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- PDB-1hcv: LLAMA HEAVY CHAIN VARIABLE DOMAIN AGAINST ALPHA SUBUNIT OF HCG (H... -

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Basic information

Entry
Database: PDB / ID: 1hcv
TitleLLAMA HEAVY CHAIN VARIABLE DOMAIN AGAINST ALPHA SUBUNIT OF HCG (HUMAN CHORIONIC GONADOTROPIN)
ComponentsIMMUNOGLOBULIN G
KeywordsIMMUNOGLOBULIN / CAMELIDS
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSpinelli, S. / Cambillau, C. / Tegoni, M.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: The crystal structure of a llama heavy chain variable domain.
Authors: Spinelli, S. / Frenken, L. / Bourgeois, D. / de Ron, L. / Bos, W. / Verrips, T. / Anguille, C. / Cambillau, C. / Tegoni, M.
#1: Journal: Nat.Struct.Biol. / Year: 1996
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. / Hamers, R. / Muyldermans, S. / Wyns, L.
#2: Journal: Nat.Struct.Biol. / Year: 1996
Title: Redefining the Minimal Antigen-Binding Fragment
Authors: Sheriff, S. / Constantine, K.L.
#3: Journal: Protein Eng. / Year: 1994
Title: Sequence and Structure of Vh Domain from Naturally Occurring Camel Heavy Chain Immunoglobulins Lacking Light Chains
Authors: Muyldermans, S. / Atarhouch, T. / Saldanha, J. / Barbosa, J.A. / Hamers, R.
#4: Journal: Nature / Year: 1993
Title: Naturally Occurring Antibodies Devoid of Light Chains
Authors: Hamers-Casterman, C. / Atarhouch, T. / Muyldermans, S. / Robinson, G. / Hamers, C. / Songa, E.B. / Bendahman, N. / Hamers, R.
History
DepositionJul 13, 1996Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 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: IMMUNOGLOBULIN G


Theoretical massNumber of molelcules
Total (without water)12,5091
Polymers12,5091
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.620, 41.830, 38.520
Angle α, β, γ (deg.)90.00, 95.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody IMMUNOGLOBULIN G / HC-V LLAMA


Mass: 12508.674 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN VARIABLE DOMAIN FROM LLAMA
Source method: isolated from a genetically manipulated source
Details: FROM IMMUNIZED LLAMA / Source: (gene. exp.) Lama glama (llama) / Tissue: BLOOD / Cell: LYMPHOCYTE / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: EMBL: AJ236094
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.72 Å3/Da / Density % sol: 32 %
Crystal growMethod: vapor diffusion / pH: 8
Details: VAPOR DIFFUSION, PEG 8K 25%, TRIS 0.1M, PH 8.0, vapor diffusion
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
225 %PEG80001reservoir
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 19, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 4270 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 9.03
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.4 / % possible all: 98.7
Reflection
*PLUS
Num. obs: 8077 / % possible obs: 99.8 % / Num. measured all: 92439 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.88 Å / % possible obs: 100 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 10.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: VH OF FAB FRAGMENT OF ANTIBODY AGAINST 2-PHENYL-OXAZOLONE

Resolution: 1.85→6 Å / Cross valid method: YES / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.218 844 10 %0.243
Rwork0.171 ---
obs0.171 7950 99 %-
Displacement parametersBiso mean: 16 Å2
Refinement stepCycle: LAST / Resolution: 1.85→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 0 0 99 1485
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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