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- PDB-1f2x: STRUCTURE OF THE SINGLE-DOMAIN CAMELID ANTIBODY CAB-CA05 -

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Basic information

Entry
Database: PDB / ID: 1f2x
TitleSTRUCTURE OF THE SINGLE-DOMAIN CAMELID ANTIBODY CAB-CA05
ComponentsANTIBODY HEAVY CHAIN
KeywordsIMMUNE SYSTEM / immunoglobulin fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDecanniere, K. / Muyldermans, S. / Wyns, L.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Canonical antigen-binding loop structures in immunoglobulins: more structures, more canonical classes?
Authors: Decanniere, K. / Muyldermans, S. / Wyns, L.
#1: Journal: To be Published
Title: Structure of the Camelid Single-Domain Antibody Fragment cAb-CA05: Free and Complexed Structure
Authors: Desmeyter, A. / Decanniere, K. / Muyldermans, S. / Wyns, L.
History
DepositionMay 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_residues / Item: _diffrn_source.type
Revision 1.4Aug 9, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
K: ANTIBODY HEAVY CHAIN
L: ANTIBODY HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)29,4672
Polymers29,4672
Non-polymers00
Water2,108117
1
K: ANTIBODY HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)14,7331
Polymers14,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L: ANTIBODY HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)14,7331
Polymers14,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.980, 43.860, 87.950
Angle α, β, γ (deg.)90.00, 93.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody ANTIBODY HEAVY CHAIN / VHH


Mass: 14733.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Cell: LYMPHOCYTES / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 1.96 Å3/Da / Density % sol: 37.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25 % (w/v) PEG8000, 0.1 M Na citrate pH 5.6, protein concentration 1.7 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 45 %
Crystal grow
*PLUS
pH: 6.4 / Details: Desmyter, A., (1996) Nature Struct. Biol., 3, 803.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein complex1drop
215-20 %(w/v)PEG80001drop
30.1 Mpotassium phosphate1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→31 Å / Num. all: 13523 / Num. obs: 13256 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 4.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1878 / % possible all: 99.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BZQ

1bzq


Resolution: 2.1→31 Å / SU B: 5.7 / SU ML: 0.15 / σ(F): 0 / σ(I): 0 / ESU R: 0.27 / ESU R Free: 0.23 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood target using F's
RfactorNum. reflection% reflectionSelection details
Rfree0.27 666 -5%, random
Rwork0.19 ---
all0.19 12819 --
obs0.19 12786 99.7 %-
Refinement stepCycle: LAST / Resolution: 2.1→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 0 117 1990
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_planar_d0.0260.05
X-RAY DIFFRACTIONp_mcbond_it1.662
X-RAY DIFFRACTIONp_mcangle_it2.713
X-RAY DIFFRACTIONp_scbond_it1.732
X-RAY DIFFRACTIONp_scangle_it2.83
X-RAY DIFFRACTIONp_planar_tor3.17
X-RAY DIFFRACTIONp_staggered_tor16.715
X-RAY DIFFRACTIONp_transverse_tor36.520
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.19 / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_mcbond_it1.662
X-RAY DIFFRACTIONp_scbond_it1.732
X-RAY DIFFRACTIONp_mcangle_it2.713
X-RAY DIFFRACTIONp_scangle_it2.83

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