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- PDB-4ra7: Structure of a putative peptidoglycan glycosyltransferase from At... -

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Basic information

Entry
Database: PDB / ID: 4ra7
TitleStructure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with nafcillin
ComponentsPeptidoglycan glycosyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / penicillin-binding protein / TRANSFERASE-TRANSFERASE INHIBITOR complex
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-NXU / Peptidoglycan glycosyltransferase
Similarity search - Component
Biological speciesAtopobium parvulum DSM 20469 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 nafcillin
Authors: Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Clancy, S. / Joachimiak, A. / Anderson, W.F.
History
DepositionSep 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 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)94,9574
Polymers94,1762
Non-polymers7812
Water6,612367
1
A: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4792
Polymers47,0881
Non-polymers3901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4792
Polymers47,0881
Non-polymers3901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.399, 70.059, 114.567
Angle α, β, γ (deg.)90.00, 96.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptidoglycan glycosyltransferase /


Mass: 47088.102 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-NXU / (2R,4S)-2-[(1R)-2-hydroxy-1-{[(2-hydroxynaphthalen-1-yl)carbonyl]amino}ethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid


Mass: 390.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H22N2O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium Iodide, 0.1 M Bis-Tris propane, 20 % PEG3350, 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-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2013 / Details: MIRROR
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. all: 79452 / Num. obs: 79452 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 29.3
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / % possible all: 94.4

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.8.0069refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JBF

4jbf


Resolution: 1.94→30 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 8.384 / SU ML: 0.11 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19901 3984 5 %RANDOM
Rwork0.1613 ---
obs0.16322 75451 99.26 %-
all-75451 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.549 Å2
Baniso -1Baniso -2Baniso -3
1-4.74 Å20 Å21.63 Å2
2---5.67 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.94→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5983 0 54 367 6404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196151
X-RAY DIFFRACTIONr_bond_other_d0.0010.025705
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.9748393
X-RAY DIFFRACTIONr_angle_other_deg0.793313099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3985827
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75224.955222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6115816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4751522
X-RAY DIFFRACTIONr_chiral_restr0.1560.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217153
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021327
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_it1.9983.0523326
X-RAY DIFFRACTIONr_mcbond_other1.9983.0513325
X-RAY DIFFRACTIONr_mcangle_it2.9934.5614147
X-RAY DIFFRACTIONr_mcangle_other2.9934.5624148
X-RAY DIFFRACTIONr_scbond_it2.7933.3992825
X-RAY DIFFRACTIONr_scbond_other2.7933.42826
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0584.9864247
X-RAY DIFFRACTIONr_long_range_B_refined7.04327.057101
X-RAY DIFFRACTIONr_long_range_B_other6.99826.5446952
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.989 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 272 -
Rwork0.269 5267 -
obs--93.72 %
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)
11.9353-2.6494-1.36017.92580.14123.5624-0.2719-0.4172-0.1516-0.24750.0612-1.08760.49330.56980.21070.15320.130.17370.24940.08770.58664.52990.7189-47.7975
25.885-2.9845-2.1913.29631.95752.5261-0.2454-0.6924-0.3814-0.14870.0352-0.59980.30080.1430.21030.38580.07360.10630.27890.12230.66531.5758-2.5404-43.2908
30.9863-1.1696-0.17351.6940.63750.97920.2985-0.1070.2644-0.47790.0154-0.4994-0.3020.117-0.31390.3356-0.02170.04020.2421-0.01410.3208-0.9899-3.6915-55.5076
41.9811-0.3412-0.23013.2691-0.90481.6631-0.0807-0.1516-0.0381-0.00910.0597-0.53980.21330.19320.02090.08480.0092-0.04520.1545-0.02950.1302-8.52319.0329-43.2427
50.9591-0.59330.19382.2804-0.15920.58790.0409-0.02430.0125-0.16940.0270.0033-0.0302-0.0172-0.06780.1038-0.02060.00630.14790.0020.0092-27.260722.7278-51.494
62.07230.3630.00933.0133-0.38031.6508-0.1035-0.27610.14270.31670.0995-0.2429-0.0264-0.04620.0040.13110.0007-0.0390.1822-0.04350.0359-20.613122.0099-37.555
72.12543.68221.84527.59152.14686.2578-0.29150.4151-0.0003-0.25810.1894-0.7446-0.7410.89010.10210.1741-0.1828-0.02870.39120.16490.8261-2.543747.1938-8.8964
80.3543-1.0956-0.33483.65420.73521.8565-0.1346-0.03240.23640.39180.2365-0.75260.12480.1551-0.10190.1952-0.00860.12890.1404-0.01930.4975-11.284949.3929-9.8409
95.2645.9872.53086.92082.88891.26460.6763-0.46220.12070.9844-0.59570.3150.4551-0.1583-0.08060.6136-0.02470.00280.3856-0.04540.8392.612354.89665.4162
103.36641.78383.17762.8440.20145.1483-0.20290.2296-0.0985-0.39410.1313-0.8815-0.3840.17660.07160.27030.0060.30270.23230.0070.6242-10.99236.9797-13.3061
112.19150.74730.14963.7253-1.73243.2539-0.07610.14230.3153-0.26210.2181-0.3605-0.23440.0346-0.1420.14330.010.12710.16180.00270.2546-19.903939.3498-14.3894
120.93110.1749-0.2043.09440.01460.62840.06490.04570.1523-0.0116-0.00390.2240.0226-0.016-0.0610.03160.0237-0.00310.13750.02060.0524-33.970124.7302-5.9494
132.3562-0.4479-0.16183.81250.2641.32790.07580.19310.1778-0.64180.0513-0.1573-0.04540.0079-0.12720.20040.01240.04310.15230.02370.03-27.32926.4186-18.708
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A523 - 545
2X-RAY DIFFRACTION2A546 - 561
3X-RAY DIFFRACTION3A562 - 602
4X-RAY DIFFRACTION4A603 - 667
5X-RAY DIFFRACTION5A668 - 877
6X-RAY DIFFRACTION6A878 - 950
7X-RAY DIFFRACTION7B523 - 545
8X-RAY DIFFRACTION8B546 - 580
9X-RAY DIFFRACTION9B581 - 603
10X-RAY DIFFRACTION10B604 - 628
11X-RAY DIFFRACTION11B629 - 668
12X-RAY DIFFRACTION12B669 - 884
13X-RAY DIFFRACTION13B885 - 950

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