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Yorodumi- PDB-1hcv: LLAMA HEAVY CHAIN VARIABLE DOMAIN AGAINST ALPHA SUBUNIT OF HCG (H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hcv | ||||||
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Title | LLAMA HEAVY CHAIN VARIABLE DOMAIN AGAINST ALPHA SUBUNIT OF HCG (HUMAN CHORIONIC GONADOTROPIN) | ||||||
Components | IMMUNOGLOBULIN G | ||||||
Keywords | IMMUNOGLOBULIN / CAMELIDS | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : Function and homology information | ||||||
Biological species | Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Spinelli, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hcv.cif.gz | 44.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hcv.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 1hcv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hcv_validation.pdf.gz | 359.2 KB | Display | wwPDB validaton report |
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Full document | 1hcv_full_validation.pdf.gz | 362 KB | Display | |
Data in XML | 1hcv_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 1hcv_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/1hcv ftp://data.pdbj.org/pub/pdb/validation_reports/hc/1hcv | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.72 Å3/Da / Density % sol: 32 % | ||||||||||||||||||||
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Crystal grow | Method: 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
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 19, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Displacement parameters | Biso mean: 16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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