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- PDB-4jbf: Crystal structure of peptidoglycan glycosyltransferase from Atopo... -

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Basic information

Entry
Database: PDB / ID: 4jbf
TitleCrystal structure of peptidoglycan glycosyltransferase from Atopobium parvulum DSM 20469.
ComponentsPeptidoglycan glycosyltransferase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI / 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
Peptidoglycan glycosyltransferase
Similarity search - Component
Biological speciesAtopobium parvulum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F. ...Filippova, E.V. / Wawrzak, Z. / 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: Crystal structure of peptidoglycan glycosyltransferase from Atopobium parvulum DSM 20469.
Authors: Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural ...Authors: Filippova, E.V. / Wawrzak, Z. / 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)
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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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)101,4923
Polymers101,2982
Non-polymers1941
Water8,377465
1
A: Peptidoglycan glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)50,6491
Polymers50,6491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidoglycan glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8432
Polymers50,6491
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.927, 70.167, 114.820
Angle α, β, γ (deg.)90.00, 97.35, 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 (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-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.7 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Ammonium Chloride, 0.1 M HEPES pH 7, 20% PEG 6000, 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: Jan 30, 2013 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.92→30 Å / Num. all: 77602 / Num. obs: 77602 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 14.2
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.75 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.92→29.48 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.349 / SU ML: 0.095 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23679 4010 5 %RANDOM
Rwork0.1954 ---
obs0.19746 75977 98.52 %-
all-75977 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.439 Å2
Baniso -1Baniso -2Baniso -3
1-57.11 Å20 Å219.01 Å2
2---44.57 Å2-0 Å2
3----12.54 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.92→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5876 0 7 465 6348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196002
X-RAY DIFFRACTIONr_bond_other_d0.0010.025589
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.9668183
X-RAY DIFFRACTIONr_angle_other_deg0.84312836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1665812
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.30925.115217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.27815799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2891521
X-RAY DIFFRACTIONr_chiral_restr0.1130.2982
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216971
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021278
LS refinement shellResolution: 1.916→1.966 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 254 -
Rwork0.365 4744 -
obs--83.89 %

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