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- PDB-6lor: crystal structure of alpha-momorcharin in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 6lor
Titlecrystal structure of alpha-momorcharin in complex with ADP
ComponentsRibosome-inactivating protein momordin I
KeywordsPLANT PROTEIN / alpha-momorcharin / Alpha-MMC / ribosome-inactivating protein / rRNA N-glycosidase / ADP
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
ADENOSINE-5'-DIPHOSPHATE / Ribosome-inactivating protein momordin I
Similarity search - Component
Biological speciesMomordica charantia (bitter melon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 1.2Nov 6, 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)32,2113
Polymers31,5631
Non-polymers6482
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint1 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.361, 130.361, 39.333
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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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 / Details: ADP / Source: (natural) Momordica charantia (bitter melon) / References: UniProt: P16094, rRNA N-glycosylase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#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.: 238 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
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: 1.349→50 Å / Num. obs: 52449 / % possible obs: 95.7 % / Redundancy: 3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16
Reflection shellResolution: 1.35→1.4 Å / Rmerge(I) obs: 0.587 / Num. unique obs: 5445 / CC1/2: 0.723

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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: 1.35→24.509 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.081 / SU ML: 0.061 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2511 2591 4.94 %
Rwork0.2179 --
all0.219 --
obs-52449 95.664 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.379 Å2
Baniso -1Baniso -2Baniso -3
1--0.566 Å2-0.283 Å2-0 Å2
2---0.566 Å20 Å2
3---1.838 Å2
Refinement stepCycle: LAST / Resolution: 1.35→24.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 41 238 2203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132020
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171890
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.6772755
X-RAY DIFFRACTIONr_angle_other_deg1.4361.5844372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9445248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9421.442104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94815335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1971516
X-RAY DIFFRACTIONr_chiral_restr0.0750.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022243
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02428
X-RAY DIFFRACTIONr_nbd_refined0.2050.2406
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.21773
X-RAY DIFFRACTIONr_nbtor_refined0.170.21005
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2913
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2163
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0410.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.214
X-RAY DIFFRACTIONr_nbd_other0.240.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1130.210
X-RAY DIFFRACTIONr_mcbond_it1.0611.865989
X-RAY DIFFRACTIONr_mcbond_other1.0561.863988
X-RAY DIFFRACTIONr_mcangle_it1.6142.7941238
X-RAY DIFFRACTIONr_mcangle_other1.6142.7961239
X-RAY DIFFRACTIONr_scbond_it1.6032.1241031
X-RAY DIFFRACTIONr_scbond_other1.6022.1271032
X-RAY DIFFRACTIONr_scangle_it2.5433.1131517
X-RAY DIFFRACTIONr_scangle_other2.5433.1161518
X-RAY DIFFRACTIONr_lrange_it4.81523.8652342
X-RAY DIFFRACTIONr_lrange_other4.81523.872343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3840.3322030.3323816X-RAY DIFFRACTION99.7766
1.384-1.4220.2842203716X-RAY DIFFRACTION99.9746
1.422-1.4630.3091630.2833713X-RAY DIFFRACTION100
1.463-1.5090.3081870.2753529X-RAY DIFFRACTION99.9193
1.509-1.5580.2471770.2423454X-RAY DIFFRACTION99.9174
1.558-1.6130.2481630.2313302X-RAY DIFFRACTION99.8847
1.613-1.6730.2731680.2253226X-RAY DIFFRACTION99.8529
1.673-1.7420.2821750.2233062X-RAY DIFFRACTION99.692
1.742-1.8190.2611700.2192953X-RAY DIFFRACTION99.522
1.819-1.9080.2611440.2112798X-RAY DIFFRACTION98.924
1.908-2.0110.2491320.2072619X-RAY DIFFRACTION97.7959
2.011-2.1330.2141180.2092501X-RAY DIFFRACTION97.6874
2.133-2.280.231220.1962298X-RAY DIFFRACTION96.0699
2.28-2.4620.2081170.1962138X-RAY DIFFRACTION95.8758
2.462-2.6970.225830.1891979X-RAY DIFFRACTION95.6401
2.697-3.0150.259850.2071681X-RAY DIFFRACTION90.7036
3.015-3.480.243760.2151374X-RAY DIFFRACTION84.1067
3.48-4.2590.262430.21890X-RAY DIFFRACTION64.1678
4.259-6.010.293300.25575X-RAY DIFFRACTION54.0661
6.01-100.34415234X-RAY DIFFRACTION39.9679
Refinement TLS params.Method: refined / Origin x: -0.7554 Å / Origin y: -23.9883 Å / Origin z: 0.0407 Å
111213212223313233
T0.0215 Å2-0.0094 Å2-0.0142 Å2-0.0243 Å20.0001 Å2--0.0546 Å2
L1.4131 °2-0.4716 °2-0.2095 °2-1.1112 °20.5694 °2--0.2953 °2
S-0.1278 Å °0.0277 Å °-0.0298 Å °0.0006 Å °0.1349 Å °0.0212 Å °0.0008 Å °0.0744 Å °-0.007 Å °
Refinement TLS groupSelection: ALL

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