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- PDB-1bzq: COMPLEX OF A DROMEDARY SINGLE-DOMAIN VHH ANTIBODY FRAGMENT WITH R... -

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Basic information

Entry
Database: PDB / ID: 1bzq
TitleCOMPLEX OF A DROMEDARY SINGLE-DOMAIN VHH ANTIBODY FRAGMENT WITH RNASE A
Components
  • PROTEIN (ANTIBODY CAB-RN05)
  • PROTEIN (RNASE A)
KeywordsHYDROLASE/IMMUNE SYSTEM / IMMUNOGLUBULIN / ANTIBODY COMPLEX / RIBONUCLEASE / 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
PHOSPHATE ION / Ribonuclease pancreatic
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDecanniere, K. / Desmyter, A. / Gahroudhi, M. / Lauwereys, M. / Muyldermans, S. / Wyns, L.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: A single-domain antibody fragment in complex with RNase A: non-canonical loop structures and nanomolar affinity using two CDR loops.
Authors: Decanniere, K. / Desmyter, A. / Lauwereys, M. / Ghahroudi, M.A. / Muyldermans, S. / Wyns, L.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal Structure of a Camel Single-Domain VH Antibody Fragment in Complex with Lysozyme
Authors: Desmyter, A. / Transue, T.R. / Ghahroudi, M.A. / Thi, M.H. / Poortmans, F. / Hmaers, R. / Muyldermans, S. / WYNS, L.
History
DepositionNov 3, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (RNASE A)
B: PROTEIN (RNASE A)
C: PROTEIN (RNASE A)
D: PROTEIN (RNASE A)
K: PROTEIN (ANTIBODY CAB-RN05)
L: PROTEIN (ANTIBODY CAB-RN05)
M: PROTEIN (ANTIBODY CAB-RN05)
N: PROTEIN (ANTIBODY CAB-RN05)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,54012
Polymers108,1608
Non-polymers3804
Water00
1
A: PROTEIN (RNASE A)
L: PROTEIN (ANTIBODY CAB-RN05)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1353
Polymers27,0402
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (RNASE A)
N: PROTEIN (ANTIBODY CAB-RN05)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1353
Polymers27,0402
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (RNASE A)
M: PROTEIN (ANTIBODY CAB-RN05)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1353
Polymers27,0402
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PROTEIN (RNASE A)
K: PROTEIN (ANTIBODY CAB-RN05)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1353
Polymers27,0402
Non-polymers951
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.520, 66.820, 69.340
Angle α, β, γ (deg.)91.43, 117.34, 97.33
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9999, -0.0076, 0.01192), (0.00766, -0.99996, 0.00492), (0.01189, 0.00501, 0.99992)40.10823, 21.82327, 0.24119
2given(-0.14133, 0.98996, 0.00297), (0.98994, 0.14131, 0.00667), (0.00618, 0.00388, -0.99997)18.14327, 27.06758, 23.75913
3given(0.13524, -0.99078, 0.00744), (-0.99061, -0.13536, -0.01911), (0.01994, -0.00479, -0.99979)43.21379, 3.47927, 24.06191
4given(-0.99947, -0.03237, 0.00219), (0.03239, -0.99942, 0.01079), (0.00184, 0.01085, 0.99994)39.81419, 22.21932, 0.08047
5given(-0.15541, 0.98784, -0.00411), (0.98782, 0.15543, 0.00735), (0.0079, -0.00292, -0.99996)17.90425, 27.18056, 23.90588
6given(0.13324, -0.99108, -0.00256), (-0.99102, -0.13321, -0.01167), (0.01122, 0.00409, -0.99993)43.05147, 3.49825, 23.9054

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Components

#1: Protein
PROTEIN (RNASE A)


Mass: 13708.326 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: RNASE A SUPPLIED BY SIGMA / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P61823, EC: 3.1.27.5
#2: Antibody
PROTEIN (ANTIBODY CAB-RN05)


Mass: 13331.775 Da / Num. of mol.: 4 / Fragment: VARIABLE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Cell: B-LYMPHOCYTES / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 50.77 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.4
Details: HANGING DROP METHOD. 5 MG/ML OF THE COMPLEX RESERVOIR SOLUTION IS 0.1 M POTASSIUM PHOSPHATE PH 6.4 15 TO 20% W/V PEG 8000, vapor diffusion - hanging drop
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
215-20 %(w/v)PEG80001reservoir
30.1 Mpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 25413 / % possible obs: 99.2 % / Redundancy: 3.8 % / Rsym value: 0.111 / Net I/σ(I): 8.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.336 / % possible all: 98.2
Reflection
*PLUS
Rmerge(I) obs: 0.111
Reflection shell
*PLUS
% possible obs: 98.2 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RUV AND PDB ENTRY 1MEL

1ruv

1mel


Resolution: 2.8→20 Å / SU ML: 0.32428 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.45252
Details: CHAINS A, B, C AND D ARE RNASE A MOLECULES CHAINS K, L, M AND N ARE ANTIBODY MOLECULES SEPARATE NCS WAS APPLIED TO EACH GROUP OF MOLECULES
RfactorNum. reflection% reflectionSelection details
Rfree0.28244 1298 5 %RANDOM
Rwork0.22234 ---
obs-25796 98.5 %-
Displacement parametersBiso mean: 27.26 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7544 0 20 0 7564
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0210.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8332
X-RAY DIFFRACTIONp_mcangle_it1.5243
X-RAY DIFFRACTIONp_scbond_it0.812
X-RAY DIFFRACTIONp_scangle_it1.393
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.0940.15
X-RAY DIFFRACTIONp_singtor_nbd0.1830.3
X-RAY DIFFRACTIONp_multtor_nbd0.2350.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1830.3
X-RAY DIFFRACTIONp_planar_tor3.27
X-RAY DIFFRACTIONp_staggered_tor25.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor25.820
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 25412 / Rfactor all: 0.225 / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.006
X-RAY DIFFRACTIONp_angle_d0.025
X-RAY DIFFRACTIONp_planar_d0.02

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