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- PDB-1gik: POKEWEED ANTIVIRAL PROTEIN FROM SEEDS -

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Basic information

Entry
Database: PDB / ID: 1gik
TitlePOKEWEED ANTIVIRAL PROTEIN FROM SEEDS
ComponentsANTIVIRAL PROTEIN S
KeywordsHYDROLASE / ALPHA+BETA
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / defense response to virus / negative regulation of translation
Similarity search - Function
Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPhytolacca americana (American pokeweed)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZeng, Z.H. / He, X.L. / Li, H.M. / Hu, Z. / Wang, D.C.
Citation
Journal: J.Struct.Biol. / Year: 2003
Title: Crystal structure of pokeweed antiviral protein with well-defined sugars from seeds at 1.8 angstrom resolution
Authors: Zeng, Z.H. / He, X.L. / Li, H.M. / Hu, Z. / Wang, D.C.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1998
Title: CRYSTALLIZATION AND PERLIMINARY CRYSTALLOGRAPHIC ANALYSES OF POKEWEED ANTIVIRAL PROTEIN FROM SEEDS
Authors: Li, H.M. / Zeng, Z.H. / Hu, Z. / Wang, D.C.
#2: Journal: SCI.CHINA, SER.C: LIFE SCI. / Year: 1998
Title: CRYSTAL STRUCTURE OF A POKEWEED ANTIVIRAL PROTEIN FROM SEEDS OF PHYTOLACCA AMERICANA AT 0.25 NM
Authors: Zeng, Z.H. / JIN, L. / LI, H.M. / HU, Z. / Wang, D.C.
#3: Journal: Eur.J.Biochem. / Year: 1994
Title: X-ray Structure of a Pokeweed Antiviral Protein, Coded by a New Genomic Clone, at 0.23 nm resolution. A Model Structure Provides a Suitable Electrostatic Field for Substrate Binding
Authors: Ago, H. / Kataoka, J. / Tsuge, H. / Habuka, N. / Inagaki, E. / Noma, M. / Miyano, M.
#4: Journal: J.Mol.Biol. / Year: 1993
Title: The 2.5 A Structure of Pokeweed Antiviral Protein
Authors: Monzingo, A.F. / Collins, E.J. / Erust, S.R. / Irvin, J.D. / Robertus, J.D.
History
DepositionFeb 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTIVIRAL PROTEIN S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8984
Polymers29,2341
Non-polymers6643
Water10,701594
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.76, 78.05, 91.57
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-327-

HOH

21A-433-

HOH

31A-550-

HOH

41A-553-

HOH

51A-556-

HOH

61A-895-

HOH

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Components

#1: Protein ANTIVIRAL PROTEIN S / RIBOSOME-INACTIVATING PROTEIN


Mass: 29234.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phytolacca americana (American pokeweed) / References: UniProt: P23339, rRNA N-glycosylase
#2: 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.: 3
Source method: isolated from a genetically manipulated source
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 305 K / Method: evaporation / pH: 5.5
Details: PEG6000 SODIUM PHOSPHATE, pH 5.5, EVAPORATION, temperature 305K
Crystal grow
*PLUS
Temperature: 306 K / Method: vapor diffusion
Details: Li, H.M., (1998) ACTA CRYSTALLOGR.,SECT.D, 54, 137.
PH range low: 6 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1100 mg/mlprotein1drop
20.03 N1dropNaCl
330 %(w/v)PEG60001drop
40.2 M1dropNaH2PO4pH5.0-6.0
530 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Apr 22, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 19809 / Num. obs: 19619 / % possible obs: 69.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.062
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2 % / % possible all: 52.5
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 23204 / % possible obs: 82 % / Num. measured all: 68617
Reflection shell
*PLUS
Lowest resolution: 1.88 Å / % possible obs: 69.5 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 8.5

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Processing

Software
NameVersionClassification
WEISdata scaling
CCP4data reduction
AMoREphasing
X-PLOR3.851refinement
WEISdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PAF

1paf


Resolution: 1.8→19.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2754268.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1894 9.7 %RANDOM
Rwork0.183 ---
obs0.183 19619 68.8 %-
all-28503 --
Displacement parametersBiso mean: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 42 594 2689
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.04
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 270 10.9 %
Rwork0.294 2198 -
obs--53 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 23204 / σ(F): 0 / Rfactor Rfree: 0.242 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.698
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.04
LS refinement shell
*PLUS
Lowest resolution: 1.88 Å / Rfactor Rfree: 0.294 / Rfactor Rwork: 0.288

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