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- PDB-2iwb: MecR1 unbound extracellular antibiotic-sensor domain. -

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Basic information

Entry
Database: PDB / ID: 2iwb
TitleMecR1 unbound extracellular antibiotic-sensor domain.
Components
  • METHICILLIN RESISTANCE MECR1 PROTEIN
  • TETRAPEPTIDE
KeywordsANTIBIOTIC RESISTANCE / BACTERIAL ANTIBIOTIC RESISTANCE / METHICILLIN RESISTANCE / BETA-LACTAMIC ANTIBIOTICS / MRSA / BETA-LACTAMASE / 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
NICKEL (II) ION / Methicillin resistance mecR1 protein
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.1Dec 28, 2016Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: METHICILLIN RESISTANCE MECR1 PROTEIN
B: TETRAPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1097
Polymers29,6822
Non-polymers4275
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.560, 80.790, 58.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein METHICILLIN RESISTANCE MECR1 PROTEIN


Mass: 29250.361 Da / Num. of mol.: 1
Fragment: EXTRACELLULAR PENICILLIN-SENSOR DOMAIN, RESIDUES 340-585
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: N315 / Plasmid: PET28A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P0A0B0
#2: Protein/peptide TETRAPEPTIDE


Mass: 431.487 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GLY-HIS-MET-SER. TENTATIVLEY ASSIGNED CLEAVED TAG / Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PET28A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: EQUIVOLUMETRIC HANGING DROPS CONSISTING OF 1.8M TRIBASIC AMMONIUM CITRATE AT PH7.0 AND PROTEIN SOLUTION AT 6.8MG/ML RENDERED CRYSTALS OF UNBOUND MECR1-PBD AT 20 DEGREES., pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1.0096
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0096 Å / Relative weight: 1
ReflectionResolution: 1.8→47.6 Å / Num. obs: 26121 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 7.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 31.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 10.5 / % possible all: 100

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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 1XA1

1xa1


Resolution: 1.8→47.6 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.665 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.203 652 2.5 %RANDOM
Rwork0.16 ---
obs0.162 25437 99.9 %-
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: 19.76 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å20 Å2
2--1.58 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2093 0 25 198 2316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222172
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.9362920
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0385248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20225.84125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51215395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.045155
X-RAY DIFFRACTIONr_chiral_restr0.1040.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021671
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.21330
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21547
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2263
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0061.51257
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65821997
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.89631040
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.594.5923
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 52
Rwork0.202 1833
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)
10.88410.07640.22040.9034-0.24420.5895-0.00790.0515-0.06480.0059-0.0291-0.07250.0135-0.00960.037-0.0784-0.00430.0192-0.0451-0.0006-0.078642.038914.854115.6437
20.97930.00530.10320.8014-0.32240.8552-0.00770.0462-0.0719-0.008-0.0345-0.06850.02070.02410.0422-0.0595-0.00460.0097-0.0558-0.0074-0.053842.304214.64915.6609
31.01840.1796-0.07270.7522-0.04230.79730.0229-0.023-0.15020.081-0.0395-0.10010.05760.02030.01650.0531-0.0002-0.00330.03480.00360.060143.516312.834617.6224
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A340 - 585
2X-RAY DIFFRACTION2A340 - 585
3X-RAY DIFFRACTION3A2001 - 2196
4X-RAY DIFFRACTION3B1 - 4

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