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- PDB-2rnf: X-RAY CRYSTAL STRUCTURE OF HUMAN RIBONUCLEASE 4 IN COMPLEX WITH D(UP) -

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Basic information

Entry
Database: PDB / ID: 2rnf
TitleX-RAY CRYSTAL STRUCTURE OF HUMAN RIBONUCLEASE 4 IN COMPLEX WITH D(UP)
ComponentsRIBONUCLEASE 4
KeywordsHYDROLASE / RIBONUCLEASE / PHOSPHODIESTERASE
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / ribonuclease A activity / RNA nuclease activity / antibacterial humoral response / nucleic acid binding / defense response to Gram-positive bacterium / extracellular space / 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
2'-DEOXYURIDINE 3'-MONOPHOSPHATE / Ribonuclease 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTerzyan, S.S. / Peracaula, R. / De Llorens, R. / Tsushima, Y. / Yamada, H. / Seno, M. / Gomis-Ruth, F.X. / Coll, M.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: The three-dimensional structure of human RNase 4, unliganded and complexed with d(Up), reveals the basis for its uridine selectivity.
Authors: Terzyan, S.S. / Peracaula, R. / de Llorens, R. / Tsushima, Y. / Yamada, H. / Seno, M. / Gomis-Ruth, F.X. / Coll, M.
History
DepositionNov 3, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 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: RIBONUCLEASE 4
B: RIBONUCLEASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5744
Polymers27,9582
Non-polymers6162
Water2,000111
1
A: RIBONUCLEASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2872
Polymers13,9791
Non-polymers3081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RIBONUCLEASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2872
Polymers13,9791
Non-polymers3081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.830, 94.330, 40.660
Angle α, β, γ (deg.)90.00, 107.20, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.518, 0.643, 0.564), (0.745, 0.663, -0.072), (0.42, 0.383, -0.822)
Vector: 4.731, 9.284, 16.586)

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Components

#1: Protein RIBONUCLEASE 4 / RNASE 4


Mass: 13979.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P34096, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical ChemComp-UM3 / 2'-DEOXYURIDINE 3'-MONOPHOSPHATE / D(UP)


Mass: 308.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.2 Å3/Da / Density % sol: 42.81 %
Crystal growpH: 6.9 / Details: pH 6.9
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2PEG 400011
3PEG 400012
Crystal grow
*PLUS
pH: 6.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
230 %(v/v)PEG40001reservoir
30.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 36143 / Num. obs: 36143 / % possible obs: 85.8 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 7.8
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 2.76 / % possible all: 89.2
Reflection
*PLUS
Num. obs: 7980 / Num. measured all: 36143
Reflection shell
*PLUS
% possible obs: 89.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RAT

2rat


Resolution: 2.4→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.215 -6 %
Rwork0.16 --
obs0.16 6404 73.5 %
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 40 111 2091
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.512
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 2 / Num. reflection Rfree: 411 / % reflection Rfree: 6 % / Rfactor obs: 0.16 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS

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