY331, HIS332 AND MET333, ARE THE RESULT OF THE CLONING STRATEGY APPLIED ...THE FIRST THREE RESIDUES, GLY331, HIS332 AND MET333, ARE THE RESULT OF THE CLONING STRATEGY APPLIED AND DO NOT CORRESPOND TO THE CHEMICAL SEQUENCE OF THE PROTEIN.

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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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growpH: 6.5 / Details: 1.8M TRIBASIC AMMONIUM CITRATE AT PH6.5, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→45.8 Å / Num. obs: 15723 / % possible obs: 99.7 % / Observed criterion σ(I): 1.5 / Redundancy: 7.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.6 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
COMBATdata scaling
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IWB

2iwb


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 11.392 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 719 4.6 %RANDOM
Rwork0.187 ---
obs0.189 14941 99.8 %-
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: 34.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2---0.67 Å20 Å2
3---1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 0 66 2222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212209
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.942983
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1335252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82325.952126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86915396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.168154
X-RAY DIFFRACTIONr_chiral_restr0.090.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021720
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.2920
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21490
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2102
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7171.51308
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18822036
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.88431061
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9154.5947
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.321 59
Rwork0.212 1026
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)
12.0638-0.0306-0.41911.25170.0661.45210.2020.1150.0269-0.0212-0.13950.0483-0.0319-0.2841-0.0625-0.14360.01270.0333-0.11190.0213-0.148427.63886.925587.0066
22.26290.1739-0.05871.83930.37071.96220.14140.09020.0055-0.0662-0.12180.0135-0.0284-0.2947-0.0196-0.13490.01680.033-0.12220.0175-0.137527.96516.342587.1146
31.90430.01580.06091.39410.23551.61440.14160.0769-0.0341-0.0965-0.1101-0.05820.1192-0.0973-0.03150.18060.00890.02710.1611-0.00280.16829.93266.331887.4154
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A331 - 585
2X-RAY DIFFRACTION2A331 - 585
3X-RAY DIFFRACTION3W701 - 766

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