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- PDB-4bjp: Crystal structure of E. coli penicillin binding protein 3 -

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Basic information

Entry
Database: PDB / ID: 4bjp
TitleCrystal structure of E. coli penicillin binding protein 3
ComponentsPENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
KeywordsTRANSFERASE
Function / homologyBeta-Lactamase - #330 / Beta-Lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSauvage, E. / Joris, M. / Herman, R. / Kerff, F. / Rocaboy, M. / Charlier, P.
CitationJournal: Plos One / Year: 2014
Title: Crystal Structure of Penicillin-Binding Protein 3 (Pbp3) from Escherichia Coli.
Authors: Sauvage, E. / Derouaux, A. / Fraipont, C. / Joris, M. / Herman, R. / Rocaboy, M. / Schloesser, M. / Dumas, J. / Kerff, F. / Nguyen-Disteche, M. / Charlier, P.
History
DepositionApr 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Dec 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 / 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 / _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: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,09530
Polymers55,3781
Non-polymers2,71729
Water2,432135
1
A: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
hetero molecules

A: PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,19160
Polymers110,7562
Non-polymers5,43558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area10420 Å2
ΔGint-82.2 kcal/mol
Surface area37230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.025, 119.025, 139.251
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PENICILLIN BINDING PROTEIN TRANSPEPTIDASE DOMAIN PROTEIN / DD-TRANSPEPTIDASE


Mass: 55378.129 Da / Num. of mol.: 1 / Fragment: RESIDUES 67-577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: J2XFH0, peptidoglycan glycosyltransferase

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Non-polymers , 6 types, 164 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.4 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97628
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.5→82.7 Å / Num. obs: 20753 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 14 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 13.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 4.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EQU

3equ


Resolution: 2.5→59.51 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.898 / SU B: 15.026 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24493 1038 5 %RANDOM
Rwork0.19876 ---
obs0.20107 19669 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.164 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.5→59.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3105 0 169 135 3409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223304
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4152.0084443
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.435403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82123.333126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46415522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1891525
X-RAY DIFFRACTIONr_chiral_restr0.10.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212365
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_it0.5551.52034
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01123282
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.74231270
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8594.51161
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: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 81 -
Rwork0.212 1371 -
obs--97.12 %
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)
10.83120.44841.01470.89480.12311.5167-0.1641-0.23910.23070.25550.02040.2541-0.3625-0.4170.14380.23480.1440.01780.1901-0.00330.1913-20.777563.813130.5576
20.3235-0.0508-0.25524.5993-2.89892.0827-0.3814-0.00870.55760.36361.1936-0.2151-0.2959-1.0459-0.81220.16610.22070.07170.6553-0.0920.9795-40.52472.044528.5654
31.2466-0.20660.02911.0563-0.09651.2209-0.0107-0.14070.09650.099-0.00040.125-0.1232-0.1830.01110.13610.0205-0.00060.10640.01040.1284-17.081753.046923.1296
41.2024-0.4054-0.50331.1950.36061.18770.03640.1284-0.1356-0.1034-0.06650.07840.035-0.09440.03010.1322-0.0086-0.01130.13120.01160.1379-3.518927.483616.3364
51.0405-0.422-0.01191.04050.021.71370.010.05380.059-0.06-0.01610.0065-0.0034-0.04340.00610.1309-0.0050.01630.11260.01840.15163.067340.537815.9496
63.21520.98040.41363.32870.36182.3241-0.00220.0806-0.008-0.12270.0050.04610.0222-0.0357-0.00270.17490.06710.02120.15610.01910.101-6.625242.502710.4974
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A71 - 92
2X-RAY DIFFRACTION2A113 - 151
3X-RAY DIFFRACTION3A163 - 285
4X-RAY DIFFRACTION4A286 - 432
5X-RAY DIFFRACTION5A433 - 502
6X-RAY DIFFRACTION6A503 - 567

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