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- PDB-7zvb: Crystal Structure of the mature form of the glutamic-class prolyl... -

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Basic information

Entry
Database: PDB / ID: 7zvb
TitleCrystal Structure of the mature form of the glutamic-class prolyl-endopeptidase neprosin at 2.35 A resolution.
ComponentsC-terminal peptidase
KeywordsHYDROLASE / glutamic endopeptidase / coeliac disease therapy / plant protease / pitcher plant
Function / homologyTRIETHYLENE GLYCOL
Function and homology information
Biological speciesNepenthes ventricosa x Nepenthes alata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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
Revision 1.2Oct 16, 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

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Assembly

Deposited unit
A: C-terminal peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2395
Polymers28,6441
Non-polymers1,5954
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint30 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.760, 49.950, 59.860
Angle α, β, γ (deg.)90.000, 106.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: 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
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 1000, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.005 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2.35→52.5 Å / Num. obs: 13077 / % possible obs: 99.6 % / Redundancy: 6.46 % / CC1/2: 0.99 / Net I/σ(I): 5.6
Reflection shellResolution: 2.35→2.434 Å / Num. unique obs: 1292 / CC1/2: 0.653 / % possible all: 98.85

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTER2.10.3 (20-MAY-2020)refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZU8

7zu8


Resolution: 2.35→52.49 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.383 / SU Rfree Blow DPI: 0.244 / SU Rfree Cruickshank DPI: 0.241
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 479 3.66 %RANDOM
Rwork0.1953 ---
obs0.1972 13077 99.7 %-
Displacement parametersBiso max: 68.64 Å2 / Biso mean: 39.57 Å2 / Biso min: 23.44 Å2
Baniso -1Baniso -2Baniso -3
1--2.9262 Å20 Å2-5.6874 Å2
2--11.1402 Å20 Å2
3----8.214 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 2.35→52.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 106 171 2288
Biso mean--52.93 43.33 -
Num. residues----258
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d920SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes371HARMONIC5
X-RAY DIFFRACTIONt_it2195HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion296SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1980SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2195HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3011HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion4.14
X-RAY DIFFRACTIONt_other_torsion2.67
LS refinement shellResolution: 2.35→2.38 Å / Rfactor Rfree error: 0 / Total num. of bins used: 24
RfactorNum. reflection% reflection
Rfree0.3932 18 3.16 %
Rwork0.2415 551 -
all0.2455 569 -
obs--97.78 %
Refinement TLS params.Method: refined / Origin x: -18.6497 Å / Origin y: 9.2656 Å / Origin z: -6.6764 Å
111213212223313233
T-0.0571 Å2-0.0142 Å20.028 Å2--0.1563 Å2-0.039 Å2--0.0027 Å2
L0.7249 °2-0.2306 °2-0.0071 °2-1.2822 °2-0.6026 °2--0.8145 °2
S-0.0348 Å °-0.0253 Å °0.0726 Å °-0.0703 Å °0.0642 Å °-0.1152 Å °0.0685 Å °0.0282 Å °-0.0294 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|132 - 380}A132 - 380
2X-RAY DIFFRACTION1{A|401 - 409}A401 - 409
3X-RAY DIFFRACTION1{A|501 - 501}A501
4X-RAY DIFFRACTION1{B|1 - 6}B1 - 6

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