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- PDB-2jbf: Structure of PBP-A, L158E mutant. Acyl-enzyme complex with penici... -

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Basic information

Entry
Database: PDB / ID: 2jbf
TitleStructure of PBP-A, L158E mutant. 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: 1.7 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
DepositionDec 6, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 13, 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)132,7199
Polymers131,2814
Non-polymers1,4385
Water16,286904
1
A: TLL2115 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2493
Polymers32,8201
Non-polymers4292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TLL2115 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1572
Polymers32,8201
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TLL2115 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1572
Polymers32,8201
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TLL2115 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1572
Polymers32,8201
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.579, 91.525, 145.708
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(-0.11818, -0.98464, 0.1285), (0.99149, -0.1099, 0.06976), (-0.05457, 0.13565, 0.98925)5.29888, 41.16547, 29.82107
2given(0.12322, 0.98958, -0.07444), (0.98936, -0.12834, -0.0685), (-0.07734, -0.0652, -0.99487)-25.58715, 26.50705, -33.64796
3given(-0.99982, 0.01752, 0.00738), (-0.0166, -0.99371, 0.11079), (0.00927, 0.11065, 0.99382)-12.02198, 4.58945, -6.29139

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Components

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


Mass: 32820.270 Da / Num. of mol.: 4 / Fragment: RESIDUES 93-368 / Mutation: YES
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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 904 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 249 TO GLU ENGINEERED RESIDUE IN CHAIN B, LEU 249 TO GLU ...ENGINEERED RESIDUE IN CHAIN A, LEU 249 TO GLU ENGINEERED RESIDUE IN CHAIN B, LEU 249 TO GLU ENGINEERED RESIDUE IN CHAIN C, LEU 249 TO GLU ENGINEERED RESIDUE IN CHAIN D, LEU 249 TO GLU
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 growpH: 7.5 / Details: SEE ENTRY 2J9O, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.843
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 14, 2005
Details: MIRROR 1, FLAT PRE-MIRROR. MIRROR 2, BENT, VERTICALLY FOCUSSING
RadiationMonochromator: SI 111, HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.843 Å / Relative weight: 1
ReflectionResolution: 1.7→28 Å / Num. obs: 126686 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.7
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

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

Resolution: 1.7→77.61 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.856 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 6364 5.03 %RANDOM
Rwork0.178 ---
obs0.18 126686 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.913 Å20 Å20 Å2
2---0.502 Å20 Å2
3----0.411 Å2
Refinement stepCycle: LAST / Resolution: 1.7→77.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8213 0 98 904 9215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228453
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.99411480
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.61451063
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.67924.638373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81114.9671459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7861568
X-RAY DIFFRACTIONr_chiral_restr0.0920.21322
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029375
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.21885
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.1730.24196
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2661
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.280
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0751.56877
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21828601
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.48733479
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7794.52879
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: 7.57→77.61 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.198 75
Rwork0.175 1381
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)
12.3746-0.42780.8471.69460.29083.06490.1758-0.0456-0.13750.01490.01370.270.5797-0.3638-0.1895-0.0229-0.091-0.0347-0.12150.0576-0.149-12.51932.554-3.444
21.20991.341-0.2913.5157-0.37940.96530.0276-0.0932-0.1879-0.0465-0.064-0.12580.05410.15560.0364-0.23660.0203-0.0095-0.11860.0267-0.1003-5.63524.95531.45
30.98-1.00550.10584.47420.01820.9475-0.0232-0.0699-0.06860.14090.0448-0.07310.0697-0.076-0.0215-0.2228-0.0187-0.0375-0.17860.0044-0.19465.20410.231-31.286
42.1283-0.17610.02051.2761-0.53151.7024-0.04760.06180.03590.18490.0111-0.0795-0.38480.04290.0364-0.0224-0.0524-0.0051-0.17130.0067-0.20240.885-28.307-5.735
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 274
2X-RAY DIFFRACTION2B10 - 274
3X-RAY DIFFRACTION3C11 - 274
4X-RAY DIFFRACTION4D2 - 274

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