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- PDB-2p4a: X-ray structure of a camelid affinity matured single-domain vhh a... -

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Basic information

Entry
Database: PDB / ID: 2p4a
TitleX-ray structure of a camelid affinity matured single-domain vhh antibody fragment in complex with RNASE A
Components
  • ANTIBODY CAB-RN05
  • Ribonuclease pancreatic
KeywordsHYDROLASE/IMMUNE SYSTEM / CAMELID SINGLE-DOMAIN ANTIBODY / VHH / CAB-RN05 / RNASE A / PARATOPE / YEAST SURFACE DISPLAY / HYDROLASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


immunoglobulin complex / pancreatic ribonuclease / ribonuclease A activity / immunoglobulin mediated immune response / RNA nuclease activity / antigen binding / nucleic acid binding / blood microparticle / 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 / Immunoglobulin V-Type ...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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hi113 protein / Ribonuclease pancreatic
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTereshko, V. / Koide, A. / Uysal, S. / Koide, S.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Exploring the capacity of minimalist protein interfaces: interface energetics and affinity maturation to picomolar KD of a single-domain antibody with a flat paratope.
Authors: Koide, A. / Tereshko, V. / Uysal, S. / Margalef, K. / Kossiakoff, A.A. / Koide, S.
History
DepositionMar 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE 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
C: Ribonuclease pancreatic
D: ANTIBODY CAB-RN05
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2696
Polymers53,0774
Non-polymers1922
Water6,503361
1
A: Ribonuclease pancreatic
B: ANTIBODY CAB-RN05
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6353
Polymers26,5392
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ribonuclease pancreatic
D: ANTIBODY CAB-RN05
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6353
Polymers26,5392
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.027, 131.623, 137.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF two VHH-RNASE A COMPLEXes.

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Components

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


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Antibody ANTIBODY CAB-RN05


Mass: 12830.278 Da / Num. of mol.: 2 / Fragment: TRUNCATED AT RESIDUE 121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli) / References: UniProt: A2KD57*PLUS
#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.: 361 / 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: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.5
Details: HAMPTON RESEARCH INDEX SCREEN, SOLUTION #67, pH 5.5, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 48836 / Num. obs: 48836 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 %

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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 2P49

2p49


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.876 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.133 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21807 2484 5.1 %RANDOM
Rwork0.18417 ---
all0.18587 48836 --
obs0.18587 46352 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.164 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å20 Å20 Å2
2---1.55 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3704 0 10 361 4075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193830
X-RAY DIFFRACTIONr_bond_other_d0.0010.023267
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.8885182
X-RAY DIFFRACTIONr_angle_other_deg0.7352.1277646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9395486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25224.176170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70415632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2461523
X-RAY DIFFRACTIONr_chiral_restr0.060.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024331
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02778
X-RAY DIFFRACTIONr_nbd_refined0.1940.2644
X-RAY DIFFRACTIONr_nbd_other0.1920.23227
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.22062
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1840.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8121.53134
X-RAY DIFFRACTIONr_mcbond_other0.1321.51022
X-RAY DIFFRACTIONr_mcangle_it0.91723876
X-RAY DIFFRACTIONr_scbond_it1.51131677
X-RAY DIFFRACTIONr_scangle_it2.1034.51304
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.953 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.245 146
Rwork0.212 2632
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)
10.2238-0.01420.31921.2205-1.38792.59420.0029-0.0489-0.0823-0.18130.0001-0.07410.2327-0.0357-0.003-0.08920.0068-0.0064-0.02640.0036-0.012616.8268-16.864550.2346
21.26890.0509-0.29061.6646-0.52233.7915-0.05970.05560.0087-0.39060.0526-0.029-0.07560.11770.0070.0117-0.0592-0.0059-0.0825-0.0117-0.098918.33580.050322.2423
30.3165-0.3208-0.05712.6475-1.23291.70060.04690.05730.0247-0.3131-0.0366-0.17270.16210.0833-0.0103-0.07950.01230.0008-0.02980.0047-0.007917.809447.2416-17.4632
41.01520.44380.35554.7291-1.04881.85180.0596-0.03080.02940.0027-0.09110.12110.4051-0.07910.03150.03420.0177-0.0033-0.0669-0.0187-0.088615.647819.81350.8749
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1241 - 124
4X-RAY DIFFRACTION2BB1 - 1211 - 121
7X-RAY DIFFRACTION3CC1 - 1241 - 124
10X-RAY DIFFRACTION4DD1 - 1211 - 121

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