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- PDB-4r3j: Structure of a putative peptidoglycan glycosyltransferase from At... -

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Basic information

Entry
Database: PDB / ID: 4r3j
TitleStructure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with cefapirin
ComponentsPeptidoglycan glycosyltransferase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / penicillin-binding protein
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / penicillin binding / regulation of cell shape / cell division / membrane
Similarity search - Function
Probable peptidoglycan glycosyltransferase FtsW/RodA / Cell cycle protein / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like ...Probable peptidoglycan glycosyltransferase FtsW/RodA / Cell cycle protein / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CFU / PHOSPHATE ION / Peptidoglycan glycosyltransferase
Similarity search - Component
Biological speciesAtopobium parvulum DSM 20469 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsFilippova, E.V. / Minasov, G. / Kiryukhina, O. / Clancy, S. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with cefapirin
Authors: Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Clancy, S. / Joachimiak, A. / Anderson, W.F.
History
DepositionAug 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan glycosyltransferase
B: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,37510
Polymers101,2982
Non-polymers1,0788
Water3,207178
1
A: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1895
Polymers50,6491
Non-polymers5404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1865
Polymers50,6491
Non-polymers5374
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.633, 119.836, 82.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Peptidoglycan glycosyltransferase /


Mass: 50648.797 Da / Num. of mol.: 2 / Fragment: UNP residues 505-954
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Atopobium parvulum DSM 20469 (bacteria)
Strain: ATCC 33793 / DSM 20469 / JCM 10300 / VPI 0546 / Gene: Apar_1344 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic
References: UniProt: C8W8H7, peptidoglycan glycosyltransferase
#2: Chemical ChemComp-CFU / (2R)-2-[(1R)-1-(acetylamino)-2-oxoethyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid


Mass: 258.294 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2O4S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.075 M HEPES Sodium Salt, 1.125 M Lithium sulfate, 25% Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2013 / Details: Beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.44→30 Å / Num. all: 37197 / Num. obs: 37197 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 56.2 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 19.2
Reflection shellResolution: 2.44→2.49 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1827 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N1X

4n1x


Resolution: 2.44→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 15.546 / SU ML: 0.173 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.317 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23068 1858 5 %RANDOM
Rwork0.1706 ---
obs0.17364 35300 99.68 %-
all-35300 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.212 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å2-0 Å2
2---0.43 Å20 Å2
3---0.57 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.44→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5826 0 67 178 6071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195993
X-RAY DIFFRACTIONr_bond_other_d0.0010.025574
X-RAY DIFFRACTIONr_angle_refined_deg1.641.9768167
X-RAY DIFFRACTIONr_angle_other_deg0.796312814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5685808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83925.278216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31815800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8821520
X-RAY DIFFRACTIONr_chiral_restr0.0840.2974
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216960
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021266
X-RAY DIFFRACTIONr_mcbond_it2.1913.4173253
X-RAY DIFFRACTIONr_mcbond_other2.1893.4173252
X-RAY DIFFRACTIONr_mcangle_it3.3445.1154054
X-RAY DIFFRACTIONr_mcangle_other3.3445.1154055
X-RAY DIFFRACTIONr_scbond_it3.5933.8422740
X-RAY DIFFRACTIONr_scbond_other3.5383.8282728
X-RAY DIFFRACTIONr_scangle_other4.8045.5814096
X-RAY DIFFRACTIONr_long_range_B_refined6.37328.796781
X-RAY DIFFRACTIONr_long_range_B_other6.35528.7376760
LS refinement shellResolution: 2.44→2.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 137 -
Rwork0.223 2505 -
obs--97.35 %
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)
12.37880.4666-0.15281.718-0.562.1788-0.0128-0.71540.19920.1578-0.0511-0.1753-0.2524-0.02330.06390.0883-0.0092-0.03830.2341-0.06750.07051.13244.26390.8115
21.06410.26750.67870.78860.38441.8114-0.0293-0.23340.0871-0.0342-0.08270.0850.0062-0.29230.1120.0512-0.01-0.00280.0948-0.00570.0295-13.213838.097-14.8051
32.7056-1.60220.332810.72091.28911.3409-0.1878-0.12460.17190.81990.04140.6498-0.0716-0.68810.14650.09420.10020.03040.4219-0.01180.0849-39.103529.1458-28.5596
40.79160.43680.55190.60380.48581.56610.0676-0.13590.0183-0.0464-0.11310.06680.2175-0.31890.04550.105-0.0447-0.00860.08430.01520.0442-16.058430.5462-24.8726
53.64570.91791.02041.49240.38291.7431-0.1866-0.17290.3194-0.2249-0.00940.2208-0.1029-0.39590.1960.0780.0366-0.03880.1105-0.02540.0886-18.293544.5855-22.3174
64.56170.1-0.04012.51420.00572.77890.1610.4337-0.479-0.40980.0033-0.17740.16850.2123-0.16440.19280.0846-0.02310.0973-0.0890.1083-14.651965.0181-41.9766
71.0767-2.2193-0.78366.1997-0.0282.232-0.0992-0.0362-0.1130.2458-0.08890.12860.02210.18750.18810.11850.0695-0.02430.0697-0.01240.0334-23.290671.6691-51.1755
81.8424-0.22230.3340.9990.88922.91140.14730.0768-0.1659-0.1048-0.13690.10.0914-0.1774-0.01040.14880.0611-0.05950.0447-0.0190.0872-25.093468.4796-34.229
91.5718-0.6344-0.37851.08130.75841.79320.0607-0.1504-0.0998-0.0163-0.11220.18970.0703-0.33930.05150.0328-0.0036-0.01210.1168-0.00920.0396-35.778278.3038-14.8571
106.7853-2.52521.64942.4983-0.14450.68880.1597-0.0414-0.4561-0.0185-0.07250.12570.2543-0.1121-0.08730.2991-0.08980.01170.1269-0.0060.1427-32.55561.9236-20.4089
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A526 - 579
2X-RAY DIFFRACTION2A580 - 708
3X-RAY DIFFRACTION3A709 - 725
4X-RAY DIFFRACTION4A726 - 885
5X-RAY DIFFRACTION5A886 - 954
6X-RAY DIFFRACTION6B526 - 566
7X-RAY DIFFRACTION7B567 - 572
8X-RAY DIFFRACTION8B573 - 673
9X-RAY DIFFRACTION9B674 - 918
10X-RAY DIFFRACTION10B919 - 953

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