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- PDB-4k7l: Crystal structure of RNase S variant (K7C/Q11C) -

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Basic information

Entry
Database: PDB / ID: 4k7l
TitleCrystal structure of RNase S variant (K7C/Q11C)
Components(Ribonuclease pancreaticPancreatic ribonuclease family) x 2
KeywordsHYDROLASE / S-peptide
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / 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
Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsGenz, M. / Straeter, N.
CitationJournal: To be Published
Title: Crystal structure of RNase S with a [Hg(Cys2)] metal center in the S-peptide as a template for structure-based design of artificial metalloenzymes using peptide-protein complementation
Authors: Genz, M. / Singer, D. / Hey-Hawkins, E. / Hoffmann, R. / Straeter, N.
History
DepositionApr 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4504
Polymers13,2582
Non-polymers1922
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-30 kcal/mol
Surface area6710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.810, 43.810, 96.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-392-

HOH

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Components

#1: Protein/peptide Ribonuclease pancreatic / Pancreatic ribonuclease family / RNase 1 / RNase A


Mass: 1701.921 Da / Num. of mol.: 1 / Fragment: unp residues 27-41 / Mutation: K7C, Q11C / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Protein Ribonuclease pancreatic / Pancreatic ribonuclease family


Mass: 11555.981 Da / Num. of mol.: 1 / Fragment: unp residues 47-150 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.36 %
Crystal growTemperature: 292 K / pH: 4
Details: 0.1 M Citric Acid, 2.4 M Ammonium Sulfate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 2, 2009
RadiationMonochromator: SI - 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.38→24.49 Å / Num. obs: 22633 / % possible obs: 99.5 % / Biso Wilson estimate: 18.61 Å2
Reflection shellResolution: 1.38→1.42 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2RNS

2rns


Resolution: 1.38→24.51 Å / Cor.coef. Fo:Fc: 0.9671 / Cor.coef. Fo:Fc free: 0.9635 / SU R Cruickshank DPI: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 237 1.05 %RANDOM
Rwork0.1669 ---
obs0.1671 22633 99.56 %-
Displacement parametersBiso mean: 24.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.4621 Å20 Å20 Å2
2---0.4621 Å20 Å2
3---0.9242 Å2
Refine analyzeLuzzati coordinate error obs: 0.183 Å
Refinement stepCycle: LAST / Resolution: 1.38→24.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms905 0 10 152 1067
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01998HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.121365HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d372SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes30HARMONIC2
X-RAY DIFFRACTIONt_gen_planes154HARMONIC5
X-RAY DIFFRACTIONt_it998HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.39
X-RAY DIFFRACTIONt_other_torsion16.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion143SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1380SEMIHARMONIC4
LS refinement shellResolution: 1.38→1.45 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2062 39 1.32 %
Rwork0.2148 2920 -
all0.2147 2959 -
obs--99.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.08731.85971.31394.13081.18513.8101-0.0762-0.00710.18710.10230.04430.0341-0.32-0.06450.03190.06020.0847-0.0236-0.0513-0.0043-0.0292-15.4362-2.999113.9995
20.5339-0.40170.34131.0441-0.50711.0332-0.01270.06430.01450.0161-0.0128-0.03290.01480.10240.02550.0050.0562-0.001-0.0232-0.0042-0.046-13.1406-8.77286.5766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|15 }A1 - 15
2X-RAY DIFFRACTION2{ B|23 - B|124 }B23 - 124

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