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- PDB-4r23: Structure of a putative peptidoglycan glycosyltransferase from At... -

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Basic information

Entry
Database: PDB / ID: 4r23
TitleStructure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with dicloxacillin
ComponentsPeptidoglycan glycosyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / penicillin-binding protein / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan L,D-transpeptidase activity / glycosyltransferase activity / penicillin binding / cell wall organization / regulation of cell shape / cell division / plasma membrane
Similarity search - Function
: / Penicillin binding protein A dimerisation domain / 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 ...: / Penicillin binding protein A dimerisation domain / 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-DXU / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Peptidoglycan glycosyltransferase
Similarity search - Component
Biological speciesAtopobium parvulum DSM 20469 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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 dicloxacillin
Authors: Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Clancy, S. / Joachimiak, A. / Anderson, W.F.
History
DepositionAug 8, 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.5May 28, 2025Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)103,21413
Polymers101,2982
Non-polymers1,91611
Water7,674426
1
A: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8008
Polymers50,6491
Non-polymers1,1517
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4145
Polymers50,6491
Non-polymers7654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.611, 69.882, 114.251
Angle α, β, γ (deg.)90.00, 96.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999938, 0.001857, 0.011), (0.001726, -0.999928, 0.011912), (0.011021, -0.011892, -0.999869)6.8026, 48.3396, -56.08216

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Components

#1: Protein Peptidoglycan glycosyltransferase


Mass: 50648.797 Da / Num. of mol.: 2 / Fragment: 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-DXU / Dicloxacillin, open form / dicloxacillin - open form / (3R,4R,5R)-3-(2,6-dichlorophenyl)-N-{(1R)-1-[(2R,4S)-4-(dihydroxymethyl)-5,5-dimethyl-1,3-thiazolidin-2-yl]-2-oxoethyl}-5-methyl-1,2-oxazolidine-4-carboxamide


Mass: 478.390 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H25Cl2N3O5S
#3: Chemical
ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Tri-Sodium Citrate, 0.1 M Tris, 15% PEG400, pH 8.5, 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: 1.84→30 Å / Num. all: 91253 / Num. obs: 91253 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2 / Num. unique all: 4542 / % possible all: 99.8

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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: 4QJG

4qjg


Resolution: 1.84→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 5.784 / SU ML: 0.082 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19183 4501 5 %RANDOM
Rwork0.15541 ---
obs0.15717 85416 98.19 %-
all-85416 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.516 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å2-0.27 Å2
2--0.4 Å20 Å2
3----0.05 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.84→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5950 0 105 426 6481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196158
X-RAY DIFFRACTIONr_bond_other_d0.0010.025748
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.9818380
X-RAY DIFFRACTIONr_angle_other_deg0.802313213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4175821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13424.977221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12815817
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7691522
X-RAY DIFFRACTIONr_chiral_restr0.0960.2997
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217097
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021309
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_it1.9592.7153305
X-RAY DIFFRACTIONr_mcbond_other1.9592.7143304
X-RAY DIFFRACTIONr_mcangle_it2.8664.0524119
X-RAY DIFFRACTIONr_mcangle_other2.8664.0534120
X-RAY DIFFRACTIONr_scbond_it3.1843.2152853
X-RAY DIFFRACTIONr_scbond_other3.1843.2152853
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6944.6614262
X-RAY DIFFRACTIONr_long_range_B_refined7.86424.3147065
X-RAY DIFFRACTIONr_long_range_B_other7.79123.8216898
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 313 -
Rwork0.274 5489 -
obs--85.76 %
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)
11.46170.7430.40714.20520.04050.7235-0.0746-0.0397-0.1237-0.44120.0408-0.72330.16090.16990.03380.11310.04060.04810.0757-0.0070.2201-0.5418-0.9816-47.6297
25.6662-6.1019-2.57667.10443.25461.62380.56220.30350.183-0.6574-0.2537-0.4066-0.3562-0.037-0.30850.30320.01380.17240.1402-0.01920.29328.0693-6.08-61.3784
31.3322-0.2693-0.2372.6235-0.68611.191-0.0836-0.1511-0.03640.07620.0886-0.37430.12250.1479-0.0050.04870.0126-0.02550.0717-0.02830.0928-9.4489.8955-42.4339
40.7108-0.55830.1821.9424-0.20650.49080.0337-0.0261-0.0346-0.09680.03430.0542-0.0107-0.0113-0.0680.0691-0.01810.01450.05040.00370.0205-27.13722.4115-52.0645
51.816-0.1392-0.76863.4096-0.12272.588-0.0734-0.24960.04840.23830.15310.0208-0.0557-0.1-0.07970.10660.0104-0.00290.0903-0.01650.0195-25.777325.9181-37.5618
61.0460.080.2382.00890.09851.1976-0.0547-0.18650.08110.29030.099-0.2340.0340.0197-0.04420.10860.0077-0.00970.0981-0.03050.0718-18.01321.8688-37.7622
70.4217-0.04230.07553.688-1.20790.452-0.03170.10520.06590.325-0.113-0.7683-0.17280.08290.14470.1326-0.05540.07030.0876-0.03770.4226-7.16449.2527-9.9203
88.2717.48342.23776.81562.18411.22050.434-0.2614-0.2290.4892-0.1755-0.28730.43920.2276-0.25850.35780.0594-0.11410.2055-0.02190.3681-1.225353.00932.912
91.45180.22560.11983.2459-1.01521.365-0.03920.12810.0395-0.16380.1241-0.4542-0.13130.0952-0.0850.0897-0.0030.07770.0606-0.02610.1368-16.121135.8553-14.291
100.77030.3788-0.28672.5674-0.1510.64110.04470.03250.10630.02560.03160.1391-0.0003-0.0366-0.07640.04830.0205-0.00460.04380.01140.0269-33.3225.6558-6.1749
112.6465-0.68850.38214.41320.03741.48560.02920.12120.1099-0.36710.06940.0311-0.0168-0.0507-0.09860.1029-0.0020.01820.07350.01380.0212-29.306825.9692-16.1463
128.6679-1.04621.61162.0782-0.29551.0913-0.05560.51560.0054-0.6280.1331-0.2966-0.1704-0.0149-0.07750.2678-0.02090.10790.1115-0.02340.0736-23.88827.7633-22.7061
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A522 - 580
2X-RAY DIFFRACTION2A581 - 603
3X-RAY DIFFRACTION3A605 - 667
4X-RAY DIFFRACTION4A668 - 865
5X-RAY DIFFRACTION5A866 - 901
6X-RAY DIFFRACTION6A902 - 950
7X-RAY DIFFRACTION7B523 - 576
8X-RAY DIFFRACTION8B577 - 603
9X-RAY DIFFRACTION9B606 - 655
10X-RAY DIFFRACTION10B656 - 884
11X-RAY DIFFRACTION11B885 - 923
12X-RAY DIFFRACTION12B924 - 950

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