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- PDB-7zvc: Second crystal form of the mature glutamic-class prolyl-endopepti... -

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Basic information

Entry
Database: PDB / ID: 7zvc
TitleSecond crystal form of the mature glutamic-class prolyl-endopeptidase neprosin at 1.85 A resolution.
Components
  • C-terminal peptidase
  • GLY-GLY-GLY-GLY
KeywordsHYDROLASE / glutamic endopeptidase / mature form / coeliac disease therapy / plant protease / pitcher plant
Function / homologyGLYCINE / NICKEL (II) ION
Function and homology information
Biological speciesNepenthes ventricosa x Nepenthes alata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRodriguez-Banqueri, A. / Eckhard, U. / Del Amo-Maestro, L. / Mendes, S.R. / Guevara, T. / Gomis-Ruth, F.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Molecular and in vivo studies of a glutamate-class prolyl-endopeptidase for coeliac disease therapy.
Authors: Del Amo-Maestro, L. / Mendes, S.R. / Rodriguez-Banqueri, A. / Garzon-Flores, L. / Girbal, M. / Rodriguez-Lagunas, M.J. / Guevara, T. / Franch, A. / Perez-Cano, F.J. / Eckhard, U. / Gomis-Ruth, F.X.
History
DepositionMay 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 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: C-terminal peptidase
C: GLY-GLY-GLY-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1209
Polymers28,8902
Non-polymers1,2307
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.86, 40.63, 64.63
Angle α, β, γ (deg.)90, 107.98, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein C-terminal peptidase


Mass: 28644.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Mature form (S129-Q380) of the glutamic endopeptidase neprosin after autolytic removal of the N-terminal pro-domain at low pH. Of note, N-terminus after maturation was confirmed by Edman degradation.
Source: (gene. exp.) Nepenthes ventricosa x Nepenthes alata (plant)
Plasmid: pCMV-Sport 6
Cell (production host): Suspension-adapted 293 human embryonic kidney (HEK) cells
Production host: Homo sapiens (human)
#2: Protein/peptide GLY-GLY-GLY-GLY


Mass: 246.222 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nepenthes ventricosa x Nepenthes alata (plant)
Production host: Homo sapiens (human)

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Sugars , 2 types, 2 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 255 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H5NO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate tribasic pH 5.6, 0.5 M ammonium sulphate, 1 M lithium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.85→61.5 Å / Num. obs: 24437 / % possible obs: 97.1 % / Redundancy: 6.55 % / CC1/2: 0.998 / Net I/σ(I): 12.4
Reflection shellResolution: 1.85→1.916 Å / Num. unique obs: 2007 / CC1/2: 0.729

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTERrefinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZU8

7zu8


Resolution: 1.85→20.66 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.127 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.136 / SU Rfree Blow DPI: 0.121 / SU Rfree Cruickshank DPI: 0.117
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 690 -RANDOM
Rwork0.1728 ---
obs0.1736 24416 97.2 %-
Displacement parametersBiso mean: 27.86 Å2
Baniso -1Baniso -2Baniso -3
1--8.3054 Å20 Å21.4056 Å2
2--0.7278 Å20 Å2
3---7.5776 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.85→20.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 91 250 2334
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112161HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.072968HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d893SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes376HARMONIC5
X-RAY DIFFRACTIONt_it2161HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion282SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance2HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact1996SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion5.05
X-RAY DIFFRACTIONt_other_torsion2.39
LS refinement shellResolution: 1.85→1.88 Å
RfactorNum. reflection% reflection
Rfree0.4625 14 -
Rwork0.3055 --
obs0.3079 719 74.72 %
Refinement TLS params.

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)
10.94040.00420.73790.67610.00341.83590.02140.00360.00070.00360.0137-0.14410.0007-0.1441-0.0351-0.0803-0.01080.0234-0.06350.0062-0.06331.87827.10820.4769
27.6862-3.64594.03571.0016-5.340512.18520.06360.1948-0.57480.19480.3832-0.3681-0.5748-0.3681-0.44690.1459-0.01770.0190.08740.00340.0796-11.316625.7763-7.3719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|132 - 379 }A132 - 379
2X-RAY DIFFRACTION2{A|380 - 380 A|401 - 408}A380 - 408

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