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- PDB-2j8y: Structure of PBP-A acyl-enzyme complex with penicillin-G -

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Basic information

Entry
Database: PDB / ID: 2j8y
TitleStructure of PBP-A acyl-enzyme complex with penicillin-G
ComponentsTLL2115 PROTEIN
KeywordsHYDROLASE / PENICILLIN-BINDING PROTEIN / LACTAMASE / THIOESTERASE / DD-PEPTIDASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / response to antibiotic
Similarity search - Function
Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
OPEN FORM - PENICILLIN G / Tll2115 protein
Similarity search - Component
Biological speciesSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.9 Å
AuthorsEvrard, C. / Declercq, J.P.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure of Pbp-A from Thermosynechococcus Elongatus, a Penicillin-Binding Protein Closely Related to Class a Beta-Lactamases.
Authors: Urbach, C. / Evrard, C. / Pudzaitis, V. / Fastrez, J. / Soumillion, P. / Declercq, J.P.
History
DepositionOct 31, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / 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 / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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

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Assembly

Deposited unit
A: TLL2115 PROTEIN
B: TLL2115 PROTEIN
C: TLL2115 PROTEIN
D: TLL2115 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,5638
Polymers131,2174
Non-polymers1,3464
Water14,826823
1
A: TLL2115 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1412
Polymers32,8041
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TLL2115 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1412
Polymers32,8041
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TLL2115 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1412
Polymers32,8041
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TLL2115 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1412
Polymers32,8041
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.692, 91.873, 147.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.12896, -0.98439, 0.11974), (0.98878, -0.11847, 0.09097), (-0.07537, 0.13013, 0.98863)25.13467, 42.03495, 30.27861
2given(0.13328, 0.98903, -0.06367), (0.98955, -0.13636, -0.04679), (-0.05496, -0.05677, -0.99687)-25.22124, 27.23692, -34.23551
3given(-0.99999, 0.0047, 0.00255), (-0.00443, -0.99512, 0.09858), (0.003, 0.09857, 0.99513)-12.23039, 4.86071, -5.81488

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Components

#1: Protein
TLL2115 PROTEIN / SERINE-TYPE CARBOXYPEPTIDASE FROM THERMOSYNECHOCOCCUS ELONGATUS


Mass: 32804.316 Da / Num. of mol.: 4 / Fragment: RESIDUES 93-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: BP-1 / Description: CYANOBASE / Plasmid: PBAD-MYC-HIS-TETR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP 10
References: UniProt: Q8DH45, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical
ChemComp-PNM / OPEN FORM - PENICILLIN G


Mass: 336.406 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H20N2O4S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 823 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCRYSTALLINE FORM WITHOUT PUTATIVE TRANSMEMBRANE SEGMENT (92 AMINO ACIDS)

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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: 2.27 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP. PROTEIN 7 MG/ML. RESERVOIR 500 UL HEPES 0.1M PH 7.5, AMMONIUM ACETATE 0.2M, PEG-3350 25% AND NAN3 0.02% (W/V). DROP 1 UL PROTEIN AND 1 UL RESERVOIR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.22
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 22, 2004 / Details: RH COATED, ZERODUR, VERTICALLY FOCUSSING
RadiationMonochromator: FIXED EXIT DOUBLE CRYSTAL SI 111, HORIZONTALLY FOCUSSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.22 Å / Relative weight: 1
ReflectionResolution: 1.9→24 Å / Num. obs: 91292 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.34 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.6 / % possible all: 88.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.9→24 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 7.946 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 4607 5 %RANDOM
Rwork0.187 ---
obs0.19 86685 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.86 Å20 Å2
3---1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8210 0 92 823 9125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228445
X-RAY DIFFRACTIONr_bond_other_d0.0020.025750
X-RAY DIFFRACTIONr_angle_refined_deg1.581.99511473
X-RAY DIFFRACTIONr_angle_other_deg1.0543.00213998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97551063
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.61724.58369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6114.9671459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4241568
X-RAY DIFFRACTIONr_chiral_restr0.0910.21327
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029359
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021553
X-RAY DIFFRACTIONr_nbd_refined0.2130.21716
X-RAY DIFFRACTIONr_nbd_other0.1980.26048
X-RAY DIFFRACTIONr_nbtor_refined0.1650.24013
X-RAY DIFFRACTIONr_nbtor_other0.0840.24208
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2528
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3430.2136
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8891.56899
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03628602
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0433472
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9574.52871
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 296
Rwork0.273 5820
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)
11.97810.23960.5491.41290.57621.76850.06560.00240.00430.13790.01720.16960.3229-0.1066-0.08290.0056-0.02610.0043-0.06770.0347-0.1066-12.74632.514-3.648
21.17070.6569-0.13852.1001-0.2390.6195-0.0052-0.0981-0.2054-0.0464-0.004-0.04460.06390.05090.0093-0.12290.0083-0.0195-0.05450.0271-0.0555-5.64125.2531.851
31.2502-0.4644-0.12732.57920.09270.8743-0.02330.0669-0.05230.09440.0042-0.04850.0633-0.07290.0191-0.1159-0.0103-0.0193-0.0812-0.0049-0.15135.39510.403-31.702
41.82010.1598-0.34271.3621-0.45841.3403-0.03240.08060.06270.02660.0459-0.0394-0.1431-0.0119-0.01360.001-0.0306-0.0157-0.06210.0029-0.12610.518-28.31-5.619
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 300
2X-RAY DIFFRACTION2B10 - 300
3X-RAY DIFFRACTION3C11 - 300
4X-RAY DIFFRACTION4D2 - 300

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