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- PDB-1mwu: Structure of methicillin acyl-Penicillin binding protein 2a from ... -

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Basic information

Entry
Database: PDB / ID: 1mwu
TitleStructure of methicillin acyl-Penicillin binding protein 2a from methicillin resistant Staphylococcus aureus strain 27r at 2.60 A resolution.
Componentspenicillin-binding protein 2a
KeywordsBIOSYNTHETIC PROTEIN / penicillin binding protein / beta-lactam / d / d-transpeptidase / d-carboxypeptidase / methicillin
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan L,D-transpeptidase activity / glycosyltransferase activity / penicillin binding / cell wall organization / response to antibiotic / plasma membrane
Similarity search - Function
Penicillin-binding protein 2a; domain 3 / NTF2-like; domain 1 / NTF2-like N-terminal transpeptidase / NTF2-like N-terminal transpeptidase domain / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Ribosomal Protein L30; Chain: A, / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily ...Penicillin-binding protein 2a; domain 3 / NTF2-like; domain 1 / NTF2-like N-terminal transpeptidase / NTF2-like N-terminal transpeptidase domain / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Ribosomal Protein L30; Chain: A, / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Roll / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7EP / : / Penicillin-binding protein 2
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsLim, D.C. / Strynadka, N.C.J.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structural basis for the beta lactam resistance of PBP2a from methicillin-resistant Staphylococcus aureus.
Authors: Lim, D. / Strynadka, N.C.
History
DepositionOct 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 15, 2012Group: Non-polymer description
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE At the time of processing, the sequence for this strain was not present in a sequence ... SEQUENCE At the time of processing, the sequence for this strain was not present in a sequence database. However, the protein crystallized contains the engineered mutation Y23M and the first 22 residues were deleted.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: penicillin-binding protein 2a
B: penicillin-binding protein 2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,02313
Polymers147,5552
Non-polymers1,46911
Water1,20767
1
A: penicillin-binding protein 2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4205
Polymers73,7771
Non-polymers6434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: penicillin-binding protein 2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6038
Polymers73,7771
Non-polymers8267
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.672, 103.210, 186.494
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein penicillin-binding protein 2a / SauPBP2a


Mass: 73777.250 Da / Num. of mol.: 2 / Fragment: residues 23-668 / Mutation: Y23M, delta 1-22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 lamda DE3 / References: UniProt: Q93IC2
#2: Chemical ChemComp-7EP / (2R,4S)-2-[(1R)-1-{[(2,6-dimethoxyphenyl)carbonyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / methicillin, bound form


Mass: 382.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H22N2O6S
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: CdCl2, PEG550MME, HEPES, NaCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlprotein1drop
220 %(v/v)PEG550 MME1reservoir
30.88 M1reservoirNaCl
4100 mMHEPES1reservoirpH7.
516 mM1reservoirCdCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 13, 2002 / Details: Osmic
RadiationMonochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. all: 47895 / Num. obs: 47895 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 37.6 Å2 / Rsym value: 0.054 / Net I/σ(I): 12.7
Reflection shellResolution: 2.6→2.7 Å / Mean I/σ(I) obs: 2 / Num. unique all: 4786 / Rsym value: 0.387 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 25 Å / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.387

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementResolution: 2.6→24.68 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1943628.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.303 2383 5 %RANDOM
Rwork0.242 ---
obs0.242 47643 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.3984 Å2 / ksol: 0.305723 e/Å3
Displacement parametersBiso mean: 62.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.2 Å20 Å20 Å2
2--19.19 Å20 Å2
3----23.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.6→24.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9981 0 61 67 10109
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.241.5
X-RAY DIFFRACTIONc_mcangle_it4.912
X-RAY DIFFRACTIONc_scbond_it4.862
X-RAY DIFFRACTIONc_scangle_it6.632.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.441 380 4.8 %
Rwork0.374 7542 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CAMC_REP.PARAMMCAMC.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor obs: 0.242 / Rfactor Rfree: 0.302 / Rfactor Rwork: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0048
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.67
LS refinement shell
*PLUS
Rfactor Rfree: 0.441 / Rfactor Rwork: 0.374

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