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- PDB-6loq: crystal structure of alpha-momorcharin in complex with cAMP -

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Basic information

Entry
Database: PDB / ID: 6loq
Titlecrystal structure of alpha-momorcharin in complex with cAMP
ComponentsRibosome-inactivating protein momordin I
KeywordsPLANT PROTEIN / alpha-momorcharin / Alpha-MMC / ribosome-inactivating protein / rRNA N-glycosidase / cAMP
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-3',5'-CYCLIC-MONOPHOSPHATE / Ribosome-inactivating protein momordin I
Similarity search - Component
Biological speciesMomordica charantia (bitter melon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.331 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

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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)31,8922
Polymers31,5631
Non-polymers3291
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-0 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.471, 130.471, 39.673
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: cAMP / Source: (natural) Momordica charantia (bitter melon) / References: UniProt: P16094, rRNA N-glycosylase
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.26 %
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: 1.33→50 Å / Num. obs: 55352 / % possible obs: 96 % / Redundancy: 5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.044 / Rrim(I) all: 0.092 / Net I/σ(I): 14.2
Reflection shellResolution: 1.33→1.38 Å / Rmerge(I) obs: 0.943 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5700 / CC1/2: 0.683 / Rpim(I) all: 0.46

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000V718data reduction
HKL-2000V718data scaling
MOLREPV11.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F8Q

1f8q


Resolution: 1.331→24.604 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.857 / WRfactor Rfree: 0.279 / WRfactor Rwork: 0.236 / SU B: 2.801 / SU ML: 0.053 / Average fsc free: 0.8302 / Average fsc work: 0.8321 / Cross valid method: FREE R-VALUE / ESU R: 0.066 / ESU R Free: 0.071
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2572 2788 5.037 %
Rwork0.2157 52564 -
all0.218 --
obs-55352 95.879 %
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: 25.452 Å2
Baniso -1Baniso -2Baniso -3
1--0.802 Å2-0.401 Å20 Å2
2---0.802 Å20 Å2
3---2.602 Å2
Refinement stepCycle: LAST / Resolution: 1.331→24.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1932 0 22 196 2150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131993
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171875
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.6642713
X-RAY DIFFRACTIONr_angle_other_deg1.4251.5754333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8385245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86321.442104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97315334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9991516
X-RAY DIFFRACTIONr_chiral_restr0.0720.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
X-RAY DIFFRACTIONr_nbd_refined0.210.2379
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.21788
X-RAY DIFFRACTIONr_nbtor_refined0.170.2997
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2855
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2129
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.060.23
X-RAY DIFFRACTIONr_nbd_other0.1670.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1260.26
X-RAY DIFFRACTIONr_mcbond_it1.1012.081983
X-RAY DIFFRACTIONr_mcbond_other1.12.079982
X-RAY DIFFRACTIONr_mcangle_it1.6413.121227
X-RAY DIFFRACTIONr_mcangle_other1.6413.1221228
X-RAY DIFFRACTIONr_scbond_it1.7222.4181010
X-RAY DIFFRACTIONr_scbond_other1.7222.4181010
X-RAY DIFFRACTIONr_scangle_it2.6683.5511486
X-RAY DIFFRACTIONr_scangle_other2.6673.5561487
X-RAY DIFFRACTIONr_lrange_it4.4926.1692268
X-RAY DIFFRACTIONr_lrange_other4.48926.1752269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.331-1.3660.3751870.3533975X-RAY DIFFRACTION97.3795
1.366-1.4030.3331860.3233970X-RAY DIFFRACTION100
1.403-1.4440.3111970.293835X-RAY DIFFRACTION100
1.444-1.4880.2622320.2563702X-RAY DIFFRACTION100
1.488-1.5370.2511730.2223660X-RAY DIFFRACTION100
1.537-1.5910.2311990.2013515X-RAY DIFFRACTION100
1.591-1.6510.2371860.23344X-RAY DIFFRACTION100
1.651-1.7180.2231840.1933217X-RAY DIFFRACTION100
1.718-1.7940.231790.1933096X-RAY DIFFRACTION100
1.794-1.8820.2191470.1973005X-RAY DIFFRACTION99.9683
1.882-1.9840.191252806X-RAY DIFFRACTION98.6869
1.984-2.1040.2181350.1972693X-RAY DIFFRACTION99.894
2.104-2.2490.2221480.1942451X-RAY DIFFRACTION98.1866
2.249-2.4290.2321170.1922240X-RAY DIFFRACTION95.6575
2.429-2.660.2651290.1992111X-RAY DIFFRACTION98.0736
2.66-2.9740.2361110.2031818X-RAY DIFFRACTION94.0517
2.974-3.4330.262630.2251463X-RAY DIFFRACTION84.7778
3.433-4.2010.306440.233776X-RAY DIFFRACTION53.1432
4.201-5.9290.26531617X-RAY DIFFRACTION54.9153
5.929-100.775150.346270X-RAY DIFFRACTION43.7788
Refinement TLS params.Method: refined / Origin x: -20.4672 Å / Origin y: -12.6721 Å / Origin z: 0.0318 Å
111213212223313233
T0.0246 Å2-0.0159 Å2-0.0057 Å2-0.0259 Å20.0119 Å2--0.0245 Å2
L0.9848 °2-0.178 °2-0.3474 °2-0.5506 °2-0.0482 °2--0.1529 °2
S0.0436 Å °0.0518 Å °-0.0459 Å °0.0708 Å °-0.0437 Å °0.0183 Å °-0.0316 Å °-0.018 Å °0 Å °
Refinement TLS groupSelection: ALL

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