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- PDB-3qsk: 5 Histidine Variant of the anti-RNase A VHH in Complex with RNAse A -

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Basic information

Entry
Database: PDB / ID: 3qsk
Title5 Histidine Variant of the anti-RNase A VHH in Complex with RNAse A
Components
  • Engineered 5 Histidine anti-RNase A Camelid VHH Antibody Domain Variant
  • Ribonuclease pancreatic
KeywordsHYDROLASE/IMMUNE SYSTEM / Antibody / Single Domain / Camelid / VHH / sdAb / RNase A / Ribonuclease A / pH / Sensitivity / Switch / Dependence / Linked / Equilibria / Equilibrium / Protein Engineering / Combinatorial / Histidine / Scanning / Phage Display / Dual-Function / Protein-Protein Interaction / Proton Binding / HYDROLASE-IMMUNE SYSTEM complex
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 / Immunoglobulins ...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 / Immunoglobulins / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ribonuclease pancreatic
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMurtaugh, M.L. / Fanning, S.W. / Sharma, T.M. / Terry, A.M. / Horn, J.R.
CitationJournal: Protein Sci. / Year: 2011
Title: A combinatorial histidine scanning library approach to engineer highly pH-dependent protein switches.
Authors: Murtaugh, M.L. / Fanning, S.W. / Sharma, T.M. / Terry, A.M. / Horn, J.R.
History
DepositionFeb 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Engineered 5 Histidine anti-RNase A Camelid VHH Antibody Domain Variant


Theoretical massNumber of molelcules
Total (without water)26,8162
Polymers26,8162
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-4 kcal/mol
Surface area12120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.787, 54.680, 48.792
Angle α, β, γ (deg.)90.00, 109.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonuclease pancreatic / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Antibody Engineered 5 Histidine anti-RNase A Camelid VHH Antibody Domain Variant


Mass: 13107.478 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Plasmid: pET21a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 1.92 Å3/Da / Density % sol: 35.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 3.350, 0.2M lithium sulfate monohydrate, 0.1M bis-tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 19497 / Num. obs: 19462 / % possible obs: 99.82 % / Observed criterion σ(I): 0.34 / Redundancy: 3.6 % / Rmerge(I) obs: 0.047
Reflection shellHighest resolution: 1.75 Å / % possible all: 99.82

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.135 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24591 1023 5 %RANDOM
Rwork0.18378 ---
obs0.1869 19462 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.668 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-1.2 Å2
2---1.04 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 0 182 2020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211887
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.9272552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0445243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2824.18686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30515307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7931510
X-RAY DIFFRACTIONr_chiral_restr0.1420.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211451
X-RAY DIFFRACTIONr_mcbond_it1.2331.51197
X-RAY DIFFRACTIONr_mcangle_it1.96121908
X-RAY DIFFRACTIONr_scbond_it2.953690
X-RAY DIFFRACTIONr_scangle_it4.5114.5642
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 61 -
Rwork0.194 1423 -
obs--99.87 %
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)
11.401-1.96570.69552.9959-1.45191.4191-0.3283-0.09450.09720.49650.134-0.205-0.10180.02640.19430.21860.0105-0.02890.1253-0.0050.089122.1393-20.996417.8069
21.3241-0.60790.38941.4917-0.1180.5713-0.01790.00390.0144-0.0352-0.01090.1095-0.02640.01180.02880.02670.00460.0220.05710.00410.04951.881-2.89580.5542
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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