1RZ8

CRYSTAL STRUCTURE OF HUMAN ANTI-HIV-1 GP120-REACTIVE ANTIBODY 17B

> Summary

Summary for 1RZ8

Related1RZ7 1RZF 1RZG 1RZI 1RZJ 1RZK
DescriptorFab 17b light and heavy chains
Functional Keywordshiv-1; gp120; cd4i; antibodies; tyrosine sulfation; vh-gene usage, immune system
Biological sourceHomo sapiens (human)
Total number of polymer chains4
Total molecular weight95456.91
Authors
Primary citation
Huang, C.C.,Venturi, M.,Majeed, S.,Moore, M.J.,Phogat, S.,Zhang, M.-Y.,Dimitrov, D.S.,Hendrickson, W.A.,Robinson, J.,Sodroski, J.,Wyatt, R.,Choe, H.,Farzan, M.,Kwong, P.D.
Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120
Proc.Natl.Acad.Sci.USA, 101:2706-2711, 2004
PubMed: 14981267
DOI: 10.1073/pnas.0308527100
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.3 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.262150.8%4.1%3.3%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1rz8
no rotation
Molmil generated image of 1rz8
rotated about x axis by 90°
Molmil generated image of 1rz8
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 1rz8
no rotation
Molmil generated image of 1rz8
rotated about x axis by 90°
Molmil generated image of 1rz8
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (1rz8.pdb1.gz [75.33 KB])
Coordinate files for Biological unit (1rz8.pdb2.gz [76.33 KB])

> Structural details

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight95456.9
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight95456.9
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.3 Å)

Cell axes63.212117.460154.813
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits19.99 - 2.30
the highest resolution shell value2.440 - 2.300
R-factor0.2121
R-work0.21200
the highest resolution shell value0.300
R-free0.26200
the highest resolution shell value0.332
RMSD bond length0.006
RMSD bond angle1.400 (1.408*)

Data Collection Statistics

Resolution limits20.00 - 2.20
the highest resolution shell value -
Number of reflections55222
Number of measurements228323*
Rmerge_l_obs0.086*
Completeness93.1*
the highest resolution shell value70.8*
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP6.5 (7.0*)293unknown*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11dropTris-HCl2.5 (mM)
21drop0.35 (M)
31drop0.02 (%(v/v))pH7.0
41dropprotein4-8 (mg/ml)
51reservoirammonium sulfate50 (%sat)
61reservoirMPD10 (%)
71reservoirimidazole0.1 (M)pH6.5
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
PS002902Immunoglobulins and major histocompatibility complex proteins signature. [FY]-{L}-C-{PGAD}-[VA]-{LC}-H
ChainResidueDetails
BNA*
DNA*

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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb1rz8.ent.gz (151.46 KB)
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all (no-compress)pdb1rz8.ent (615.65 KB)
header onlypdb1rz8.ent.gz (7.95 KB)
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PDBx/mmCIF1rz8.cif.gz (187.25 KB)
PDBMLall1rz8.xml.gz (291.62 KB)
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no-atom1rz8-noatom.xml.gz (41.51 KB)
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ext-atom1rz8-extatom.xml.gz (170.3 KB)
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PDBMLplusall1rz8-plus.xml.gz (293.56 KB)
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no-atom1rz8-plus-noatom.xml.gz (43.46 KB)
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add only1rz8-add.xml.gz (1.94 KB)
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RDF1rz8.rdf.gz (85.13 KB)
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Structure factorsr1rz8sf.ent.gz (758.08 KB)
Biological unit (PDB format)1rz8.pdb1.gz (75.33 KB) (A,B)
*author and software defined assembly, 2 molecule(s) (dimeric)
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1rz8.pdb2.gz (76.33 KB) (C,D)
*author and software defined assembly, 2 molecule(s) (dimeric)
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Validation reportsPDF1rz8​_validation.pdf.gz (270.98 KB)
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PDF-full1rz8​_full​_validation.pdf.gz (291.19 KB)
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XML1rz8​_validation.xml.gz (41.55 KB)
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PNG1rz8​_multipercentile​_validation.png.gz (150.9 KB)
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SVG1rz8​_multipercentile​_validation.svg.gz (951 B)
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Sequence (fasta)1rz8​_seq.txt
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