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- PDB-3ku0: Structure of GAP31 with adenine at its binding pocket -

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Basic information

Entry
Database: PDB / ID: 3ku0
TitleStructure of GAP31 with adenine at its binding pocket
ComponentsRibosome-inactivating protein gelonin
KeywordsHYDROLASE / Plant seeds / glycosidase / Disulfide bond / Glycoprotein / Plant defense / Protein synthesis inhibitor / Toxin
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / carbohydrate binding / negative regulation of translation / protein homodimerization activity
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
ADENINE / Ribosome-inactivating protein gelonin
Similarity search - Component
Biological speciesGelonium multiflorum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKong, X.-P.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: A new activity of anti-HIV and anti-tumor protein GAP31: DNA adenosine glycosidase--structural and modeling insight into its functions.
Authors: Li, H.G. / Huang, P.L. / Zhang, D. / Sun, Y. / Chen, H.C. / Zhang, J. / Huang, P.L. / Kong, X.P. / Lee-Huang, S.
History
DepositionNov 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Derived calculations / Category: chem_comp / reflns / struct_conn
Item: _chem_comp.type / _reflns.pdbx_Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome-inactivating protein gelonin
B: Ribosome-inactivating protein gelonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1316
Polymers56,4182
Non-polymers7134
Water3,153175
1
A: Ribosome-inactivating protein gelonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5663
Polymers28,2091
Non-polymers3562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribosome-inactivating protein gelonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5663
Polymers28,2091
Non-polymers3562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.373, 44.395, 137.270
Angle α, β, γ (deg.)90.000, 98.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribosome-inactivating protein gelonin / rRNA N-glycosidase


Mass: 28209.184 Da / Num. of mol.: 2 / Fragment: (UNP RESIDUES 47-297) / Source method: isolated from a natural source
Details: The enzyme is isolated from seeds of Gelonium multiflorum. The DNA oligo is synthesized by a commercial source.
Source: (natural) Gelonium multiflorum (plant) / Strain: Gelonium multiflorum / References: UniProt: P33186, rRNA N-glycosylase
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl, pH 8.5, 2.0 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11251
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12B11
SYNCHROTRONNSLS X26C21
SYNCHROTRONAPS 19-BM31
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 1, 2003
RadiationMonochromator: CCD / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→47.35 Å / Num. all: 48417 / Num. obs: 46674 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.041
Reflection shellResolution: 1.9→2.02 Å / % possible all: 71

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.35 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 521827 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2061 4.9 %RANDOM
Rwork0.2 ---
all0.2 46674 --
obs0.2 41738 90.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.488 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 79.66 Å2 / Biso mean: 21.911 Å2 / Biso min: 8.59 Å2
Baniso -1Baniso -2Baniso -3
1-6.76 Å20 Å22.48 Å2
2--0.58 Å20 Å2
3----7.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3976 0 48 175 4199
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it2.382
X-RAY DIFFRACTIONc_scangle_it3.632.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.245 288 5.3 %
Rwork0.247 5132 -
all-5420 -
obs--71 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4dna-rna_rep.paramcarbohydrate.top

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