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- PDB-2p48: Complex of a camelid single-domain vhh antibody fragment with RNA... -

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Basic information

Entry
Database: PDB / ID: 2p48
TitleComplex of a camelid single-domain vhh antibody fragment with RNASE A at 2.3A resolution: SE5B-tetra 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 / defense response to Gram-positive bacterium / lyase activity / 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 ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ribonuclease pancreatic
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 / 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
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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-33.3 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.324, 42.324, 352.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
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 (domestic 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.: 76 / 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: 2.92 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.5
Details: HAMPTON RESEARCH INDEX SCREEN, SOLUTION #66: (NH4)2SO4, PEG 3350, BIS-TRIS, 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: 0.97926 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: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 15006 / Num. obs: 15006 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 %

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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 entry 2P45

2p45


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.881 / SU B: 20.231 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.338 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29651 1525 10.2 %RANDOM
Rwork0.24054 ---
all0.24611 15006 --
obs0.24611 13481 97.08 %-
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: 43.852 Å2
Baniso -1Baniso -2Baniso -3
1-3.01 Å20 Å20 Å2
2--3.01 Å20 Å2
3----6.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 10 76 1944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191903
X-RAY DIFFRACTIONr_bond_other_d0.0010.021611
X-RAY DIFFRACTIONr_angle_refined_deg1.0791.8962569
X-RAY DIFFRACTIONr_angle_other_deg0.7472.1543771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8815241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47324.28684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.08815317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.251511
X-RAY DIFFRACTIONr_chiral_restr0.070.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02383
X-RAY DIFFRACTIONr_nbd_refined0.2150.2391
X-RAY DIFFRACTIONr_nbd_other0.2080.21619
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.2960
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1110.210
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0080.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2711.51485
X-RAY DIFFRACTIONr_mcbond_other0.2281.5511
X-RAY DIFFRACTIONr_mcangle_it1.59521923
X-RAY DIFFRACTIONr_scbond_it2.6863800
X-RAY DIFFRACTIONr_scangle_it3.744.5646
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.285 74
Rwork0.283 789
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)
11.01030.3423-0.43451.4684-0.26631.4245-0.0655-0.0613-0.1306-0.05130.09310.00930.1895-0.0778-0.0276-0.29010.0191-0.01470.0389-0.01450.054424.350423.131143.5119
21.1525-0.0974-0.5910.9952-0.15793.85940.07850.03130.0146-0.2141-0.0079-0.02950.24950.1603-0.0706-0.0922-0.00230.03480.0099-0.0433-0.050733.805725.620711.9662
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1241 - 124
4X-RAY DIFFRACTION2BB1 - 1213 - 123

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