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- PDB-2j7v: Structure of PBP-A -

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Basic information

Entry
Database: PDB / ID: 2j7v
TitleStructure of PBP-A
ComponentsTLL2115 PROTEIN
KeywordsHYDROLASE / PENICILLIN-BINDING PROTEIN / LACTAMASE / DD-PEPTIDASE / THIOESTERASE
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
Biological speciesSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 17, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 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 / 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
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)131,2174
Polymers131,2174
Non-polymers00
Water15,673870
1
A: TLL2115 PROTEIN


Theoretical massNumber of molelcules
Total (without water)32,8041
Polymers32,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TLL2115 PROTEIN


Theoretical massNumber of molelcules
Total (without water)32,8041
Polymers32,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TLL2115 PROTEIN


Theoretical massNumber of molelcules
Total (without water)32,8041
Polymers32,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TLL2115 PROTEIN


Theoretical massNumber of molelcules
Total (without water)32,8041
Polymers32,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.790, 91.900, 147.270
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(-0.14043, -0.98558, 0.09439), (0.98763, -0.13272, 0.08352), (-0.06979, 0.10495, 0.99203)25.1811, 41.16818, 30.92813
2given(0.15398, 0.98703, -0.04546), (0.98805, -0.15351, 0.01366), (0.00651, -0.04702, -0.99887)-24.52435, 28.50231, -33.96877
3given(-0.99719, 0.00546, -0.07466), (-0.01593, -0.98997, 0.14041), (-0.07315, 0.1412, 0.98727)-10.71017, 3.95332, -7.79352

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 870 / Source method: isolated from a natural source / Formula: H2O
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 10 MG/ML. RESERVOIR 500 UL HEPES 0.1 M PH 7.5, PROLINE 0.2 M, PEG-3350 10% (W/V) AND NAN3 0.02% (W/V). DROP 1UL PROTEIN AND 1 UL RESERVOIR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8414
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 2, 2004
Details: MIRROR 1, FLAT PRE-MIRROR. MIRROR 2, BENT, VERTICALLY FOCUSSING
RadiationMonochromator: SI , HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8414 Å / Relative weight: 1
ReflectionResolution: 1.9→39.2 Å / Num. obs: 94191 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PRE-ALIGNED STRUCTURES WITH PDB ENTRIES 1MF0, 1E25, 1BSG, 1ERM, 1I2S

1mf0

1e25

1bsg

1erm

1i2s


Resolution: 1.9→39.2 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.475 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 4726 5 %RANDOM
Rwork0.172 ---
obs0.174 89464 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2---0.74 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8255 0 0 870 9125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228391
X-RAY DIFFRACTIONr_bond_other_d0.0020.025729
X-RAY DIFFRACTIONr_angle_refined_deg1.511.98511389
X-RAY DIFFRACTIONr_angle_other_deg0.996314033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84351070
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.13224.58369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.835151466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8561568
X-RAY DIFFRACTIONr_chiral_restr0.0880.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029330
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021554
X-RAY DIFFRACTIONr_nbd_refined0.220.21870
X-RAY DIFFRACTIONr_nbd_other0.2070.26454
X-RAY DIFFRACTIONr_nbtor_refined0.1730.24167
X-RAY DIFFRACTIONr_nbtor_other0.090.24456
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2677
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3170.2160
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.252
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0161.56925
X-RAY DIFFRACTIONr_mcbond_other0.2141.52156
X-RAY DIFFRACTIONr_mcangle_it1.13528662
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2833364
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2724.52727
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% reflection
Rfree0.298 339 -
Rwork0.22 6560 -
obs--99.7 %
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)
11.8643-0.38930.2571.43040.6632.24610.0047-0.01090.00080.1257-0.00950.11110.241-0.21560.0048-0.0948-0.03030.0093-0.08210.013-0.143-12.07232.49-3.53
21.02070.3385-0.18172.0878-0.41190.802-0.0613-0.0517-0.1001-0.00930.0177-0.02070.03690.02940.0437-0.14680.0177-0.0126-0.12470.0098-0.113-5.45124.62431.64
31.0563-0.3581-0.08572.91610.57751.1076-0.036-0.0167-0.1255-0.02530.032-0.00270.1013-0.02990.0041-0.1371-0.0206-0.0118-0.1068-0.013-0.12546.10811.441-32.266
42.14350.0130.15461.7431-0.17691.6669-0.14780.1242-0.0205-0.19470.054-0.3492-0.59950.12820.09390.2732-0.08450.0334-0.0541-0.0027-0.02581.593-29.029-5.131
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 274
2X-RAY DIFFRACTION2B11 - 275
3X-RAY DIFFRACTION3C6 - 275
4X-RAY DIFFRACTION4D1 - 274

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