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- PDB-8ura: Crystal structure of Corynebacterium ulcerans endo-beta-N-acetylg... -

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Basic information

Entry
Database: PDB / ID: 8ura
TitleCrystal structure of Corynebacterium ulcerans endo-beta-N-acetylglucosaminidase catalytically inactive CU43 D187A-E189A at 2.6 A resolution (space group P21)
ComponentsCorynebacterial protease CP40
KeywordsHYDROLASE / Endoglycosidase / GH18 family / endo-beta-N-acetylglucosaminidase / single-domain IgG-specific
Function / homology:
Function and homology information
Biological speciesCorynebacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsSastre, D.E. / Sultana, N. / Sundberg, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell / Year: 2024
Title: Potent efficacy of an IgG-specific endoglycosidase against IgG-mediated pathologies.
Authors: Sastre, D.E. / Bournazos, S. / Du, J. / Boder, E.J. / Edgar, J.E. / Azzam, T. / Sultana, N. / Huliciak, M. / Flowers, M. / Yoza, L. / Xu, T. / Chernova, T.A. / Ravetch, J.V. / Sundberg, E.J.
History
DepositionOct 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 11, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Corynebacterial protease CP40
B: Corynebacterial protease CP40


Theoretical massNumber of molelcules
Total (without water)92,2152
Polymers92,2152
Non-polymers00
Water1,00956
1
A: Corynebacterial protease CP40


Theoretical massNumber of molelcules
Total (without water)46,1071
Polymers46,1071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Corynebacterial protease CP40


Theoretical massNumber of molelcules
Total (without water)46,1071
Polymers46,1071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.514, 70.897, 73.734
Angle α, β, γ (deg.)90.00, 92.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Corynebacterial protease CP40


Mass: 46107.309 Da / Num. of mol.: 2 / Mutation: D187A, E189A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium ulcerans (bacteria) / Gene: cpp, CULC0211_20780 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A830QWM5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 1.66 Å3/Da / Density % sol: 25.77 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Ammonium acetate 0.1 M BIS-TRIS pH 5.5 17% (w/v) PEG 10,000 (JCSG+,H6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 18310 / % possible obs: 96.6 % / Redundancy: 6.5 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.056 / Rrim(I) all: 0.144 / Rsym value: 0.132 / Χ2: 0.833 / Net I/σ(I): 14.15
Reflection shellResolution: 2.59→2.64 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.632 / Num. unique obs: 1810 / CC1/2: 0.852 / CC star: 0.959 / Rpim(I) all: 0.272 / Rrim(I) all: 0.689 / Rsym value: 0.632 / Χ2: 0.387 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→44.84 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2494 1809 9.93 %
Rwork0.1913 --
obs0.1971 18218 95.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5089 0 0 56 5145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075210
X-RAY DIFFRACTIONf_angle_d1.0727049
X-RAY DIFFRACTIONf_dihedral_angle_d12.8081894
X-RAY DIFFRACTIONf_chiral_restr0.063751
X-RAY DIFFRACTIONf_plane_restr0.009920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.650.30751230.26551201X-RAY DIFFRACTION90
2.65-2.730.28871400.24251187X-RAY DIFFRACTION91
2.73-2.820.29211280.22081182X-RAY DIFFRACTION90
2.82-2.920.25471520.2251277X-RAY DIFFRACTION98
2.92-3.040.28511230.23071301X-RAY DIFFRACTION99
3.04-3.180.32491630.21831289X-RAY DIFFRACTION99
3.18-3.340.27641410.20461289X-RAY DIFFRACTION99
3.34-3.550.24931570.18971306X-RAY DIFFRACTION99
3.55-3.830.27041420.17831301X-RAY DIFFRACTION99
3.83-4.210.23851380.16781282X-RAY DIFFRACTION97
4.21-4.820.17651250.16111240X-RAY DIFFRACTION93
4.82-6.070.23361240.17131215X-RAY DIFFRACTION90
6.07-44.840.21861530.17991339X-RAY DIFFRACTION99
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)
13.3878-0.1513-0.22631.8202-1.45392.8524-0.06330.19670.56280.04510.0725-0.0149-0.2966-0.038-0.0340.369-0.0550.03130.274-0.01270.298-2.7-3.102-33.154
26.8155-1.0766-0.34721.39690.11090.9908-0.14880.4393-0.3471-0.1277-0.00680.17080.1148-0.21460.13460.3777-0.04230.0450.4641-0.03860.2383-30.58819.178-10.7
31.93690.8366-0.22321.31480.21914.8053-0.1102-0.1271-0.18310.0744-0.077-0.03590.24920.02610.18940.23540.09010.04350.32120.02010.3985-22.25318.5847.863
43.8827-0.1690.13081.4418-0.43172.6932-0.13110.7333-0.1176-0.1569-0.0743-0.00880.04070.2760.25140.3104-0.02530.04270.45560.02050.2766-15.85227.195-12.761
53.7711-0.2954-2.18121.8680.50062.0745-0.0114-0.3752-0.26450.04790.1025-0.26190.1839-0.0376-0.06310.3096-0.0723-0.00180.3354-0.05280.3009-3.416-13.56-28.106
62.68320.27480.07320.58230.03722.9571-0.09140.04360.1302-0.01950.01010.0936-0.1339-0.2709-0.00030.2961-0.01770.0190.237-0.02260.2903-14.486-13.822-22.287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 246:368 )A246 - 368
2X-RAY DIFFRACTION2( CHAIN B AND RESID 48:140 )B48 - 140
3X-RAY DIFFRACTION3( CHAIN B AND RESID 141:245 )B141 - 245
4X-RAY DIFFRACTION4( CHAIN B AND RESID 246:369 )B246 - 369
5X-RAY DIFFRACTION5( CHAIN A AND RESID 40:71 )A40 - 71
6X-RAY DIFFRACTION6( CHAIN A AND RESID 72:245 )A72 - 245

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