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- PDB-6loz: crystal structure of alpha-momorcharin in complex with adenine -

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Basic information

Entry
Database: PDB / ID: 6loz
Titlecrystal structure of alpha-momorcharin in complex with adenine
ComponentsRibosome-inactivating protein momordin I
KeywordsPLANT PROTEIN / alpha-momorcharin / ribosome-inactivating protein / rRNA N-glycosidase / adenine
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / negative regulation of translation
Similarity search - Function
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
Similarity search - Domain/homology
ADENINE / Ribosome-inactivating protein momordin I
Similarity search - Component
Biological speciesMomordica charantia (bitter melon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsFan, X. / Jin, T.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Atomic-resolution structures of type I ribosome inactivating protein alpha-momorcharin with different substrate analogs.
Authors: Fan, X. / Wang, Y. / Guo, F. / Zhang, Y. / Jin, T.
History
DepositionJan 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 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: Ribosome-inactivating protein momordin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9193
Polymers31,5631
Non-polymers3562
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint7 kcal/mol
Surface area11420 Å2
Unit cell
Length a, b, c (Å)131.167, 131.167, 37.145
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-676-

HOH

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Components

#1: Protein Ribosome-inactivating protein momordin I / Alpha-momorcharin / Alpha-MMC / rRNA N-glycosidase


Mass: 31562.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Momordica charantia (bitter melon) / References: UniProt: P16094, rRNA N-glycosylase
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#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: 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.: 276 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.95 Å3/Da / Density % sol: 36.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Magnesium Acetate, 20% PEG 8000, 0.1 M Sodium cacodylate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.08→50 Å / Num. obs: 96174 / % possible obs: 93.9 % / Redundancy: 3.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.084 / Net I/σ(I): 11
Reflection shellResolution: 1.08→1.12 Å / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2 / Num. unique obs: 10245 / CC1/2: 0.649

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F8Q

1f8q


Resolution: 1.08→24.038 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.204 / SU ML: 0.028 / Cross valid method: FREE R-VALUE / ESU R: 0.038 / ESU R Free: 0.039
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2215 4939 5.135 %
Rwork0.2024 --
all0.203 --
obs-96174 93.841 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.437 Å2
Baniso -1Baniso -2Baniso -3
1--0.259 Å2-0.129 Å2-0 Å2
2---0.259 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.08→24.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 24 276 2224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132032
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171913
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.6612770
X-RAY DIFFRACTIONr_angle_other_deg1.5751.584424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8755255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88321.442104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27815341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4481516
X-RAY DIFFRACTIONr_chiral_restr0.090.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022293
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02438
X-RAY DIFFRACTIONr_nbd_refined0.2190.2413
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.21844
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21032
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2976
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2133
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2450.212
X-RAY DIFFRACTIONr_nbd_other0.1850.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1050.214
X-RAY DIFFRACTIONr_mcbond_it0.9031.3121008
X-RAY DIFFRACTIONr_mcbond_other0.8991.3111007
X-RAY DIFFRACTIONr_mcangle_it1.3631.9721267
X-RAY DIFFRACTIONr_mcangle_other1.3631.9731268
X-RAY DIFFRACTIONr_scbond_it1.611.5391024
X-RAY DIFFRACTIONr_scbond_other1.6091.541025
X-RAY DIFFRACTIONr_scangle_it2.4582.231503
X-RAY DIFFRACTIONr_scangle_other2.4572.2311504
X-RAY DIFFRACTIONr_lrange_it3.80816.7822347
X-RAY DIFFRACTIONr_lrange_other3.58116.0872287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.1070.373890.347197X-RAY DIFFRACTION99.8815
1.107-1.1380.3114020.3087000X-RAY DIFFRACTION99.9055
1.138-1.1710.2763380.276804X-RAY DIFFRACTION99.7347
1.171-1.2070.2643740.246595X-RAY DIFFRACTION99.5714
1.207-1.2460.2293630.2276359X-RAY DIFFRACTION99.5262
1.246-1.290.2173220.2116137X-RAY DIFFRACTION99.2014
1.29-1.3390.2163400.25951X-RAY DIFFRACTION99.2428
1.339-1.3930.2113030.1935691X-RAY DIFFRACTION98.7642
1.393-1.4550.2082850.1795448X-RAY DIFFRACTION98.7087
1.455-1.5260.1892950.1675172X-RAY DIFFRACTION98.6289
1.526-1.6090.1952600.1664937X-RAY DIFFRACTION97.8719
1.609-1.7060.1882620.1734655X-RAY DIFFRACTION97.4049
1.706-1.8240.1912050.1734312X-RAY DIFFRACTION97.0146
1.824-1.970.1941940.1813992X-RAY DIFFRACTION95.3531
1.97-2.1580.2121900.1753542X-RAY DIFFRACTION92.5825
2.158-2.4120.1961740.1813009X-RAY DIFFRACTION87.5894
2.412-2.7850.2361280.2072372X-RAY DIFFRACTION78.0275
2.785-3.4090.241830.2471389X-RAY DIFFRACTION53.9985
3.409-4.8150.387260.352443X-RAY DIFFRACTION22.3866
4.815-100.97960.603230X-RAY DIFFRACTION20.38
Refinement TLS params.Method: refined / Origin x: -20.4994 Å / Origin y: -12.5941 Å / Origin z: -0.0161 Å
111213212223313233
T0.014 Å2-0.0055 Å20.0015 Å2-0.03 Å20.009 Å2--0.0057 Å2
L0.5383 °2-0.0486 °2-0.1692 °2-0.1108 °2-0.0147 °2--0.1079 °2
S-0.0309 Å °0.0172 Å °-0.0147 Å °0.0116 Å °0.0155 Å °-0.0022 Å °0.0246 Å °-0.0059 Å °0.0153 Å °
Refinement TLS groupSelection: ALL

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