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- PDB-1bk7: RIBONUCLEASE MC1 FROM THE SEEDS OF BITTER GOURD -

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Basic information

Entry
Database: PDB / ID: 1bk7
TitleRIBONUCLEASE MC1 FROM THE SEEDS OF BITTER GOURD
ComponentsPROTEIN (RIBONUCLEASE MC1)
KeywordsHYDROLASE / HYDROLASE (NUCLEIC ACID / RNA)
Function / homology
Function and homology information


ribonuclease T2 / ribonuclease T2 activity / RNA catabolic process / RNA binding / extracellular region
Similarity search - Function
Ribonuclease T2, eukaryotic / Ribonuclease T2, His active site 1 / Ribonuclease T2 family histidine active site 1. / Ribonuclease T2-like / Ribonuclease T2 family / Ribonuclease Rh; Chain A / Ribonuclease T2-like / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily ...Ribonuclease T2, eukaryotic / Ribonuclease T2, His active site 1 / Ribonuclease T2 family histidine active site 1. / Ribonuclease T2-like / Ribonuclease T2 family / Ribonuclease Rh; Chain A / Ribonuclease T2-like / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesMomordica charantia (bitter melon)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.75 Å
AuthorsNakagawa, A. / Tanaka, I.
Citation
Journal: Biochim.Biophys.Acta / Year: 1999
Title: Crystal structure of a ribonuclease from the seeds of bitter gourd (Momordica charantia) at 1.75 A resolution.
Authors: Nakagawa, A. / Tanaka, I. / Sakai, R. / Nakashima, T. / Funatsu, G. / Kimura, M.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of a Plant Ribonuclease from the Seeds of the Bitter Gourd Momordica Charantia
Authors: De, A. / Funatsu, G.
#2: Journal: FEBS Lett. / Year: 1991
Title: The Complete Amino Acid Sequence of Ribonuclease from the Seeds of Bitter Gourd
Authors: Ide, H. / Kimura, M. / Arai, M. / Funatsu, G.
#3: Journal: FEBS Lett. / Year: 1991
Title: The Complete Amino Acid Sequence of Ribonuclease from the Seeds of Bitter Gourd
Authors: Ide, H. / Kimura, M. / Arai, M. / Funatsu, G.
History
DepositionJul 15, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (RIBONUCLEASE MC1)


Theoretical massNumber of molelcules
Total (without water)21,2271
Polymers21,2271
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.800, 67.970, 75.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (RIBONUCLEASE MC1) / RNASE MC1


Mass: 21227.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Momordica charantia (bitter melon) / Tissue: SEED / References: UniProt: P23540, EC: 3.1.27.1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47 %
Crystal growpH: 6.7
Details: PROTEN WAS CRYSTALLIZED FROM THE 1:1 MIXTURE OF 10MG/ML PROTEIN SOLUTION IN 5MM TRIS-HCL PH7.2 AND 30% PEG 6000, 0.2M NA-ACETATE, 0.1M NA-CACODYLATE PH 6.7
Crystal grow
*PLUS
Method: other / Details: De, A., (1991) J. Mol. Biol., 228, 1271.

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 15, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.75 Å / Num. obs: 69704 / % possible obs: 98.4 % / Observed criterion σ(I): 4 / Redundancy: 3.4 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.1
Reflection shellResolution: 1.75→1.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 3.5 / % possible all: 98.2
Reflection
*PLUS
Num. obs: 20323 / Num. measured all: 69704
Reflection shell
*PLUS
% possible obs: 98.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
SHARPphasing
X-PLOR3.851refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.75→100 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1031 5.1 %RANDOM
Rwork0.192 ---
obs0.192 20257 97.6 %-
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.75→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 0 187 1683
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.62
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.511.5
X-RAY DIFFRACTIONx_mcangle_it2.272
X-RAY DIFFRACTIONx_scbond_it2.832
X-RAY DIFFRACTIONx_scangle_it4.382.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.364 168 5.2 %
Rwork0.327 3042 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2WAT.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.62
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.364 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.327

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