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- PDB-1f8q: CRYSTAL STRUCTURE OF ALPHA-MOMORCHARIN IN ACETONITRILE-WATER MIXTURE -

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Basic information

Entry
Database: PDB / ID: 1f8q
TitleCRYSTAL STRUCTURE OF ALPHA-MOMORCHARIN IN ACETONITRILE-WATER MIXTURE
ComponentsALPHA-MOMORCHARIN
KeywordsHYDROLASE / RIBOSOME-INACTIVATING PROTEIN / ORGANIC SLOVENT / MOMORCHARIN
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / negative regulation of translation
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
ACETONITRILE / PENTANEDIAL / Ribosome-inactivating protein momordin I
Similarity search - Component
Biological speciesMomordica charantia (bitter melon)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsZhu, G. / Huang, Q. / Qian, M. / Tang, Y.
Citation
Journal: BIOCHIM.BIOPHYS.ACTA / Year: 2001
Title: Crystal structure of alpha-momorcharin in 80% acetonitrile--water mixture
Authors: Zhu, G. / Huang, Q. / Qian, M. / Tang, Y.
#1: Journal: BIOCHEM.J. / Year: 1995
Title: Studies on Crystal Structures, Active-Centre Geometry and Depurinating Mechanism of Two Ribosome-Inactivating Proteins
Authors: Huang, Q. / Liu, S. / Tang, Y. / Jin, S. / Wang, Y.
History
DepositionJul 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-MOMORCHARIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2197
Polymers29,1181
Non-polymers1,1016
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.510, 131.510, 39.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-395-

HOH

21A-396-

HOH

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Components

#1: Protein ALPHA-MOMORCHARIN


Mass: 29117.975 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: Polysaccharide alpha-D-xylopyranose-(1-2)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-xylopyranose-(1-2)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 718.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-2DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a212h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c2-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Xylp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-PTD / PENTANEDIAL / Glutaraldehyde


Mass: 100.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H8O2
#4: Chemical ChemComp-CCN / ACETONITRILE / Acetonitrile


Mass: 41.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3N
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: PEG 3350, Tris-HCl, ATP, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 4.1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mMHAc-NaAc1droppH4.1
23 mMATP1drop
314 mg/mlprotein1drop
420 mMTris-HCl1reservoir
520 %(w/v)PEG33501reservoirpH7.12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22941
Diffraction source
SourceTypeIDWavelength
ROTATING ANODERIGAKU RU30011.54178
ROTATING ANODERIGAKU RU30021.54178
Detector
TypeIDDetectorDate
RIGAKU RAXIS IIC1IMAGE PLATENov 22, 1999
RIGAKU RAXIS IIC2IMAGE PLATEJan 3, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→66 Å / Num. all: 12473 / Num. obs: 11526 / % possible obs: 85.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.252 / Num. unique all: 946 / % possible all: 70.2
Reflection
*PLUS
% possible obs: 85.2 % / Rmerge(I) obs: 0.056

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementResolution: 2.2→8 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.272 1033 RANDOM
Rwork0.198 --
all0.204 11256 -
obs0.204 11256 -
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 75 96 2102
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.42
X-RAY DIFFRACTIONx_dihedral_angle_d23.5
X-RAY DIFFRACTIONx_improper_angle_d1.28
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 11526 / σ(F): 2 / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.28

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