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- PDB-6vot: Crystal structure of Pseudomonas aerugonisa PBP3 complexed to gam... -

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Basic information

Entry
Database: PDB / ID: 6vot
TitleCrystal structure of Pseudomonas aerugonisa PBP3 complexed to gamma-lactam YU253434
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsHYDROLASE / Inhibitor complex / penicillin-binding protein / ANTIBIOTIC
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane
Similarity search - Function
Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-R7G / Peptidoglycan D,D-transpeptidase FtsI / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
Authorsvan den Akker, F.
CitationJournal: J.Med.Chem. / Year: 2020
Title: A gamma-Lactam Siderophore Antibiotic Effective against Multidrug-Resistant Gram-Negative Bacilli.
Authors: Goldberg, J.A. / Nguyen, H. / Kumar, V. / Spencer, E.J. / Hoyer, D. / Marshall, E.K. / Cmolik, A. / O'Shea, M. / Marshall, S.H. / Hujer, A.M. / Hujer, K.M. / Rudin, S.D. / Domitrovic, T.N. / ...Authors: Goldberg, J.A. / Nguyen, H. / Kumar, V. / Spencer, E.J. / Hoyer, D. / Marshall, E.K. / Cmolik, A. / O'Shea, M. / Marshall, S.H. / Hujer, A.M. / Hujer, K.M. / Rudin, S.D. / Domitrovic, T.N. / Bethel, C.R. / Papp-Wallace, K.M. / Logan, L.K. / Perez, F. / Jacobs, M.R. / van Duin, D. / Kreiswirth, B.M. / Bonomo, R.A. / Plummer, M.S. / van den Akker, F.
History
DepositionJan 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.country ..._chem_comp.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan D,D-transpeptidase FtsI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0182
Polymers58,3291
Non-polymers6891
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.107, 83.813, 89.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein 3 / PBP-3


Mass: 58329.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: pbpB, ftsI, ftsI_2, ALP65_00912, CAZ10_21230, CGU42_01090, DZ934_06595, DZ962_00565, E4V10_06485, ECC04_026610, ERJ99_003095, FCG96_14995, FLI88_02250, IPC1481_11065, IPC1482_17070, IPC165_ ...Gene: pbpB, ftsI, ftsI_2, ALP65_00912, CAZ10_21230, CGU42_01090, DZ934_06595, DZ962_00565, E4V10_06485, ECC04_026610, ERJ99_003095, FCG96_14995, FLI88_02250, IPC1481_11065, IPC1482_17070, IPC165_24935, IPC170_23205, IPC669_10550, RW109_RW109_05757
Production host: Escherichia coli (E. coli)
References: UniProt: Q51504, UniProt: G3XD46*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-R7G / 1-[(2S)-2-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetyl]amino}-3-oxopropyl]-4-{[2-(5,6 -dihydroxy-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)ethyl]carbamoyl}-2,5-dihydro-1H-pyrazole-3-carboxylic acid / YU253434


Mass: 688.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28N8O12S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4000, 0.2 M MgCl2, and 0.1 M Tris pH 8.5. Crystal was soaked for 15 minutes in 5 mM YU253434 in mother liquor.
Temp details: RT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 20549 / % possible obs: 99.7 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.049 / Rrim(I) all: 0.145 / Χ2: 1.037 / Net I/σ(I): 10.9 / Num. measured all: 167804
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.446.80.5889870.9370.2350.6340.767100
2.44-2.496.70.5359950.9420.2180.580.74698.7
2.49-2.537.40.54310040.950.2070.5820.7798.3
2.53-2.598.60.42610160.9770.150.4530.737100
2.59-2.648.60.41410160.9790.1440.4390.708100
2.64-2.78.80.45210110.9730.1550.4790.77100
2.7-2.778.70.37510080.9860.130.3980.772100
2.77-2.858.60.33710180.9860.1180.3570.79699.9
2.85-2.938.60.29710170.9860.1050.3160.82100
2.93-3.028.50.21810170.9920.0780.2320.868100
3.02-3.138.20.19610290.9860.0710.2091.067100
3.13-3.267.30.16710180.9910.0650.1791.17398.5
3.26-3.418.70.15510190.9910.0550.1651.23899.6
3.41-3.588.90.13910340.9910.0480.1481.265100
3.58-3.818.70.12610300.9950.0440.1331.599100
3.81-4.18.60.09110300.9960.0320.0961.333100
4.1-4.5280.07410460.9960.0280.0791.26399.7
4.52-5.177.40.06910500.9960.0260.0741.289100
5.17-6.518.60.07110650.9970.0250.0751.46199.5
6.51-507.40.05211390.9990.020.0561.13399.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PBQ

3pbq


Resolution: 2.4→39.59 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.111 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.464 / ESU R Free: 0.26
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 1057 5.2 %RANDOM
Rwork0.182 ---
obs0.185 19446 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 112.6 Å2 / Biso mean: 34.263 Å2 / Biso min: 13.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.03 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.4→39.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 48 85 3943
Biso mean--57.2 31.93 -
Num. residues----499
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133946
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173757
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.6615360
X-RAY DIFFRACTIONr_angle_other_deg1.2611.5848677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1675501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.83720.842202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.07215651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7141536
X-RAY DIFFRACTIONr_chiral_restr0.0660.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02830
LS refinement shellResolution: 2.402→2.464 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 60 -
Rwork0.239 1367 -
all-1427 -
obs--95.58 %

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