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- PDB-1ucg: Crystal structure of Ribonuclease MC1 N71T mutant -

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Basic information

Entry
Database: PDB / ID: 1ucg
TitleCrystal structure of Ribonuclease MC1 N71T mutant
ComponentsRibonuclease MC
KeywordsHYDROLASE / alpha plus beta
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSuzuki, A. / Numata, T. / Yao, M. / Tanaka, I. / Kimura, M.
Citation
Journal: Biochemistry / Year: 2003
Title: Crystal structures of the ribonuclease MC1 mutants N71T and N71S in complex with 5'-GMP: structural basis for alterations in substrate specificity
Authors: Numata, T. / Suzuki, A. / Kakuta, Y. / Kimura, K. / Yao, M. / Tanaka, I. / Yoshida, Y. / Ueda, T. / Kimura, M.
#1: Journal: Biochemistry / Year: 2001
Title: Amino acid residues in ribonuclease MC1 from bitter gourd seeds which are essential for uridine specificity
Authors: Numata, T. / Suzuki, A. / Yao, M. / Tanaka, I. / Kimura, M.
History
DepositionApr 14, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 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: Ribonuclease MC
B: Ribonuclease MC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6166
Polymers42,3962
Non-polymers2204
Water4,161231
1
A: Ribonuclease MC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3083
Polymers21,1981
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease MC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3083
Polymers21,1981
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.79, 135.90, 52.39
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212
DetailsThere are two monomers in the asymmetric unit, each monomer is a biological unit.

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Components

#1: Protein Ribonuclease MC / Ribonuclease MC1


Mass: 21198.033 Da / Num. of mol.: 2 / Mutation: N71T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Momordica charantia (bitter melon) / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P23540, EC: 3.1.27.1
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 1540, Manganese Cloride tetrahydrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112-16 mg/mlprotein1drop
210 mM1reservoirMgCl2
330 %(w/v)PEG15401reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 25, 2001 / Details: mirrors
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→19.96 Å / Num. all: 50912 / Num. obs: 50884 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 7.6 % / Biso Wilson estimate: 36.31 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.05 / Net I/σ(I): 9.1
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 3.8 / Num. unique all: 7159 / Rsym value: 0.189 / % possible all: 97.3
Reflection
*PLUS
Lowest resolution: 35.81 Å / Num. obs: 50905 / Redundancy: 8.5 % / Num. measured all: 434769
Reflection shell
*PLUS
% possible obs: 97.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 22.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BK7

1bk7


Resolution: 1.65→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.196 5096 -RANDOM
Rwork0.181 ---
all-51103 --
obs-50618 99.1 %-
Displacement parametersBiso mean: 23.94 Å2
Baniso -1Baniso -2Baniso -3
1--2.822 Å20 Å20 Å2
2--3.355 Å20 Å2
3----0.532 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2984 0 4 231 3219
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.257
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_dihedral_angle_d23.049
X-RAY DIFFRACTIONc_improper_angle_d0.778
LS refinement shellResolution: 1.65→1.71 Å
RfactorNum. reflection% reflection
Rfree0.213 483 -
Rwork0.222 --
obs-4834 0.961 %
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.049
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.778

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