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- PDB-4ktd: Fab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE1... -

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Basic information

Entry
Database: PDB / ID: 4ktd
TitleFab fragment of HIV vaccine-elicited CD4bs-directed antibody, GE136, from non-human primate
Components
  • GE136 Heavy Chain Fab
  • GE136 Light Chain Fab
KeywordsIMMUNE SYSTEM / Antibody Affinity / Antibody Specificity / Vaccine Elicited Antibodies / Fab fragment / AIDS Vaccines
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPoulsen, C. / Tran, K. / Standfield, R. / Wyatt, R.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Vaccine-elicited primate antibodies use a distinct approach to the HIV-1 primary receptor binding site informing vaccine redesign.
Authors: Tran, K. / Poulsen, C. / Guenaga, J. / de Val Alda, N. / Wilson, R. / Sundling, C. / Li, Y. / Stanfield, R.L. / Wilson, I.A. / Ward, A.B. / Karlsson Hedestam, G.B. / Wyatt, R.T.
History
DepositionMay 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: GE136 Heavy Chain Fab
L: GE136 Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4787
Polymers48,0062
Non-polymers4725
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-70 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.920, 71.500, 154.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody GE136 Heavy Chain Fab


Mass: 24620.561 Da / Num. of mol.: 1 / Fragment: Fab fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: CMV-R expression plasmid / Cell line (production host): 293F / Production host: Homo sapiens (human)
#2: Antibody GE136 Light Chain Fab


