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- PDB-4nuz: Crystal structure of a glycosynthase mutant (D233Q) of EndoS, an ... -

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Basic information

Entry
Database: PDB / ID: 4nuz
TitleCrystal structure of a glycosynthase mutant (D233Q) of EndoS, an endo-beta-N-acetyl-glucosaminidase from Streptococcus pyogenes
ComponentsEndo-beta-N-acetylglucosaminidase F2
KeywordsHYDROLASE / glycosynthase / endo-beta-N-acetylglucosaminidase S / endoglycosidase S / immunoglobulin G
Function / homology:
Function and homology information
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.905 Å
AuthorsTrastoy, B. / Guenther, S. / Snyder, G.A. / Sundberg, E.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies.
Authors: Trastoy, B. / Lomino, J.V. / Pierce, B.G. / Carter, L.G. / Gunther, S. / Giddens, J.P. / Snyder, G.A. / Weiss, T.M. / Weng, Z. / Wang, L.X. / Sundberg, E.J.
History
DepositionDec 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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

Downloads & links

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Assembly

Deposited unit
A: Endo-beta-N-acetylglucosaminidase F2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5432
Polymers101,5031
Non-polymers401
Water15,277848
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.769, 96.388, 141.545
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endo-beta-N-acetylglucosaminidase F2


Mass: 101503.344 Da / Num. of mol.: 1 / Mutation: D233Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Gene: endoS, M5005_Spy1540 / Production host: Escherichia coli (E. coli)
References: UniProt: Q48WW7, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
#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.: 848 / 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: 3.12 Å3/Da / Density % sol: 60.54 %
Crystal growTemperature: 298 K / Method: liquid diffusion
Details: Crystals were grown through liquid-liquid diffusion using the Crystal Former from Microlytic, 20% polyethylene glycol (PEG) 3350, 0.2 M Lithium acetate at 298 K , LIQUID DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979340, 0.97870, 0.91837, 0.97951
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 19, 2013
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.97871
30.918371
40.979511
ReflectionResolution: 1.905→30 Å / Num. obs: 98581 / % possible obs: 96.8 % / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.85-3.28195.4
2.55-2.84197.8
2.33-2.54199
2.16-2.32199.4
2.02-2.15199.5
1.9-2.01195.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
RESOLVE2.13phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
JBluIce-EPICSdata collection
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 1.905→29.685 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8279 / SU ML: 0.25 / σ(F): 1.33 / Phase error: 24.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 1984 2.02 %RANDOM
Rwork0.1923 ---
obs0.1932 98436 98.7 %-
all-98436 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.33 Å2 / Biso mean: 38.5665 Å2 / Biso min: 11.47 Å2
Refinement stepCycle: LAST / Resolution: 1.905→29.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7047 0 1 848 7896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0167189
X-RAY DIFFRACTIONf_angle_d1.5089718
X-RAY DIFFRACTIONf_chiral_restr0.1111069
X-RAY DIFFRACTIONf_plane_restr0.0081258
X-RAY DIFFRACTIONf_dihedral_angle_d14.5032716
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9046-1.95220.36411430.31256549669295
1.9522-2.0050.32061360.27769197055100
2.005-2.0640.29571470.247168947041100
2.064-2.13060.27151450.237668326977100
2.1306-2.20670.2771370.220769427079100
2.2067-2.29510.24721400.207469227062100
2.2951-2.39950.2681430.199369037046100
2.3995-2.52590.25141400.198769327072100
2.5259-2.68410.24651460.195169407086100
2.6841-2.89110.2441410.19196908704999
2.8911-3.18180.22711460.19416888703499
3.1818-3.64150.23251360.18046842697897
3.6415-4.58520.20071410.16496872701397
4.5852-29.68850.20141430.17637109725297
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)
12.414-0.7961-0.39521.89290.32951.6750.18360.3637-0.3165-0.2104-0.19560.3141-0.038-0.3247-0.00660.14640.0378-0.05980.2379-0.08120.1947-14.5717104.8124194.7038
20.1344-0.0528-0.3270.1030.30961.86150.07490.04760.0701-0.14690.1108-0.0648-0.28430.0815-0.16280.3057-0.02970.06170.188-0.03290.324725.2228109.888169.8725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:445)A4 - 445
2X-RAY DIFFRACTION2(chain A and resid 446:890)A446 - 890

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