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- PDB-3mac: crystal structure of GP41-derived protein complexed with fab 8062 -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mac | ||||||
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Title | crystal structure of GP41-derived protein complexed with fab 8062 | ||||||
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![]() | IMMUNE SYSTEM / GP41 / fab8062 | ||||||
Function / homology | Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1860 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Transmembrane glycoprotein![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, M. / Gustchina, E. / Louis, J. / Gustchina, A. / Wlodawer, A. / Clore, M. | ||||||
![]() | ![]() Title: Structural Basis of HIV-1 Neutralization by Affinity Matured Fabs Directed against the Internal Trimeric Coiled-Coil of gp41. Authors: Gustchina, E. / Li, M. / Louis, J.M. / Anderson, D.E. / Lloyd, J. / Frisch, C. / Bewley, C.A. / Gustchina, A. / Wlodawer, A. / Clore, G.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 252.2 KB | Display | ![]() |
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PDB format | ![]() | 203.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ma9C ![]() 2cmrS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24479.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 26334.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
#3: Antibody | Mass: 22640.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 14% Polyethylene glycol 10K, 0.1M ammonium sulfate, 5% ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARCCD300 / Detector: CCD / Date: Jan 1, 2009 / Details: mirror |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.5 Å / Num. obs: 23655 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rsym value: 0.082 / Net I/σ(I): 13.79 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2 / Rsym value: 0.524 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CMR Resolution: 2.5→29.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 21.692 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.602 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.229 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.502→2.567 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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