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- PDB-4n1x: Structure of a putative peptidoglycan glycosyltransferase from At... -

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Basic information

Entry
Database: PDB / ID: 4n1x
TitleStructure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with penicillin G
ComponentsPeptidoglycan glycosyltransferase
KeywordsTransferase/Antibiotic / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Susceptibility to Known Mtb Inhibitors / MTBI / glycosyltransferase / penicillin G / Transferase-Antibiotic Complex / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors
Function / homology
Function and homology information


lipid-linked peptidoglycan transporter activity / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / cell division site / 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
OPEN FORM - PENICILLIN G / Peptidoglycan glycosyltransferase
Similarity search - Component
Biological speciesAtopobium parvulum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: To be Published
Title: Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with penicillin G
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F.
History
DepositionOct 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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_ptnr2_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 1.4Dec 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)99,8184
Polymers99,1452
Non-polymers6732
Water14,412800
1
A: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9092
Polymers49,5731
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9092
Polymers49,5731
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.623, 70.141, 115.344
Angle α, β, γ (deg.)90.00, 96.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptidoglycan glycosyltransferase /


Mass: 49572.531 Da / Num. of mol.: 2 / Fragment: penicillin-binding domain, UNP residues 515-954
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Atopobium parvulum (bacteria) / Strain: DSM 20469 / 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-PNM / OPEN FORM - PENICILLIN G / Benzylpenicillin


Mass: 336.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N2O4S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 800 / 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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.085 M MES, 10.2% (w/v) PEG 20000, 10 % (w/v) Glycerol, pH 6.5, 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: Aug 20, 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→30 Å / Num. all: 70573 / Num. obs: 70573 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 26.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 4 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 9.2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JBF

4jbf


Resolution: 2→29.93 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.245 / SU ML: 0.122 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23684 3550 5 %RANDOM
Rwork0.19963 ---
obs0.20153 67015 95.92 %-
all-67015 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.239 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å2-0 Å21.44 Å2
2---2.88 Å2-0 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 2→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5925 0 46 800 6771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196106
X-RAY DIFFRACTIONr_bond_other_d0.0010.025662
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.9748333
X-RAY DIFFRACTIONr_angle_other_deg0.888313005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3495824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.824.909220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.84215806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7631522
X-RAY DIFFRACTIONr_chiral_restr0.1130.2989
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217124
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021322
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_it1.4911.2953311
X-RAY DIFFRACTIONr_mcbond_other1.4911.2943310
X-RAY DIFFRACTIONr_mcangle_it2.2611.9334130
X-RAY DIFFRACTIONr_mcangle_other2.2611.9334131
X-RAY DIFFRACTIONr_scbond_it1.91.4772795
X-RAY DIFFRACTIONr_scbond_other1.8971.4762793
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7892.1514203
X-RAY DIFFRACTIONr_long_range_B_refined6.9056.937549
X-RAY DIFFRACTIONr_long_range_B_other6.626.4167192
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 238 -
Rwork0.223 5090 -
obs--98.68 %
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)
10.9969-0.49940.69974.7052-1.34270.7132-0.20910.14930.10230.5104-0.0061-0.7207-0.22410.09440.21530.1975-0.0315-0.04290.178-0.00090.378720.000235.341249.0876
25.41662.8920.2151.97552.336111.48040.7613-0.9146-0.26090.6092-0.4851-0.18271.10040.0757-0.27610.349-0.1176-0.15990.25860.02780.501933.072844.874664.5766
31.52230.13310.02953.0487-0.90271.40710.0510.11250.0621-0.02710.074-0.3761-0.1550.1517-0.1250.0586-0.00640.03790.0926-0.01740.128812.259823.142444.1107
40.77810.2141-0.25132.3711-0.12460.64960.0150.03920.0902-0.0069-0.00910.13120.0018-0.0319-0.00590.02860.0147-0.02050.06610.00750.038-5.783812.297651.1361
51.3168-0.1588-0.25322.9870.44561.21330.00960.18780.0903-0.30540.0554-0.0297-0.02220.0054-0.0650.08020.0102-0.01290.10820.00370.02490.086813.510238.7317
61.22110.34550.44993.7211-0.36641.0614-0.001-0.0865-0.1393-0.3949-0.0723-0.76310.26650.24720.07330.22890.04490.05120.2040.00940.323226.2184-13.34899.1512
77.0501-9.8733-3.351313.85024.66431.63041.03740.55760.0911-1.4408-0.9121-0.1082-0.5982-0.1535-0.12530.71670.05470.07770.5702-0.02290.641235.7824-19.7973-4.6446
81.4205-0.1050.22343.5371-0.61870.41060.0296-0.1255-0.01680.13220.008-0.24820.08910.1731-0.03760.13010.0298-0.04450.1771-0.02850.109517.21-2.983714.3654
90.5037-0.31540.09821.7363-0.20290.52740.0447-0.0230.0006-0.05980.01290.0402-0.0161-0.0228-0.05750.0891-0.01660.01450.0682-0.00250.0118-0.005110.30145.4781
101.40180.1428-0.14742.9449-0.59111.1579-0.0447-0.22570.03580.27040.0232-0.204-0.00610.06390.02150.1419-0.0092-0.00130.1062-0.03470.02827.0079.042919.0991
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A523 - 584
2X-RAY DIFFRACTION2A585 - 603
3X-RAY DIFFRACTION3A604 - 655
4X-RAY DIFFRACTION4A656 - 884
5X-RAY DIFFRACTION5A885 - 949
6X-RAY DIFFRACTION6B523 - 580
7X-RAY DIFFRACTION7B581 - 603
8X-RAY DIFFRACTION8B605 - 668
9X-RAY DIFFRACTION9B669 - 880
10X-RAY DIFFRACTION10B881 - 950

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