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- PDB-8pn5: Crystal structure of the HC7-Glu200Ala mutant complexed to a trig... -

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Basic information

Entry
Database: PDB / ID: 8pn5
TitleCrystal structure of the HC7-Glu200Ala mutant complexed to a triglycopeptide
Components
  • DUF3472 domain-containing protein
  • Triglycopeptide
KeywordsCARBOHYDRATE / Mucinase / glycoprotease / cluster of O-glycans
Function / homology2-acetamido-2-deoxy-alpha-D-galactopyranose
Function and homology information
Biological speciesBacillus cereus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsTaleb, V. / Hurtado-Guerrero, R.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and Competitiveness Spain
CitationJournal: Nat Catal / Year: 2024
Title: A family of di-glutamate mucin-degrading enzymes that bridges glycan hydrolases and peptidases
Authors: Narimatsu, Y. / Bull, C. / Taleb, V. / Liao, Q. / Companon, I. / Sanchez-Navarro, D. / Durbesson, F. / Vincentelli, R. / Hansen, L. / Corzana, F. / Rovira, C. / Henrissat, B. / Clausen, H. / ...Authors: Narimatsu, Y. / Bull, C. / Taleb, V. / Liao, Q. / Companon, I. / Sanchez-Navarro, D. / Durbesson, F. / Vincentelli, R. / Hansen, L. / Corzana, F. / Rovira, C. / Henrissat, B. / Clausen, H. / Joshi, H.J. / Hurtado-Guerrero, R.
History
DepositionJun 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF3472 domain-containing protein
B: DUF3472 domain-containing protein
C: DUF3472 domain-containing protein
D: DUF3472 domain-containing protein
E: DUF3472 domain-containing protein
F: DUF3472 domain-containing protein
G: DUF3472 domain-containing protein
H: DUF3472 domain-containing protein
I: Triglycopeptide
J: Triglycopeptide
K: Triglycopeptide
L: Triglycopeptide
M: Triglycopeptide
N: Triglycopeptide
O: Triglycopeptide
P: Triglycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)582,18361
Polymers575,05116
Non-polymers7,13345
Water42,8762380
1
A: DUF3472 domain-containing protein
I: Triglycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7958
Polymers71,8812
Non-polymers9136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DUF3472 domain-containing protein
J: Triglycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7027
Polymers71,8812
Non-polymers8215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DUF3472 domain-containing protein
K: Triglycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7297
Polymers71,8812
Non-polymers8485
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DUF3472 domain-containing protein
L: Triglycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6376
Polymers71,8812
Non-polymers7564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: DUF3472 domain-containing protein
M: Triglycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7027
Polymers71,8812
Non-polymers8215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: DUF3472 domain-containing protein
N: Triglycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9639
Polymers71,8812
Non-polymers1,0827
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: DUF3472 domain-containing protein
O: Triglycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7688
Polymers71,8812
Non-polymers8876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: DUF3472 domain-containing protein
P: Triglycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8879
Polymers71,8812
Non-polymers1,0057
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.331, 260.637, 82.626
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide / Sugars , 3 types, 40 molecules ABCDEFGHIJKLMNOP

#1: Protein
DUF3472 domain-containing protein


Mass: 70581.906 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: MFNQRTKNGVKKILAITAASTVFSMFGSSISIIEAASAPGVYVTPKNSVSSDIISIDWSPVQTAPYTYWA VHNWNQGGEAGGYAGFQQQSGFDENGKRTLHFAVWDPISSKEAIKAEYVSPTSVASNFGGEGTGLKIQTT ...Details: MFNQRTKNGVKKILAITAASTVFSMFGSSISIIEAASAPGVYVTPKNSVSSDIISIDWSPVQTAPYTYWA VHNWNQGGEAGGYAGFQQQSGFDENGKRTLHFAVWDPISSKEAIKAEYVSPTSVASNFGGEGTGLKIQTT YDWKNYNWYRMTMRSWQENGHTKFGQWLKDVSKNQWKLIGIMDFPVPNVTFNYGQTLFQADWLGNGQDVR EARVKNGYGRNISDKKWTSWNTQSIEGQEPLNNNWDGGATSEYLWFKAGGDSRSTIGTGKTFTLNQPSQP EIGKLDYDVKSTYYENEKLNITWQLKDSSTPQFKGKIEIYNNENMTGQPINVINDIKSYQNGISQSISLP TNTYAKIVLTDIFDQTVEKKVKIKNESPNILEGDRFAWSMKGIGDFEFAKLDLNKSTEELQVSLIAGTPH NYFDSTYASIKVQDTSGKVVYNKEIYGNTQQNAESKTVPVKVGNFIELTHLEGGERATLTNLDNNKRESF DKKVIYEVTKDGLKKINQIVNPKPDTEAPTQPQGLYASNVASDSVELKWNPSTDNVGVKEYQVLRDGQLI QTVQETKVTDQNLTANKEYKYTVKAVDTAGNISVQSNILTVTTKSQNVTYEKWDPKKAYTKGDKVEYQGK FYEAVQSYQGNGDPTWIFALSLWQPFKLI
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: DN401_14795 / Production host: Escherichia coli (E. coli)
#2: Protein/peptide
Triglycopeptide


Mass: 1299.428 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: Sugar...
ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 2401 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2380 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: MES PEG 8,000 zinc acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.72→20 Å / Num. obs: 371886 / % possible obs: 99.9 % / Redundancy: 5.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.7
Reflection shellResolution: 1.72→1.81 Å / Rmerge(I) obs: 1.264 / Num. unique obs: 53889 / CC1/2: 0.641

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→19.97 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.235 --RANDOM
Rwork0.208 ---
obs-356688 99.87 %-
Refinement stepCycle: LAST / Resolution: 1.72→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22452 0 428 2388 25268

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