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- PDB-6rsa: NUCLEAR MAGNETIC RESONANCE AND NEUTRON DIFFRACTION STUDIES OF THE... -

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Basic information

Entry
Database: PDB / ID: 6rsa
TitleNUCLEAR MAGNETIC RESONANCE AND NEUTRON DIFFRACTION STUDIES OF THE COMPLEX OF RIBONUCLEASE*A WITH URIDINE VANADATE, A TRANSITION-STATE ANALOGUE
ComponentsRIBONUCLEASE A
KeywordsHYDROLASE
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
DEUTERATED WATER / URIDINE-2',3'-VANADATE / Ribonuclease pancreatic / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodNEUTRON DIFFRACTION / SOLUTION NMR / Resolution: 2 Å
AuthorsWlodawer, A.
Citation
Journal: Biochemistry / Year: 1985
Title: Nuclear magnetic resonance and neutron diffraction studies of the complex of ribonuclease A with uridine vanadate, a transition-state analogue.
Authors: Borah, B. / Chen, C.W. / Egan, W. / Miller, M. / Wlodawer, A. / Cohen, J.S.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1986
Title: Comparison of Two Independently Refined Models of Ribonuclease-A
Authors: Wlodawer, A. / Borkakoti, N. / Moss, D.S. / Howlin, B.
#2: Journal: Biochemistry / Year: 1983
Title: Structure of Ribonuclease A. Results of Joint Neutron and X-Ray Refinement at 2.0-Angstroms Resolution
Authors: Wlodawer, A. / Sjolin, L.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1983
Title: Active Site of Rnase. Neutron Diffraction Study of a Complex with Uridine Vanadate, a Transition-State Analog
Authors: Wlodawer, A. / Miller, M. / Sjolin, L.
#4: Journal: J.Biol.Chem. / Year: 1982
Title: The Refined Crystal Structure of Ribonuclease A at 2.0 Angstroms Resolution
Authors: Wlodawer, A. / Bott, R. / Sjolin, L.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Hydrogen Exchange in Rnase A. Neutron Diffraction Study
Authors: Wlodawer, A. / Sjolin, L.
#6: Journal: Acta Crystallogr.,Sect.A (Supplement) / Year: 1981
Title: Structure of Ribonuclease A. X-Ray and Neutron Refinement
Authors: Wlodawer, A. / Bott, R. / Sjolin, L.
#7: Journal: Acta Crystallogr.,Sect.A (Supplement) / Year: 1981
Title: Joint Refinement of Macromolecular Structures with X-Ray and Neutron Single-Crystal Diffraction Data
Authors: Wlodawer, A. / Hendrickson, W.A.
#8: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981
Title: Orientation of Histidine Residues in Rnase A. Neutron Diffraction Study
Authors: Wlodawer, A. / Sjolin, L.
#9: Journal: Acta Crystallogr.,Sect.B / Year: 1980
Title: Studies of Ribonuclease-A by X-Ray and Neutron Diffraction
Authors: Wlodawer, A.
History
DepositionFeb 25, 1986Processing site: BNL
Revision 1.0May 7, 1986Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Data collection / Non-polymer description
Revision 1.4Oct 5, 2011Group: Derived calculations
Revision 1.5Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700SHEET THIS STRUCTURE CONTAINS TWO SHEETS. SHEET S1 COMPRISES THREE STRANDS. IN THE SECOND STRAND OF ...SHEET THIS STRUCTURE CONTAINS TWO SHEETS. SHEET S1 COMPRISES THREE STRANDS. IN THE SECOND STRAND OF SHEET S1, RESIDUES 88 AND 89 *BULGE OUT*. IN ORDER TO REPRESENT THIS BREAK IN STRAND 2, TWO SHEETS (S1A AND S1B) ARE DEFINED BELOW. STRANDS 1 AND 3 OF *SHEETS* S1A AND S1B ARE, THEREFORE, IDENTICAL AND STRAND 2 DIFFERS. SHEET S2 COMPRISES FOUR STRANDS. RESIDUE 120 DOES NOT PROPERLY BELONG IN STRAND 4 OF SHEET S2. IN ORDER TO REPRESENT THIS BREAK IN STRAND 4, TWO SHEETS (S2A AND S2B) ARE DEFINED BELOW. STRANDS 1,2,3 OF *SHEETS* S2A AND S2B ARE, THEREFORE, IDENTICAL AND STRAND 4 DIFFERS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0512
Polymers13,7081
Non-polymers3431
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.300, 38.350, 53.700
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES 93 AND 114 ARE CIS-PROLINES.
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein RIBONUCLEASE A


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cell line: S2 / Organ: PANCREAS
References: UniProt: P00656, UniProt: P61823*PLUS, EC: 3.1.27.5
#2: Chemical ChemComp-UVC / URIDINE-2',3'-VANADATE


Mass: 343.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O9V
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: D2O
Has protein modificationY
Nonpolymer detailsCOORDINATES ARE NOT INCLUDED FOR THREE DEUTERIUMS IN HET GROUP *UVC*.

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Experimental details

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Experiment

Experiment
Method
NEUTRON DIFFRACTION
SOLUTION NMR

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.65 %
Description: DATA WERE COLLECTED ON DEUTERATED CRYSTALS. THE SOLVENT IS TERTIARY BUTANOL. AMIDE HYDROGENS WHICH EXCHANGED LESS THAN 50 PER CENT ARE ENTERED AS H, OTHERS ARE ENTERED AS D.
Crystal grow
*PLUS
pH: 5.3 / Method: unknown
Details: Wlodawer, A., (1983) Proc.Nat.Acad.Sci.USA, 80, 3628.
Components of the solutions
*PLUS
Conc.: 43 % / Common name: t-butyl alcohol

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Processing

RefinementResolution: 2→10 Å
Refine LS restraints
Refine-IDTypeDev ideal
NEUTRON DIFFRACTIONo_bond_d0.23
NEUTRON DIFFRACTIONo_bond_d_na
NEUTRON DIFFRACTIONo_bond_d_prot
NEUTRON DIFFRACTIONo_angle_d
NEUTRON DIFFRACTIONo_angle_d_na
NEUTRON DIFFRACTIONo_angle_d_prot
NEUTRON DIFFRACTIONo_angle_deg
NEUTRON DIFFRACTIONo_angle_deg_na
NEUTRON DIFFRACTIONo_angle_deg_prot
NEUTRON DIFFRACTIONo_dihedral_angle_d
NEUTRON DIFFRACTIONo_dihedral_angle_d_na
NEUTRON DIFFRACTIONo_dihedral_angle_d_prot
NEUTRON DIFFRACTIONo_improper_angle_d
NEUTRON DIFFRACTIONo_improper_angle_d_na
NEUTRON DIFFRACTIONo_improper_angle_d_prot
NEUTRON DIFFRACTIONo_mcbond_it
NEUTRON DIFFRACTIONo_mcangle_it
NEUTRON DIFFRACTIONo_scbond_it
NEUTRON DIFFRACTIONo_scangle_it
NMR ensembleConformers submitted total number: 1
Refinement
*PLUS
Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS

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