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

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Basic information

Entry
Database: PDB / ID: 4qjg
TitleStructure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with penicillin V
ComponentsPeptidoglycan glycosyltransferase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / glycosyltransferase
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-35P / Peptidoglycan glycosyltransferase
Similarity search - Component
Biological speciesAtopobium parvulum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 penicillin V
Authors: Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Clancy, S. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionJun 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references / Structure summary
Revision 1.2Aug 12, 2015Group: Non-polymer description
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Sep 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.pdbx_ptnr1_label_alt_id / _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 1.6Dec 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)102,0024
Polymers101,2982
Non-polymers7052
Water10,449580
1
A: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0012
Polymers50,6491
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0012
Polymers50,6491
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.723, 70.019, 114.625
Angle α, β, γ (deg.)90.00, 96.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999949, 0.003942, 0.009334), (0.003771, -0.999825, 0.018316), (0.009404, -0.01828, -0.999789)6.78855, 48.18832, -56.11718

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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 (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-35P / (2R,4S)-5,5-dimethyl-2-{(1R)-2-oxo-1-[(phenoxyacetyl)amino]ethyl}-1,3-thiazolidine-4-carboxylic acid / OPEN FORM - PENICILLIN V


Mass: 352.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N2O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M NaCl, 0.1 M Bis-Tris, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 89289 / Num. obs: 89289 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.7
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.7 / % possible all: 97.7

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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: 4JBF

4jbf


Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.723 / SU ML: 0.099 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20568 4423 5 %RANDOM
Rwork0.17479 ---
obs0.17631 84846 99.58 %-
all-84846 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.064 Å2
Baniso -1Baniso -2Baniso -3
1-4.26 Å2-0 Å22.13 Å2
2---3.57 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6012 0 48 580 6640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196234
X-RAY DIFFRACTIONr_bond_other_d0.0020.025783
X-RAY DIFFRACTIONr_angle_refined_deg1.821.9728513
X-RAY DIFFRACTIONr_angle_other_deg0.894313288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3165841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.77624.957230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.98715834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4861524
X-RAY DIFFRACTIONr_chiral_restr0.1080.21006
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0217289
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021355
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_it2.7312.3633364
X-RAY DIFFRACTIONr_mcbond_other2.7292.3633363
X-RAY DIFFRACTIONr_mcangle_it3.8493.5184205
X-RAY DIFFRACTIONr_mcangle_other3.8493.5194206
X-RAY DIFFRACTIONr_scbond_it4.192.782870
X-RAY DIFFRACTIONr_scbond_other4.1892.7812871
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7414.0234309
X-RAY DIFFRACTIONr_long_range_B_refined8.00911.5917510
X-RAY DIFFRACTIONr_long_range_B_other7.91111.2917239
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 311 -
Rwork0.256 6002 -
obs--95.7 %
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)
11.2011-0.4932-1.02986.11371.44571.0698-0.2339-0.3238-0.4395-0.2157-0.0111-0.79580.14320.23850.2450.0640.07670.12260.11050.09160.45355.3247-1.0342-47.6109
20.2744-0.15020.16490.110.00670.44630.0335-0.09990.0277-0.05610.0815-0.0567-0.10270.0494-0.1150.138-0.029-0.01360.0785-0.0570.1637-2.0693-1.0267-51.9876
32.2615-1.4885-1.36.7509-0.09210.91550.24960.09260.2850.0188-0.0402-0.1558-0.1826-0.0631-0.20940.07540.03080.05120.1110.00180.175712.5734-7.4399-60.1701
40.3034-0.34630.13320.6906-0.09210.23270.0125-0.0479-0.0079-0.07690.039-0.0202-0.0071-0.0003-0.05150.0568-0.0115-0.03570.11830.00270.0793-23.160620.1786-49.7675
50.33160.29490.0250.66490.03910.5054-0.0591-0.0730.03530.06230.0849-0.0730.0266-0.0354-0.02580.07110.0096-0.05360.1474-0.02030.0914-20.62822.6029-37.3921
60.1284-0.58920.09644.337-0.59460.0896-0.09430.09320.09750.6048-0.0116-0.5565-0.08320.02950.10590.094-0.0304-0.05510.17380.03060.2255-7.304248.2517-9.2779
73.09714.17750.00266.0388-0.77761.54650.2148-0.11790.01410.1261-0.2980.03120.23330.31430.08320.13980.005-0.12520.12230.01420.27243.75155.67955.996
80.580.1854-0.0081.4666-0.39820.31110.00810.04780.01930.0080.0819-0.1267-0.03210.0366-0.08990.0556-0.0017-0.00320.1185-0.01070.1144-15.499838.1697-14.0366
90.38090.2435-0.24620.8173-0.210.17990.03230.04560.08510.12580.03760.1118-0.0012-0.0001-0.06990.08490.0226-0.02650.10550.01180.0898-33.271124.7443-6.0006
100.11540.1158-0.20090.5521-0.17060.4598-0.02420.03860.0013-0.10870.10430.0450.0236-0.0184-0.08010.0804-0.007-0.03840.14020.00060.0982-27.082926.4258-18.7347
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A524 - 552
2X-RAY DIFFRACTION2A553 - 597
3X-RAY DIFFRACTION3A598 - 606
4X-RAY DIFFRACTION4A607 - 872
5X-RAY DIFFRACTION5A873 - 950
6X-RAY DIFFRACTION6B523 - 582
7X-RAY DIFFRACTION7B583 - 603
8X-RAY DIFFRACTION8B604 - 661
9X-RAY DIFFRACTION9B667 - 884
10X-RAY DIFFRACTION10B885 - 950

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