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- PDB-6lp0: crystal structure of alpha-momorcharin in complex with AMP -

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Basic information

Entry
Database: PDB / ID: 6lp0
Titlecrystal structure of alpha-momorcharin in complex with AMP
ComponentsRibosome-inactivating protein momordin I
KeywordsPLANT PROTEIN / alpha-momorcharin / ribosome-inactivating protein / rRNA N-glycosidase / AMP
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 MONOPHOSPHATE / Ribosome-inactivating protein momordin I
Similarity search - Component
Biological speciesMomordica charantia (bitter melon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.519 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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 13, 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)32,1313
Polymers31,5631
Non-polymers5682
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint4 kcal/mol
Surface area11550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.347, 131.347, 37.297
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 / Source: (natural) Momordica charantia (bitter melon) / References: UniProt: P16094, rRNA N-glycosylase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*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.: 202 / 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: 1.96 Å3/Da / Density % sol: 37.3 %
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: 1.519→50 Å / Num. obs: 29931 / % possible obs: 81.4 % / Redundancy: 2.7 % / CC1/2: 0.969 / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.7
Reflection shellResolution: 1.52→1.57 Å / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 3.53 / Num. unique obs: 3589 / CC1/2: 0.896

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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: 1.519→15.734 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.87 / WRfactor Rfree: 0.347 / WRfactor Rwork: 0.283 / SU B: 4.672 / SU ML: 0.085 / Average fsc free: 0.8432 / Average fsc work: 0.8636 / Cross valid method: FREE R-VALUE / ESU R: 0.136 / ESU R Free: 0.137
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.299 1547 5.169 %
Rwork0.2461 28384 -
all0.249 --
obs-29931 80.812 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.449 Å2
Baniso -1Baniso -2Baniso -3
1--1.149 Å2-0.575 Å20 Å2
2---1.149 Å20 Å2
3---3.729 Å2
Refinement stepCycle: LAST / Resolution: 1.519→15.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 37 202 2163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132008
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171887
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.6722734
X-RAY DIFFRACTIONr_angle_other_deg1.4381.5844363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4155246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04121.442104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02315334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.0081516
X-RAY DIFFRACTIONr_chiral_restr0.080.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022229
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02427
X-RAY DIFFRACTIONr_nbd_refined0.2290.2431
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.21874
X-RAY DIFFRACTIONr_nbtor_refined0.170.2996
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2923
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2114
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3070.230
X-RAY DIFFRACTIONr_nbd_other0.3160.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1940.217
X-RAY DIFFRACTIONr_mcbond_it1.0841.891984
X-RAY DIFFRACTIONr_mcbond_other1.0811.889983
X-RAY DIFFRACTIONr_mcangle_it1.6322.8351230
X-RAY DIFFRACTIONr_mcangle_other1.6322.8371231
X-RAY DIFFRACTIONr_scbond_it1.7472.151024
X-RAY DIFFRACTIONr_scbond_other1.7462.1511025
X-RAY DIFFRACTIONr_scangle_it2.6913.1441504
X-RAY DIFFRACTIONr_scangle_other2.693.1461505
X-RAY DIFFRACTIONr_lrange_it4.21723.452307
X-RAY DIFFRACTIONr_lrange_other4.12523.0872278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.519-1.5580.3221230.262268X-RAY DIFFRACTION87.1673
1.558-1.6010.2921050.252530X-RAY DIFFRACTION98.3209
1.601-1.6470.2771310.2432383X-RAY DIFFRACTION97.669
1.647-1.6980.281720.2352320X-RAY DIFFRACTION97.3438
1.698-1.7530.2631220.2262220X-RAY DIFFRACTION97.0576
1.753-1.8150.2851040.2282133X-RAY DIFFRACTION94.5877
1.815-1.8830.2321090.2172038X-RAY DIFFRACTION94.4151
1.883-1.960.337910.221955X-RAY DIFFRACTION92.6211
1.96-2.0470.266780.2161753X-RAY DIFFRACTION87.149
2.047-2.1470.255920.2161564X-RAY DIFFRACTION82.9659
2.147-2.2630.272910.2141447X-RAY DIFFRACTION79.6891
2.263-2.40.274860.2411303X-RAY DIFFRACTION76.1096
2.4-2.5660.311680.2441157X-RAY DIFFRACTION72.9601
2.566-2.7710.315590.253989X-RAY DIFFRACTION66.7516
2.771-3.0350.301470.273850X-RAY DIFFRACTION60.8548
3.035-3.3920.349330.296596X-RAY DIFFRACTION47.6154
3.392-3.9150.363150.284382X-RAY DIFFRACTION34.612
3.915-4.7910.526120.304208X-RAY DIFFRACTION22.2898
4.791-6.7580.49570.359223X-RAY DIFFRACTION30.3831
6.758-100.244265X-RAY DIFFRACTION
Refinement TLS params.Method: refined / Origin x: 21.2002 Å / Origin y: 11.4001 Å / Origin z: 0.0029 Å
111213212223313233
T0.0264 Å2-0.0044 Å20.0043 Å2-0.0312 Å2-0.0052 Å2--0.002 Å2
L0.1307 °20.0803 °2-0.0422 °2-0.2662 °2-0.0998 °2--0.0444 °2
S0.007 Å °-0.0078 Å °-0.0043 Å °-0.0059 Å °-0.0105 Å °-0.0059 Å °0.0036 Å °0.0084 Å °0.0036 Å °
Refinement TLS groupSelection: ALL

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