Mass: 23384.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: CMV-R expression plasmid / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1M Citric Acid, 1.6M Ammonium Sulfate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 6, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 34482 / Num. obs: 33654 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.099 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 12.34
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.050.544.59118692470197.4
2.05-2.110.4835.12114882356197.5
2.11-2.170.4285.9116192348197.7
2.17-2.240.3626.73112862260197.6
2.24-2.310.3217.46109312168197.6
2.31-2.390.3028.14108992128197.7
2.39-2.480.2878.63106692047197.9
2.48-2.580.2299.86103691975197.8
2.58-2.70.19111.38100711894197.9
2.7-2.830.16212.7898911837196.9
2.83-2.980.13714.893511741197.8
2.98-3.160.10616.7687931620197.3
3.16-3.380.08718.5883861553196.5
3.38-3.650.07420.1977321437197.6
3.65-40.07221.2471091337196
4-4.470.06622.6165761232197.5
4.47-5.160.06323.8760271086198.1
5.16-6.320.06623.955704947199.3
6.32-8.940.0625.744974773199.9
8.94-38.8160.05726.42673445198.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
JBluIce-EPICSdata collection
XDSdata reduction
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→38.816 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8243 / SU ML: 0.24 / σ(F): 1.34 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 1673 4.98 %Random
Rwork0.2139 ---
obs0.2153 33611 97.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.12 Å2 / Biso mean: 29.5436 Å2 / Biso min: 11.14 Å2
Refinement stepCycle: LAST / Resolution: 2→38.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3223 0 27 344 3594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033334
X-RAY DIFFRACTIONf_angle_d0.8034553
X-RAY DIFFRACTIONf_chiral_restr0.051521
X-RAY DIFFRACTIONf_plane_restr0.004573
X-RAY DIFFRACTIONf_dihedral_angle_d11.5751158
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.05890.26271370.22942630276797
2.0589-2.12540.30361390.23562611275098
2.1254-2.20130.29451340.23552598273297
2.2013-2.28950.24141390.21942636277598
2.2895-2.39360.26461370.2282628276598
2.3936-2.51980.28931390.24092637277698
2.5198-2.67770.26851400.24752643278398
2.6777-2.88430.28381360.24592641277797
2.8843-3.17450.24951350.24072651278697
3.1745-3.63350.23481410.20812670281197
3.6335-4.57670.20671420.17682699284197
4.5767-38.82280.20541540.18972894304899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8929-0.1440.24754.06112.04713.2299-0.1432-0.3747-0.24110.6102-0.08930.5920.6333-0.4940.16070.2931-0.02130.10130.27230.04880.3184-3.598-23.7758-12.0145
21.6401-0.3555-1.00250.66030.28590.9792-0.0846-0.1401-0.10240.11390.05230.01070.05260.02660.02530.20480.0118-0.05080.21070.02630.206612.7873-18.5043-23.4534
33.96511.0903-0.77054.3287-0.74023.3162-0.14430.06820.2544-0.2644-0.1009-0.41950.01450.41980.21370.17490.0048-0.0490.17840.01370.224330.0217-21.4964-36.8731
47.94941.42910.36222.62930.05571.8778-0.16950.3860.1425-0.02530.2583-0.2201-0.16890.3912-0.04190.1512-0.0181-0.01620.2180.00160.13935.45883.2736-18.329
54.2743-0.98780.10952.6177-0.4952.46410.03180.08460.06780.041-0.03960.1616-0.17580.20930.03350.1101-0.0163-0.02060.2183-0.01120.118-5.62660.7958-13.8861
62.72691.3629-0.42594.4626-0.55012.5651-0.2069-0.64330.02860.47530.091-0.2227-0.1755-0.03660.09090.2003-0.0146-0.01940.323-0.02270.1172-0.20671.6359-6.5457
73.8661.6970.49773.80110.52232.809-0.1802-0.5025-0.12660.13410.1296-0.149-0.14170.52190.00050.1734-0.0063-0.03270.31220.02760.08864.6602-1.7312-11.3795
88.70836.0109-1.24126.7326-0.76851.7911-0.4624-0.0336-0.4098-0.35820.2889-0.0710.1599-0.16360.19510.13380.0123-0.01310.20660.02310.08951.5078-4.3756-16.1826
91.32690.34410.52625.35024.82646.14050.1287-0.0618-0.1765-0.1628-0.0494-0.24490.221-0.03-0.05510.15520.0099-0.02060.11760.02370.182319.8339-11.2181-39.7513
102.7791.91962.68943.38973.82844.6761-0.42560.3612-0.0828-0.14880.1320.2602-0.26130.50390.18680.116-0.0071-0.01120.20670.00720.190914.6036-2.6467-32.5934
112.06030.62131.11992.11841.04054.76-0.06770.0220.1561-0.0062-0.09720.1936-0.0274-0.04020.17650.1071-0.0083-0.00540.1865-0.03940.211315.237-7.5046-32.164
123.28281.23871.62992.4410.51922.24930.01190.44240.1134-0.5061-0.13920.43590.2138-0.16460.07510.27930.0846-0.09780.1972-0.00820.23512.2344-14.9087-46.3303
131.56940.32480.01576.66094.60386.4078-0.04320.0897-0.0454-0.63880.02890.386-0.3186-0.26070.07130.1965-0.0032-0.04950.1630.01640.228114.3866-2.1853-42.647
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN H AND (RESSEQ 2:87 )H0
2X-RAY DIFFRACTION2CHAIN H AND (RESSEQ 88:175 )H0
3X-RAY DIFFRACTION3CHAIN H AND (RESSEQ 176:213 )H0
4X-RAY DIFFRACTION4CHAIN L AND (RESSEQ 2:18 )L0
5X-RAY DIFFRACTION5CHAIN L AND (RESSEQ 19:38 )L0
6X-RAY DIFFRACTION6CHAIN L AND (RESSEQ 39:75 )L0
7X-RAY DIFFRACTION7CHAIN L AND (RESSEQ 76:92 )L0
8X-RAY DIFFRACTION8CHAIN L AND (RESSEQ 93:106A)L0
9X-RAY DIFFRACTION9CHAIN L AND (RESSEQ 107:137 )L0
10X-RAY DIFFRACTION10CHAIN L AND (RESSEQ 138:150 )L0
11X-RAY DIFFRACTION11CHAIN L AND (RESSEQ 151:173 )L0
12X-RAY DIFFRACTION12CHAIN L AND (RESSEQ 174:187 )L0
13X-RAY DIFFRACTION13CHAIN L AND (RESSEQ 188:208 )L0

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