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- PDB-4r0q: Structure of a putative peptidoglycan glycosyltransferase from At... -

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Basic information

Entry
Database: PDB / ID: 4r0q
TitleStructure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with cephalothin
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 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
CEPHALOTHIN GROUP / THIOCYANATE ION / Peptidoglycan glycosyltransferase
Similarity search - Component
Biological speciesAtopobium parvulum DSM 20469 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 cephalothin
Authors: Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Clancy, S. / Joachimiak, A. / Anderson, W.F.
History
DepositionAug 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)102,7758
Polymers101,2982
Non-polymers1,4786
Water6,395355
1
A: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3884
Polymers50,6491
Non-polymers7393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3884
Polymers50,6491
Non-polymers7393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.553, 70.002, 115.233
Angle α, β, γ (deg.)90.00, 96.76, 90.00
Int Tables number4
Space group name H-MP1211

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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-CEP / CEPHALOTHIN GROUP


Mass: 398.454 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18N2O6S2
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Potassium thiocyanate, 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-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: 2→30 Å / Num. all: 72944 / Num. obs: 72944 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 19.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.1 / % possible all: 91.7

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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→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.57 / SU ML: 0.113 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21662 3668 5 %RANDOM
Rwork0.17903 ---
obs0.18089 69023 98.53 %-
all-69023 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.261 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-0.56 Å2
2--0.96 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5938 0 88 355 6381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196131
X-RAY DIFFRACTIONr_bond_other_d0.0010.025702
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.9818352
X-RAY DIFFRACTIONr_angle_other_deg0.947313104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5055818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64325.045222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32415812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4561522
X-RAY DIFFRACTIONr_chiral_restr0.0920.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217120
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021321
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_it1.7822.1323295
X-RAY DIFFRACTIONr_mcbond_other1.7012.133292
X-RAY DIFFRACTIONr_mcangle_it2.663.1824104
X-RAY DIFFRACTIONr_mcangle_other2.663.1834105
X-RAY DIFFRACTIONr_scbond_it2.5372.4822836
X-RAY DIFFRACTIONr_scbond_other2.5342.4832836
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.783.6074249
X-RAY DIFFRACTIONr_long_range_B_refined7.56119.0317088
X-RAY DIFFRACTIONr_long_range_B_other7.56219.0377089
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 205 -
Rwork0.299 4463 -
obs--86 %
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)
10.82720.21030.4926.0554-0.54790.69050.0815-0.0924-0.1491-0.3969-0.1384-1.10880.22910.15690.05690.23010.05290.04730.22580.02240.4703-0.7603-1.198-47.5995
26.5357-5.9083-0.91566.33631.92111.34270.59070.3931-0.0336-0.5555-0.2559-0.2756-0.17760.0721-0.33480.5096-0.0090.22760.18720.02660.6187.1035-4.5696-60.4292
30.5232-0.5480.15051.8035-0.24420.10560.0143-0.014-0.03-0.0070.0207-0.0342-0.030.0004-0.0350.0743-0.01010.03450.0136-0.00360.0277-24.217320.3662-49.7972
42.60571.3361-0.46975.617-1.0161.7902-0.0369-0.1997-0.00850.40460.0145-0.1382-0.01250.00240.02240.22560.0025-0.00220.17-0.02210.1116-22.588322.5586-40.0458
58.08961.7904-2.46030.8283-1.09811.7506-0.207-0.0149-0.01710.29830.1305-0.1602-0.1948-0.18280.07650.39990.0951-0.19830.0461-0.04650.1161-17.32520.053-34.6573
67.59037.0271-0.4426.7059-0.63440.3256-0.930.8657-0.4596-0.59870.5263-0.8992-0.31160.39370.40370.992-0.4698-0.06790.97670.25981.797-3.049148.53-10.1113
71.19661.1448-0.13731.54420.43970.9330.28850.065-0.16360.32690.0355-0.57780.28560.0397-0.3240.48250.05240.14440.1859-0.01050.8255-8.440150.2026-2.8093
80.6380.4372-0.07843.49850.04850.37150.02760.03750.1538-0.20240.01340.1513-0.0252-0.0291-0.0410.24510.01760.01890.190.01750.1665-33.694828.4695-7.9309
91.17730.09730.25543.0957-0.21580.85050.06840.0870.0958-0.2838-0.0333-0.44690.06060.0535-0.0350.29620.03230.07730.21370.01140.2251-24.063723.5895-10.212
1010.684-1.76280.66971.78480.1291.35180.01420.74190.0621-0.70210.0361-0.4581-0.1482-0.0067-0.05030.46590.00260.21150.1710.00070.1677-24.142927.1714-22.7551
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A523 - 577
2X-RAY DIFFRACTION2A578 - 608
3X-RAY DIFFRACTION3A609 - 880
4X-RAY DIFFRACTION4A881 - 924
5X-RAY DIFFRACTION5A925 - 950
6X-RAY DIFFRACTION6B523 - 557
7X-RAY DIFFRACTION7B558 - 603
8X-RAY DIFFRACTION8B604 - 813
9X-RAY DIFFRACTION9B814 - 923
10X-RAY DIFFRACTION10B924 - 950

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