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- PDB-2y2l: PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL B... -

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Basic information

Entry
Database: PDB / ID: 2y2l
TitlePENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH AN ALKYL BORONATE (E06)
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 / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / outer membrane-bounded periplasmic space ...peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / outer membrane-bounded periplasmic space / proteolysis / metal ion binding / membrane
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-E06 / Penicillin-binding protein 1b
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 1.2Jan 25, 2017Group: Atomic model / Other
Revision 1.3Dec 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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PENICILLIN-BINDING PROTEIN 1B
B: PENICILLIN-BINDING PROTEIN 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,09441
Polymers108,1942
Non-polymers1,90039
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-367 kcal/mol
Surface area38610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.055, 101.628, 145.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A107 - 125
2115B107 - 125
1215A335 - 789
2215B335 - 789
1314A1000
2314B1000
1416A1100 - 1300
2416B1100 - 1300
1516A1790
2516B1790

NCS oper: (Code: given
Matrix: (-0.999413, 0.032825, -0.009768), (-0.034248, -0.957122, 0.287655), (9.3E-5, 0.28782, 0.957684)
Vector: 143.42473, 131.29225, -18.92054)

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 54096.906 Da / Num. of mol.: 2 / Fragment: TRANSPEPTIDASE DOMAIN, RESIDUES 101-125,323-791 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ALKYL BORONATE (E06) COVALENTLY BOND TO S460 / Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) PLYS
References: UniProt: Q7CRA4, peptidoglycan glycosyltransferase, Transferases; Acyltransferases; Aminoacyltransferases

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Non-polymers , 5 types, 537 molecules

#2: Chemical ChemComp-E06 / [(1R)-1-[(2,6-difluorophenyl)carbonylamino]ethyl]-trihydroxy-boron


Mass: 245.996 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11BF2NO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O

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Details

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 ENGINEERED RESIDUE IN CHAIN B, ASN 656 TO GLY ENGINEERED RESIDUE IN CHAIN B, ARG 686 TO GLN ENGINEERED RESIDUE IN CHAIN B, ARG 687 TO GLN
Has protein modificationY
Nonpolymer details(R)-(1-(2,6-DIFLUOROBENZAMIDO)ETHYL)BORONIC ACID (E06): COVALENTLY BOND TO SER 460

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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: 3.33 Å3/Da / Density % sol: 63.04 %
Description: MOLECULAR REPLACEMENT MODEL 2BG1 WITHOUT RESIDUES 654 TO 660
Crystal growpH: 7.2
Details: 50MM HEPES PH 7.2, 3M NACL, 0.6-0.9M 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→44.9 Å / Num. obs: 85632 / % possible obs: 84.7 % / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 44.533 Å2 / Rsym value: 0.05 / Net I/σ(I): 35.1
Reflection shellResolution: 2.07→2.19 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.09 / Rsym value: 0.48 / % possible all: 59.5

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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→44.92 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.017 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25614 8403 10 %RANDOM
Rwork0.18981 ---
obs0.19634 75250 95.72 %-
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: 48.694 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2--0.62 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.07→44.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7312 0 77 498 7887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227499
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.93110149
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7025945
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_restr0.1160.21115
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025608
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1891medium positional0.210.5
2B1891medium positional0.210.5
1A1758loose positional0.465
2B1758loose positional0.465
1A1891medium thermal3.552
2B1891medium thermal3.552
1A1758loose thermal4.5410
2B1758loose thermal4.5410
LS refinement shellResolution: 2.07→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 445 -
Rwork0.441 4322 -
obs--76.85 %
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)
13.4395-3.44790.17674.4716-0.21530.37570.02340.2487-0.0046-0.1553-0.0542-0.11930.02450.06580.03080.1015-0.07230.01730.2452-0.00440.023872.801670.09835.7388
20.9428-0.71910.02881.1774-0.14730.4049-0.00770.06480.05430.0351-0.0041-0.0494-0.0185-0.0230.01180.0199-0.01280.01150.0203-0.00740.012272.442173.685354.3959
30.6806-1.16710.27122.3872-0.19841.4654-0.3794-0.25870.14230.92480.119-0.0857-0.1196-0.07260.26040.4004-0.08820.02060.4808-0.13760.272.442977.74780.2947
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A104 - 125
2X-RAY DIFFRACTION1B104 - 125
3X-RAY DIFFRACTION1A337 - 393
4X-RAY DIFFRACTION1B337 - 393
5X-RAY DIFFRACTION1A585 - 601
6X-RAY DIFFRACTION1B585 - 601
7X-RAY DIFFRACTION2A394 - 584
8X-RAY DIFFRACTION2B394 - 584
9X-RAY DIFFRACTION2A602 - 722
10X-RAY DIFFRACTION2B602 - 722
11X-RAY DIFFRACTION3A723 - 790
12X-RAY DIFFRACTION3B723 - 790

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