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- PDB-2p47: Complex of a camelid single-domain vhh antibody fragment with RNA... -

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Basic information

Entry
Database: PDB / ID: 2p47
TitleComplex of a camelid single-domain vhh antibody fragment with RNASE A at 2.5A resolution: SE5B-TRI 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 / 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: 2.5 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: Advisory / Version format compliance
Revision 1.2Aug 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,0492
Polymers27,0492
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-5.3 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.011, 72.011, 98.012
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ONE VHH-RNASE A COMPLEX. EACH COMPLEX CONSISTS OF TWO CHAINS, A AND B, AND REPRESENTS ONE BIOLOGICAL UNIT.

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: HAMPTON RESEARCH INDEX SCREEN, SOLUTION #68: (NH4)SO4, PEG 3350, HEPES BUFFER, PH 7.5, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 1, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 10142 / Num. obs: 10142 / % possible obs: 96.1 % / 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
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2P45

2p45


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.903 / SU B: 39.129 / SU ML: 0.345 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.4 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29438 493 4.9 %RANDOM
Rwork0.22998 ---
all0.23295 10142 --
obs0.23295 9649 96.01 %-
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: 84.208 Å2
Baniso -1Baniso -2Baniso -3
1-4.76 Å22.38 Å20 Å2
2--4.76 Å20 Å2
3----7.14 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 0 19 1863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191880
X-RAY DIFFRACTIONr_bond_other_d0.0010.021597
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.8892538
X-RAY DIFFRACTIONr_angle_other_deg0.7452.1553735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4525241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27124.21783
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27115311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0481511
X-RAY DIFFRACTIONr_chiral_restr0.0650.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022143
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02382
X-RAY DIFFRACTIONr_nbd_refined0.2150.2345
X-RAY DIFFRACTIONr_nbd_other0.1880.21554
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.080.2940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1280.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2080.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.386 39
Rwork0.367 678
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)
12.11620.2567-3.10285.8529-8.279315.27740.5903-0.2897-0.15940.2431-0.3522-0.1433-0.38950.8503-0.2381-0.10070.05390.1214-0.17010.1204-0.131433.845129.655255.8905
24.25250.5339-4.09914.0582-3.30549.41230.6458-0.43860.34150.6244-0.245-0.048-1.56520.5508-0.40080.15290.05540.3049-0.26420.1075-0.031545.178847.220329.4538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1242 - 124
3X-RAY DIFFRACTION2BB1 - 1213 - 123

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