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- PDB-1cf5: BETA-MOMORCHARIN STRUCTURE AT 2.55 A -

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Basic information

Entry
Database: PDB / ID: 1cf5
TitleBETA-MOMORCHARIN STRUCTURE AT 2.55 A
ComponentsPROTEIN (BETA-MOMORCHARIN)
KeywordsRIBOSOME-INACTIVATING PROTEIN / RNA N-GLYCOSIDASE ACTIVITY / GLYCOPROTEIN
Function / homology
Function and homology information


regulation of defense response to virus / 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
Ribosome-inactivating protein beta-momorcharin / Ribosome-inactivating protein momordin II
Similarity search - Component
Biological speciesMomordica charantia (bitter melon)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsYuan, Y.-R. / He, Y.-N. / Xiong, J.-P. / Xia, Z.-X.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Three-dimensional structure of beta-momorcharin at 2.55 A resolution.
Authors: Yuan, Y.R. / He, Y.N. / Xiong, J.P. / Xia, Z.X.
#1: Journal: Chin.Chem.Lett. / Year: 1995
Title: The Determination and Refinement of Three-Dimensional Structure of Beta- Momorcharin at 2.4 A Resolution
Authors: Yuan, Y.-R. / Xiong, J.-P. / Xia, Z.-X.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and preliminary crystallographic study of beta-momorcharin.
Authors: Xiong, J.P. / Xia, Z.X. / Zhang, L. / Ye, G.J. / Jin, S.W. / Wang, Y.
History
DepositionMar 24, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 7, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 13, 2019Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_conn / struct_ref_seq_dif
Item: _chem_comp.type / _citation.page_last ..._chem_comp.type / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (BETA-MOMORCHARIN)
B: PROTEIN (BETA-MOMORCHARIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3004
Polymers56,2462
Non-polymers2,0542
Water1,22568
1
A: PROTEIN (BETA-MOMORCHARIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1502
Polymers28,1231
Non-polymers1,0271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (BETA-MOMORCHARIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1502
Polymers28,1231
Non-polymers1,0271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.090, 50.580, 61.120
Angle α, β, γ (deg.)72.98, 78.39, 76.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PROTEIN (BETA-MOMORCHARIN)


Mass: 28122.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Momordica charantia (bitter melon) / References: UniProt: P29339, UniProt: P24817*PLUS
#2: Polysaccharide beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1026.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-2[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a212h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-5/a3-b1_a4-c1_c4-d1_d2-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-6-deoxy-Altp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Xylp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growpH: 6.1 / Details: pH 6.10
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 %(w/v)PEG80001drop
20.1 Mphosphate1drop
31.5 %(w/v)protein1drop
428 %(w/v)PEG80001reservoir
50.2 Mphosphate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.41→40 Å / Num. obs: 17215 / % possible obs: 74 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 16
Reflection shellResolution: 2.41→2.56 Å / % possible all: 30
Reflection shell
*PLUS
% possible obs: 30 %

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Processing

Software
NameVersionClassification
MERLOTphasing
X-PLOR3.1refinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→10 Å / Rfactor Rfree error: 0.011 / Cross valid method: IN THE LATE STAGE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.278 697 5.1 %RANDOM
Rwork0.172 ---
obs0.172 13774 79.3 %-
Refinement stepCycle: LAST / Resolution: 2.55→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3982 0 138 68 4188
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.66
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.55→2.66 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.356 70 6.2 %
Rwork0.268 1125 -
obs--51.9 %
Xplor fileSerial no: 1 / Param file: A
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.66

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