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- PDB-7zva: Crystal Structure of the native zymogen form of the glutamic-clas... -

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Basic information

Entry
Database: PDB / ID: 7zva
TitleCrystal Structure of the native zymogen form of the glutamic-class prolyl-endopeptidase neprosin at 1.80 A resolution.
ComponentsC-terminal peptidase
KeywordsHYDROLASE / glutamic endopeptidase / zymogen / proform / coeliac disease therapy / plant protease
Function / homologyACETATE ION / ISOPROPYL ALCOHOL
Function and homology information
Biological speciesNepenthes ventricosa x Nepenthes alata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDel Amo-Maestro, L. / Eckhard, U. / Rodriguez-Banqueri, A. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-terminal peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,79117
Polymers43,0071
Non-polymers1,78516
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint16 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.370, 92.620, 42.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein C-terminal peptidase


Mass: 43006.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Pro-form of the glutamic endopeptidase neprosin (R25 to Q380) with an N-terminal IgK leader sequence and a C-terminal non-cleavable His6-tag.
Source: (gene. exp.) Nepenthes ventricosa x Nepenthes alata (plant)
Plasmid: pCMV-Sport 6
Cell line (production host): Suspension-adapted 293 human embryonic kidney (HEK) cells
Production host: Homo sapiens (human)

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 270 molecules

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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.99 Å3/Da / Density % sol: 38.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate pH 4.0, 22% PEG 6000, 10% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 1.005 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 1.8→63.2 Å / Num. obs: 32321 / % possible obs: 99.3 % / Redundancy: 12.6 % / CC1/2: 0.999 / Net I/σ(I): 15.3
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 2996 / CC1/2: 0.71

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTER2.10.4 (20-OCT-2021)refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZU8

7zu8


Resolution: 1.8→23.16 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.135 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.12
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 635 1.97 %RANDOM
Rwork0.1817 ---
obs0.1824 32301 99.3 %-
Displacement parametersBiso max: 82.44 Å2 / Biso mean: 35.76 Å2 / Biso min: 19.23 Å2
Baniso -1Baniso -2Baniso -3
1-7.8852 Å20 Å20 Å2
2--1.7795 Å20 Å2
3----9.6647 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.8→23.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 118 278 3004
Biso mean--58.97 47.75 -
Num. residues----335
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1203SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes482HARMONIC5
X-RAY DIFFRACTIONt_it2757HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion365SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2652SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2813HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3834HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion4.54
X-RAY DIFFRACTIONt_other_torsion2.62
LS refinement shellResolution: 1.8→1.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 32
RfactorNum. reflection% reflection
Rfree0.6657 18 1.73 %
Rwork0.3369 1024 -
all0.3423 1042 -
obs--88.33 %
Refinement TLS params.Method: refined / Origin x: 28.1314 Å / Origin y: 12.7223 Å / Origin z: 43.3187 Å
111213212223313233
T-0.0444 Å20.0049 Å20.0043 Å2--0.0249 Å2-0.001 Å2---0.0174 Å2
L1.0827 °2-0.0754 °20.0493 °2-0.9159 °2-0.1033 °2--0.2994 °2
S0.0074 Å °-0.0016 Å °-0.077 Å °0.0096 Å °0.0001 Å °0.0908 Å °-0.039 Å °-0.0147 Å °-0.0075 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|29 - 382 }A29 - 380
2X-RAY DIFFRACTION1{A|401 - 402 }A401 - 402
3X-RAY DIFFRACTION1{B|1 - 2 }B1 - 2
4X-RAY DIFFRACTION1{C|1 - 2 }C1 - 2

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