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- PDB-2p45: Complex of a camelid single-domain vhh antibody fragment with RNA... -

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Basic information

Entry
Database: PDB / ID: 2p45
TitleComplex of a camelid single-domain vhh antibody fragment with RNASE A at 1.1A resolution: SE5B-ORTHO-1 crystal form with five se-met sites (L4M, M34, M51, F68M, M83) in vhh scaffold.
Components
  • ANTIBODY CAB-RN05
  • Ribonuclease pancreatic
KeywordsHYDROLASE/IMMUNE SYSTEM / SEMET PHASING / CAMELID SINGLE-DOMAIN ANTIBODY / VHH / CAB-RN05 / RNASE A / YEAST SURFACE DISPLAY / 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 / MAD / Resolution: 1.1 Å
AuthorsTereshko, V. / Uysal, S. / Koide, A. / Margalef, K. / Koide, S. / Kossiakoff, A.A.
CitationJournal: Protein Sci. / Year: 2008
Title: Toward chaperone-assisted crystallography: protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold
Authors: Tereshko, V. / Uysal, S. / Koide, A. / Margalef, K. / Koide, S. / Kossiakoff, A.A.
History
DepositionMar 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE AT THE TIME OF PROCESSING, THE SEQUENCE OF VHH ANTIBODY IS NOT AVAILABLE AT THE UNP ...SEQUENCE AT THE TIME OF PROCESSING, THE SEQUENCE OF VHH ANTIBODY IS NOT AVAILABLE AT THE UNP SEQUENCE DATABASE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease pancreatic
B: ANTIBODY CAB-RN05
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2414
Polymers27,0492
Non-polymers1922
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-29.5 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.447, 73.070, 42.539
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: Protein ANTIBODY CAB-RN05


Mass: 13341.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.5
Details: HAMPTON RESEARCH INDEX SCREEN, SOLUTION #74: LI2SO4, PEG 3350, BIS-TRIS BUFFER, PH 5.5, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97955,0.97934
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 1, 2004 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979551
20.979341
ReflectionResolution: 1.1→20 Å / Num. all: 90838 / Num. obs: 90838 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 %

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.1→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.876 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.035 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19468 4562 5 %RANDOM
Rwork0.1726 ---
all0.17368 ---
obs0.17368 86276 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.278 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20 Å2
2--0.51 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 10 319 2212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191931
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.8972607
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2225244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.08624.23585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31615328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8971511
X-RAY DIFFRACTIONr_chiral_restr0.0950.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021459
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2840
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2229
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.246
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6031.51246
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3421945
X-RAY DIFFRACTIONr_scbond_it4.3733787
X-RAY DIFFRACTIONr_scangle_it5.1324.5661
X-RAY DIFFRACTIONr_rigid_bond_restr3.60531836
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded6.08831720
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.202 265
Rwork0.194 5039

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