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- PDB-3zfr: Crystal structure of product-like, processed N-terminal protease ... -

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Basic information

Entry
Database: PDB / ID: 3zfr
TitleCrystal structure of product-like, processed N-terminal protease Npro with iridium
ComponentsN-TERMINAL PROTEASE NPRO
KeywordsHYDROLASE / AUTO-PROCESSING CYSTEINE PROTEASE / VIRAL PROTEASE / IN CIS- CLEAVAGE / HYDROXIDE-DEPENDENT CATALYSIS / AUTO-PROTEOLYSIS / IMMUNE MODULATION / HOST-PATHOGEN INTERACTION / CONVERGENT EVOLUTION
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / viral protein processing / cysteine-type endopeptidase activity / proteolysis
Similarity search - Function
Pestivirus Npro endopeptidase C53, interaction domain / Peptidase C53, pestivirus Npro, interaction domain / Peptidase C53, pestivirus Npro / Pestivirus Npro endopeptidase C53 / Pestivirus N-terminal protease Npro domain profile. / Spermidine Synthase; Chain: A, domain 2 / Roll / Mainly Beta
Similarity search - Domain/homology
IRIDIUM (III) ION / HYDROXIDE ION / MONOTHIOGLYCEROL / Nonstructural protein
Similarity search - Component
Biological speciesPESTIVIRUS STRAIN D32/00_HOBI
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZogg, T. / Sponring, M. / Schindler, S. / Koll, M. / Schneider, R. / Brandstetter, H. / Auer, B.
CitationJournal: Structure / Year: 2013
Title: Crystal Structures of the Viral Protease Npro Imply Distinct Roles for the Catalytic Water in Catalysis
Authors: Zogg, T. / Sponring, M. / Schindler, S. / Koll, M. / Schneider, R. / Brandstetter, H. / Auer, B.
History
DepositionDec 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references / Refinement description
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-TERMINAL PROTEASE NPRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0685
Polymers16,5581
Non-polymers5104
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.770, 41.070, 43.560
Angle α, β, γ (deg.)90.00, 114.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein N-TERMINAL PROTEASE NPRO / NONSTRUCTURAL PROTEIN


Mass: 16558.031 Da / Num. of mol.: 1 / Fragment: NPRO, RESIDUES 22-168 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PESTIVIRUS STRAIN D32/00_HOBI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5L4B1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-SGM / MONOTHIOGLYCEROL


Mass: 108.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2S
#3: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#4: Chemical ChemComp-IR3 / IRIDIUM (III) ION


Mass: 192.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ir
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 8.5 / Details: 100MM NAACETATE, PH 8.5 50% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20.5 Å / Num. obs: 12457 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZFN

3zfn


Resolution: 1.8→20.54 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 145-150 DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.22836 632 5.1 %RANDOM
Rwork0.17959 ---
obs0.18199 11801 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.102 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å2-1.05 Å2
2---0.25 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 0 9 74 1245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191203
X-RAY DIFFRACTIONr_bond_other_d00.021142
X-RAY DIFFRACTIONr_angle_refined_deg1.9871.9841638
X-RAY DIFFRACTIONr_angle_other_deg3.6723.0052634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.865152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19723.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.92715194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.62158
X-RAY DIFFRACTIONr_chiral_restr0.1210.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211356
X-RAY DIFFRACTIONr_gen_planes_other0.0260.02267
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 52 -
Rwork0.307 778 -
obs--90.91 %

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