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- PDB-2je5: STRUCTURAL AND MECHANISTIC BASIS OF PENICILLIN BINDING PROTEIN IN... -

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Basic information

Entry
Database: PDB / ID: 2je5
TitleSTRUCTURAL AND MECHANISTIC BASIS OF PENICILLIN BINDING PROTEIN INHIBITION BY LACTIVICINS
ComponentsPENICILLIN-BINDING PROTEIN 1B
KeywordsDRUG-BINDING PROTEIN / PEPTIDOGLYCAN SYNTHESIS MULTIFUNCTIONAL ENZYME / CELL WALL / PEPTIDOGLYCAN / GAMMA LACTAM ANTIBIOTICS
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / outer membrane-bounded periplasmic space / proteolysis / 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-L4C / peptidoglycan glycosyltransferase
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMacheboeuf, P. / Fisher, D.S. / Brown, T.J. / Zervosen, A. / Luxen, A. / Joris, B. / Dessen, A. / Schofield, C.J.
CitationJournal: Nat.Chem.Biol. / Year: 2007
Title: Structural and Mechanistic Basis of Penicillin-Binding Protein Inhibition by Lactivicins
Authors: Macheboeuf, P. / Fisher, D.S. / Brown, T.J. / Zervosen, A. / Luxen, A. / Joris, B. / Dessen, A. / Schofield, C.J.
History
DepositionJan 15, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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 / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 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)157,77110
Polymers156,8572
Non-polymers9148
Water1,42379
1
A: PENICILLIN-BINDING PROTEIN 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8865
Polymers78,4281
Non-polymers4574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PENICILLIN-BINDING PROTEIN 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8865
Polymers78,4281
Non-polymers4574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.540, 99.830, 152.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.035, -0.962, 0.27), (0.989, -0.071, -0.126), (0.141, 0.263, 0.954)
Vector: 1.27003, 0.49157, 0.10928)

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Components

#1: Protein PENICILLIN-BINDING PROTEIN 1B


Mass: 78428.328 Da / Num. of mol.: 2 / Fragment: RESIDUES 72-791 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 / Plasmid: PGEX4T1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O70038
#2: Chemical ChemComp-L4C / (2E)-2-{[(2S)-2-(ACETYLAMINO)-2-CARBOXYETHOXY]IMINO}PENTANEDIOIC ACID / LACTIVICIN


Mass: 290.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2O8 / Comment: antibiotic*YM
#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.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 73 TO ALA ENGINEERED RESIDUE IN CHAIN A, SER 123 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, SER 73 TO ALA ENGINEERED RESIDUE IN CHAIN A, SER 123 TO LEU ENGINEERED RESIDUE IN CHAIN A, ASN 158 TO LYS ENGINEERED RESIDUE IN CHAIN A, PRO 162 TO ARG ENGINEERED RESIDUE IN CHAIN A, ARG 336 TO GLN ENGINEERED RESIDUE IN CHAIN A, ARG 686 TO GLN ENGINEERED RESIDUE IN CHAIN A, ARG 687 TO GLN ENGINEERED RESIDUE IN CHAIN B, SER 73 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 123 TO LEU ENGINEERED RESIDUE IN CHAIN B, ASN 158 TO LYS ENGINEERED RESIDUE IN CHAIN B, PRO 162 TO ARG ENGINEERED RESIDUE IN CHAIN B, ARG 336 TO GLN ENGINEERED RESIDUE IN CHAIN B, ARG 686 TO GLN ENGINEERED RESIDUE IN CHAIN B, ARG 687 TO GLN
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: 3.69 Å3/Da / Density % sol: 66.42 % / Description: NONE
Crystal growpH: 7
Details: 50 MH HEPES 3.2 M SODIUM CHLORIDE 0.8 M AMMONIUM SULFATE, pH 7

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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 / Date: Feb 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→84.52 Å / Num. obs: 46529 / % possible obs: 99.2 % / Observed criterion σ(I): 5 / Redundancy: 4.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.46
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BG1

2bg1


Resolution: 2.6→84.52 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU B: 10.87 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.475 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.298 2315 5 %RANDOM
Rwork0.26 ---
obs0.262 44214 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2--0.49 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.6→84.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7099 0 52 79 7230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0420.0227301
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.2521.9459921
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7965921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.22125.221339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.119151161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4781528
X-RAY DIFFRACTIONr_chiral_restr0.2120.21081
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.025630
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2790.23489
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3410.24982
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2312
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6761.54739
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.74927296
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.46833094
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.514.52625
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: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.424 187
Rwork0.365 3228

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