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- PDB-4ovd: Crystal structure of a putative peptidoglycan glycosyltransferase... -

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Basic information

Entry
Database: PDB / ID: 4ovd
TitleCrystal structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum DSM 20469
ComponentsPeptidoglycan glycosyltransferase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / D / D-transpeptidase
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / glycosyltransferase activity / penicillin binding / cell wall organization / plasma membrane
Similarity search - Function
Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily ...Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / 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
Peptidoglycan glycosyltransferase
Similarity search - Component
Biological speciesAtopobium parvulum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Kiryukhina, O. / Babnigg, G. / Clancy, S. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum DSM 20469
Authors: Filippova, E.V. / Wawrzak, Z. / Kiryukhina, O. / Babnigg, G. / Clancy, S. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionFeb 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5212
Polymers61,4811
Non-polymers401
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peptidoglycan glycosyltransferase
hetero molecules

A: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,0424
Polymers122,9622
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2510 Å2
ΔGint-33 kcal/mol
Surface area32900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.680, 45.510, 71.290
Angle α, β, γ (deg.)90.00, 102.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-745-

HOH

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Components

#1: Protein Peptidoglycan glycosyltransferase / D / D-transpeptidase


Mass: 61480.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Atopobium parvulum (bacteria) / Strain: DSM 20469 / Gene: Apar_0480 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic
References: UniProt: C8W9X3, peptidoglycan glycosyltransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1.98 Å3/Da / Density % sol: 37.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Calcium Chloride, 0.1 M HEPES, 20% PEG6000, pH 7, 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: Oct 21, 2013 / Details: 3.0 Undulator
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→29.17 Å / Num. all: 32538 / Num. obs: 32538 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.052 / Mean I/σ(I) obs: 2.5 / % possible all: 95.6

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.8.0049refinement
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→29.17 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.579 / SU ML: 0.128 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23269 1646 5.1 %RANDOM
Rwork0.17947 ---
obs0.18223 30883 98.94 %-
all-30883 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.813 Å2
Baniso -1Baniso -2Baniso -3
1--4.36 Å20 Å21.86 Å2
2--3.7 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 1 156 3335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193231
X-RAY DIFFRACTIONr_bond_other_d0.0010.023015
X-RAY DIFFRACTIONr_angle_refined_deg2.1071.9624377
X-RAY DIFFRACTIONr_angle_other_deg0.90836928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5015418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19725.342146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56615482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6281514
X-RAY DIFFRACTIONr_chiral_restr0.1350.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023763
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02729
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_it4.0653.0571684
X-RAY DIFFRACTIONr_mcbond_other4.0613.0551683
X-RAY DIFFRACTIONr_mcangle_it5.0574.5492098
X-RAY DIFFRACTIONr_mcangle_other5.0564.5522099
X-RAY DIFFRACTIONr_scbond_it5.9573.7061547
X-RAY DIFFRACTIONr_scbond_other5.9563.7081548
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.3335.3332280
X-RAY DIFFRACTIONr_long_range_B_refined10.06614.6463764
X-RAY DIFFRACTIONr_long_range_B_other10.05314.5763734
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 121 -
Rwork0.249 2225 -
obs--97.63 %
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)
113.749-2.30670.67730.78120.0720.3063-0.0433-0.17920.4843-0.1580.1323-0.17180.0429-0.1216-0.0890.1671-0.1201-0.0040.22020.04240.067-13.27228.1839-3.7245
23.35830.2746-1.58170.0286-0.14811.45490.0607-0.65340.24890.0158-0.02420.0113-0.01330.0383-0.03660.1465-0.0047-0.03120.2957-0.070.14349.667513.2856-13.176
33.34410.0037-0.69150.23310.14720.41640.04070.11260.1133-0.0455-0.0410.0168-0.0226-0.07170.00030.10090.0015-0.06610.01980.01910.096329.50048.5654-37.1996
43.0867-0.0597-0.59320.49790.04780.5743-0.0334-0.1653-0.09910.0134-0.03350.01520.03180.00080.0670.1085-0.0008-0.0590.03020.03270.103429.79086.1874-31.5477
52.7005-0.1888-0.06421.6977-0.72666.36020.0882-0.71150.5929-0.0029-0.03890.0530.21970.062-0.04930.056-0.0308-0.0060.1935-0.15680.150332.400818.623-18.4346
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A61 - 68
2X-RAY DIFFRACTION2A69 - 279
3X-RAY DIFFRACTION3A280 - 344
4X-RAY DIFFRACTION4A345 - 545
5X-RAY DIFFRACTION5A546 - 571

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