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- PDB-7zu8: Crystal Structure of the zymogen form of the glutamic-class proly... -

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Basic information

Entry
Database: PDB / ID: 7zu8
TitleCrystal Structure of the zymogen form of the glutamic-class prolyl-endopeptidase neprosin at 2.05 A resolution in presence of the crystallophore Lu-Xo4.
ComponentsGlutamyl endopeptidase Neprosin
KeywordsHYDROLASE / glutamic endopeptidase / zymogen / proform / coeliac disease therapy / crystallophore
Function / homologyACETATE ION / Chem-K93
Function and homology information
Biological speciesNepenthes ventricosa x Nepenthes alata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 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 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamyl endopeptidase Neprosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2677
Polymers43,0071
Non-polymers2,2606
Water3,225179
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)86.650, 93.350, 48.690
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 Glutamyl endopeptidase Neprosin


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-Q380) from Nepenthes ventrata with an N-terminal IgK leader sequence and a C-terminal non-cleavable His6-tag (AIA-HHHHHH).
Source: (gene. exp.) Nepenthes ventricosa x Nepenthes alata (plant)
Gene: NvNpr / Plasmid: pCMV-Sport 6
Cell line (production host): Suspension-adapted 293 human embryonic kidney (HEK) cells
Production host: Homo sapiens neanderthalensis (Neandertal) / References: glutamyl endopeptidase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-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 , 3 types, 183 molecules

#4: Chemical ChemComp-K93 / 12-oxidanyl-9,11$l^{3}-dioxa-1$l^{4},19$l^{4},22,27$l^{4},28$l^{4}-pentaza-10$l^{6}-lutetaoctacyclo[17.5.2.1^{3,7}.1^{10,13}.0^{1,10}.0^{10,19}.0^{10,28}.0^{17,27}]octacosa-3,5,7(28),11,13,15,17(27)-heptaen-8-one


Mass: 573.403 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24LuN5O4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate pH 4.0, 22% polyethylene glycol (PEG) 6000, 10% isopropanol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.34 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 2.05→63.51 Å / Num. obs: 25470 / % possible obs: 99.9 % / Redundancy: 12.5 % / CC1/2: 0.997 / Net I/σ(I): 9.2
Reflection shellResolution: 2.05→2.12 Å / Num. unique obs: 2500 / CC1/2: 0.918 / % possible all: 98.73

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
BUSTER2.10.4 (20-OCT-2021)refinement
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.05→63.51 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.887 / SU R Cruickshank DPI: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.207 / SU Rfree Blow DPI: 0.176 / SU Rfree Cruickshank DPI: 0.174
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 621 2.44 %RANDOM
Rwork0.2092 ---
obs0.2102 25470 99.9 %-
Displacement parametersBiso max: 119.28 Å2 / Biso mean: 48.48 Å2 / Biso min: 26.98 Å2
Baniso -1Baniso -2Baniso -3
1-15.6821 Å20 Å20 Å2
2--8.2755 Å20 Å2
3----23.9576 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.05→63.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 0 134 179 2926
Biso mean--57.3 52.66 -
Num. residues----336
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1225SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes513HARMONIC5
X-RAY DIFFRACTIONt_it2703HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion373SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance18HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2448SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2839HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg3882HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion4.05
X-RAY DIFFRACTIONt_other_torsion2.66
LS refinement shellResolution: 2.05→2.07 Å / Rfactor Rfree error: 0 / Total num. of bins used: 32
RfactorNum. reflection% reflection
Rfree0.5481 17 2.07 %
Rwork0.3656 805 -
all0.3692 822 -
obs--98.57 %
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)
12.2574-0.06330.00312.2094-0.09910.66250.04950.002-0.0025-0.0126-0.050.16870.0337-0.04130.0005-0.17340.00510.0056-0.1771-0.0240.154928.217812.90424.8913
20-0.08890.567300.39340.0282-0.00420.05910.0484-0.105-0.01080.05710.00590.06260.01510.1270.13050.15950.309-0.0265-0.378143.986514.90966.8465
30-0.26880.201800.34610.0188-0.00110.00190.00340.0182-0.00910.02650.0645-0.04740.01020.02920.0675-0.00640.0280.04550.314133.2691-3.266614.2774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|29 - 383 A|501 - 502 A|511 - 511 A|601 - 602}A29 - 383
2X-RAY DIFFRACTION1{A|29 - 383 A|501 - 502 A|511 - 511 A|601 - 602}A501 - 502
3X-RAY DIFFRACTION1{A|29 - 383 A|501 - 502 A|511 - 511 A|601 - 602}A511
4X-RAY DIFFRACTION1{A|29 - 383 A|501 - 502 A|511 - 511 A|601 - 602}A601 - 602
5X-RAY DIFFRACTION2{A|400 - 402}A400 - 402
6X-RAY DIFFRACTION3{A|403 - 404}A403 - 404

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