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- PDB-5df8: CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONA... -

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Basic information

Entry
Database: PDB / ID: 5df8
TitleCRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH CEFOPERAZONE
ComponentsCell division protein
KeywordsTRANSFERASE / cefoperazone / beta-lactam antibiotics / acyl-enzyme complex / de-acylation
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 / plasma membrane => GO:0005886 / proteolysis
Similarity search - Function
Beta-Lactamase - #330 / 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 domain / Penicillin-binding protein, transpeptidase / Beta-Lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase ...Beta-Lactamase - #330 / 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 domain / Penicillin-binding protein, transpeptidase / Beta-Lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase / Beta-lactamase/transpeptidase-like / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-59F / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsRen, J. / Nettleship, J.E. / Males, A. / Stuart, D.I. / Owens, R.J.
CitationJournal: Febs Lett. / Year: 2016
Title: Crystal structures of penicillin-binding protein 3 in complexes with azlocillin and cefoperazone in both acylated and deacylated forms.
Authors: Ren, J. / Nettleship, J.E. / Males, A. / Stuart, D.I. / Owens, R.J.
History
DepositionAug 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein
B: Cell division protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,14216
Polymers122,3052
Non-polymers1,83614
Water10,773598
1
A: Cell division protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0718
Polymers61,1531
Non-polymers9187
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell division protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0718
Polymers61,1531
Non-polymers9187
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.218, 74.374, 82.448
Angle α, β, γ (deg.)71.69, 86.06, 85.88
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A57 - 562
2010B57 - 562

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Components

#1: Protein Cell division protein / / Penicillin-binding protein 3 / Pseudomonas aeruginosa genome assembly PAE221


Mass: 61152.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (unknown)
Gene: pbpB, ftsI_2, ERS445055_04698, PAE221_03076, YQ19_27590
Production host: Escherichia coli BL21(DE3) (unknown)
References: UniProt: Q51504, peptidoglycan glycosyltransferase
#2: Chemical ChemComp-59F / (2R,4R,5R)-2-[(1R)-1-{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-(4-hydroxyphenyl)acetyl]amino}-2-oxoethyl]-5-methyl-1,3-thiazinane-4-carboxylic acid


Mass: 535.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H29N5O8S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2.5 M NaCl; 0.1 M imidazole pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 80608 / % possible obs: 92.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 6
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 1.7 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2→47.21 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.904 / SU B: 12.046 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2633 4067 5 %RANDOM
Rwork0.22611 ---
obs0.22801 76541 92.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.594 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.46 Å20.6 Å2
2--0.87 Å21.08 Å2
3----0.44 Å2
Refinement stepCycle: 1 / Resolution: 2→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7639 0 116 598 8353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197901
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.141.98310719
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.33251000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62123.182330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.909151288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4261571
X-RAY DIFFRACTIONr_chiral_restr0.0760.21200
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216007
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_it3.0975.3854009
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.8712.0415006
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.26.9763892
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.26126.43212543
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 609 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 281 -
Rwork0.38 5573 -
obs--90.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.09140.154-0.27160.3227-0.52630.95890.03110.0276-0.00390.0001-0.0384-0.008-0.0175-0.05680.00730.10060.08360.01710.16630.01580.01943.755811.4824-32.3359
20.0847-0.0574-0.17690.0780.12970.38850.0151-0.0005-0.005-0.0244-0.03260.0056-0.0260.01470.01750.05320.00540.00210.071-0.01550.07971.93952.708-13.0999
30.23980.0232-0.19690.08480.06870.5164-0.0538-0.0469-0.01380.04990.01790.00160.09940.02890.03590.08560.00290.00360.03320.00060.0615-2.9047-3.40617.9086
40.21880.0141-0.11450.7669-0.27140.1617-0.0388-0.1947-0.03060.15640.0283-0.0373-0.05650.06650.01040.10140.05290.00910.23680.06690.041932.358810.993637.0358
50.3175-0.08460.18870.0754-0.11260.30880.01470.14480.0680.0179-0.0436-00.00230.02140.02890.03940.00210.00770.10830.03650.077725.620920.8663-6.3151
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 176
2X-RAY DIFFRACTION2A177 - 292
3X-RAY DIFFRACTION3A293 - 564
4X-RAY DIFFRACTION4B57 - 224
5X-RAY DIFFRACTION5B225 - 562

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