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- PDB-2y2n: PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL B... -

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Basic information

Entry
Database: PDB / ID: 2y2n
TitlePENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (E07)
ComponentsPENICILLIN-BINDING PROTEIN 1B
KeywordsTRANSFERASE / INFECTION / CELL WALL / PEPTIDOGLYCAN / INHIBITOR
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / acyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / response to antibiotic / proteolysis / extracellular region / membrane / metal ion binding
Similarity search - Function
Rossmann fold - #12800 / Penicillin-binding protein 2a (Domain 2) - #40 / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / : / Transglycosylase / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase ...Rossmann fold - #12800 / Penicillin-binding protein 2a (Domain 2) - #40 / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / : / Transglycosylase / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-E07 / peptidoglycan glycosyltransferase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsContreras-Martel, C. / Amoroso, A. / Woon, E.C. / Zervosen, A. / Inglis, S. / Martins, A. / Verlaine, O. / Rydzik, A. / Job, V. / Luxen, A. ...Contreras-Martel, C. / Amoroso, A. / Woon, E.C. / Zervosen, A. / Inglis, S. / Martins, A. / Verlaine, O. / Rydzik, A. / Job, V. / Luxen, A. / Joris, B. / Schofield, C.J. / Dessen, A.
CitationJournal: Acs Chem.Biol. / Year: 2011
Title: Structure-Guided Design of Cell Wall Biosynthesis Inhibitors that Overcome Beta-Lactam Resistance in Staphylococcus Aureus (Mrsa).
Authors: Contreras-Martel, C. / Amoroso, A. / Woon, E.C. / Zervosen, A. / Inglis, S. / Martins, A. / Verlaine, O. / Rydzik, A. / Job, V. / Luxen, A. / Joris, B. / Schofield, C.J. / Dessen, A.
History
DepositionDec 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_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.pdbx_leaving_atom_flag / _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_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: PENICILLIN-BINDING PROTEIN 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,20025
Polymers54,0971
Non-polymers1,10324
Water4,270237
1
A: PENICILLIN-BINDING PROTEIN 1B
hetero molecules

A: PENICILLIN-BINDING PROTEIN 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,40050
Polymers108,1942
Non-polymers2,20648
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6550 Å2
ΔGint-418.9 kcal/mol
Surface area37120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.744, 147.956, 98.778
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1791-

CL

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Components

#1: Protein PENICILLIN-BINDING PROTEIN 1B / PBP1B


Mass: 54096.906 Da / Num. of mol.: 1 / Fragment: TRANSPEPTIDASE DOMAIN, RESIDUES 101-125,323-791 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ALKYL BORONATE (E07) COVALENTLY BOND TO S460 / Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS
References: UniProt: Q7CRA4, peptidoglycan glycosyltransferase, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-E07 / TRIHYDROXY-[(1S)-1-[[2-(PHENYLMETHYL)PHENYL]CARBONYLAMINO]ETHYL]BORON


Mass: 300.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19BNO4
#3: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 656 TO GLY ENGINEERED RESIDUE IN CHAIN A, ARG 686 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, ASN 656 TO GLY ENGINEERED RESIDUE IN CHAIN A, ARG 686 TO GLN ENGINEERED RESIDUE IN CHAIN A, ARG 687 TO GLN
Nonpolymer details(S)-(1-(2-BENZYLBENZAMIDO)ETHYL)BORONIC ACID IS COVALENTLY BOUND TO SER 460 AS RESIDUE E07 ...(S)-(1-(2-BENZYLBENZAMIDO)ETHYL)BORONIC ACID IS COVALENTLY BOUND TO SER 460 AS RESIDUE E07 (DERIVING FROM TRIHYDROXY- [(1S)-1-[[2-(PHENYLMETHYL)PHENYL] CARBONYLAMINO]ETHYL]BORON).

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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: 3.31 Å3/Da / Density % sol: 62.85 %
Description: MOLECULAR REPLACEMENT MODEL 2BG1 WITHOUT RESIDUES 654 TO 660.
Crystal growpH: 7.2
Details: 50 MM HEPES PH 7.2, 3M NACL, 0.6-0.9 M AMMONIUM SULFATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.07→43.9 Å / Num. obs: 40622 / % possible obs: 82.9 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Biso Wilson estimate: 34.77 Å2 / Rsym value: 0.09 / Net I/σ(I): 14.91
Reflection shellResolution: 2.07→2.19 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.86 / Rsym value: 0.5 / % possible all: 56.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0095refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BG1

2bg1


Resolution: 2.07→43.94 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.705 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 4052 10 %RANDOM
Rwork0.19141 ---
obs0.1966 36291 92.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.275 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.07→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3607 0 44 237 3888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223735
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9315061
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4675476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022818
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.07→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 195 -
Rwork0.309 1719 -
obs--61.94 %
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)
13.14890.46232.05250.07670.28893.2501-0.1568-0.06820.143-0.01890.016-0.0077-0.01090.04740.14090.1024-0.034-0.0090.1092-0.06560.136429.520538.43235.0549
21.0364-0.45380.26321.6858-0.10250.94960.0123-0.0573-0.09550.0434-0.0319-0.00150.0825-0.04160.01960.0124-0.0127-0.00120.02260.01120.014114.53618.1654-13.3732
32.862.2826-2.12414.14-0.69253.3407-0.34620.5555-0.6751-0.58740.2334-0.46410.7884-0.18520.11280.47280.1549-0.06260.253-0.16710.420520.3783-7.4039-29.1596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A104 - 119
2X-RAY DIFFRACTION1A337 - 393
3X-RAY DIFFRACTION1A585 - 601
4X-RAY DIFFRACTION2A394 - 584
5X-RAY DIFFRACTION2A602 - 722
6X-RAY DIFFRACTION3A723 - 790

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