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- PDB-1gmp: COMPLEX OF RIBONUCLEASE FROM STREPTOMYCES AUREOFACIENS WITH 2'-GM... -

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Basic information

Entry
Database: PDB / ID: 1gmp
TitleCOMPLEX OF RIBONUCLEASE FROM STREPTOMYCES AUREOFACIENS WITH 2'-GMP AT 1.7 ANGSTROMS RESOLUTION
ComponentsRIBONUCLEASE SA
KeywordsHYDROLASE(GUANYLORIBONUCLEASE)
Function / homology
Function and homology information


ribonuclease T1 / ribonuclease T1 activity / RNA endonuclease activity / lyase activity / RNA binding / extracellular region
Similarity search - Function
Microbial ribonucleases / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-2'-MONOPHOSPHATE / Guanyl-specific ribonuclease Sa
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsSevcik, J. / Hill, C. / Dauter, Z. / Wilson, K.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Complex of ribonuclease from Streptomyces aureofaciens with 2'-GMP at 1.7 A resolution.
Authors: Sevcik, J. / Hill, C.P. / Dauter, Z. / Wilson, K.S.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Continuation of the Rnase Sa Work After 1Sar and 2Sar Structures
Authors: Sevcik, J. / Dodson, E.J. / Dodson, G.G.
History
DepositionOct 1, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBONUCLEASE SA
B: RIBONUCLEASE SA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9925
Polymers21,1692
Non-polymers8233
Water8,863492
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.700, 78.800, 39.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES PRO A 27 AND PRO B 27 ARE CIS PROLINES.

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Components

#1: Protein RIBONUCLEASE SA


Mass: 10584.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / References: UniProt: P05798, EC: 3.1.27.3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-2GP / GUANOSINE-2'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHERE TOO MANY WATER MOLECULES AT BONDING DISTANCE FROM ATOMS OF 2GP B.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion / Details: referred to Acta Cryst.B47.240-253 1991
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1phosphate1reservoir
2ammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 22455 / % possible obs: 98.9 % / Num. measured all: 77200 / Rmerge(I) obs: 0.033

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.133 / Highest resolution: 1.7 Å
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1501 0 53 492 2046
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 22372 / Rfactor obs: 0.133
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.040.038
X-RAY DIFFRACTIONp_dihedral_angle_d0.050.048
X-RAY DIFFRACTIONp_plane_restr0.20.014
X-RAY DIFFRACTIONp_chiral_restr0.20.216

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