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- PDB-5whz: PGDM1400-10E8v4 CODV Fab -

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Basic information

Entry
Database: PDB / ID: 5whz
TitlePGDM1400-10E8v4 CODV Fab
Components
  • Anti-HIV CODV-Fab Heavy chain
  • Anti-HIV CODV-Fab Light chain
KeywordsIMMUNE SYSTEM / cross-over dual variable immunoglobin / multifunctional biotherapeutic format / bispecific property / CODV / HIV
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.549 Å
AuthorsLord, D.M. / Wei, R.R.
CitationJournal: Science / Year: 2017
Title: Trispecific broadly neutralizing HIV antibodies mediate potent SHIV protection in macaques.
Authors: Xu, L. / Pegu, A. / Rao, E. / Doria-Rose, N. / Beninga, J. / McKee, K. / Lord, D.M. / Wei, R.R. / Deng, G. / Louder, M. / Schmidt, S.D. / Mankoff, Z. / Wu, L. / Asokan, M. / Beil, C. / ...Authors: Xu, L. / Pegu, A. / Rao, E. / Doria-Rose, N. / Beninga, J. / McKee, K. / Lord, D.M. / Wei, R.R. / Deng, G. / Louder, M. / Schmidt, S.D. / Mankoff, Z. / Wu, L. / Asokan, M. / Beil, C. / Lange, C. / Leuschner, W.D. / Kruip, J. / Sendak, R. / Do Kwon, Y. / Zhou, T. / Chen, X. / Bailer, R.T. / Wang, K. / Choe, M. / Tartaglia, L.J. / Barouch, D.H. / O'Dell, S. / Todd, J.P. / Burton, D.R. / Roederer, M. / Connors, M. / Koup, R.A. / Kwong, P.D. / Yang, Z.Y. / Mascola, J.R. / Nabel, G.J.
History
DepositionJul 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Anti-HIV CODV-Fab Light chain
H: Anti-HIV CODV-Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)80,4012
Polymers80,4012
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-37 kcal/mol
Surface area33170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.226, 151.226, 200.595
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Antibody Anti-HIV CODV-Fab Light chain


Mass: 36878.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Anti-HIV CODV-Fab Heavy chain


Mass: 43522.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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: 4.12 Å3/Da / Density % sol: 70.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1 / Details: 1.68M ammonium sulfate 0.1M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 3.549→59.552 Å / Num. obs: 17034 / % possible obs: 100 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.035 / Net I/σ(I): 14.7
Reflection shellResolution: 3.55→3.74 Å / Redundancy: 9.5 % / Rmerge(I) obs: 3.236 / Mean I/σ(I) obs: 1 / Num. unique all: 2423 / Rpim(I) all: 0.77 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IQ9, 4RQQ

5iq9

4rqq


Resolution: 3.549→59.552 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.95
RfactorNum. reflection% reflection
Rfree0.2867 838 4.93 %
Rwork0.2394 --
obs0.2417 16983 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 399.15 Å2 / Biso mean: 220.8852 Å2 / Biso min: 95.32 Å2
Refinement stepCycle: final / Resolution: 3.549→59.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5169 0 0 0 5169
Num. residues----677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025297
X-RAY DIFFRACTIONf_angle_d0.5537207
X-RAY DIFFRACTIONf_chiral_restr0.042794
X-RAY DIFFRACTIONf_plane_restr0.005926
X-RAY DIFFRACTIONf_dihedral_angle_d6.033110
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.549-3.77130.39411500.34126072757
3.7713-4.06250.42391300.296826422772
4.0625-4.47120.28681540.226726302784
4.4712-5.11780.28241330.212126692802
5.1178-6.44670.29041510.247327012852
6.4467-59.56070.2541200.229928963016
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)
14.6297-4.49040.12416.9693-1.4983-0.80660.18390.4137-0.9176-0.60250.17290.9183-0.3783-0.1172-0.35471.5853-0.176-0.321.57040.25681.7903107.0941159.513135.1561
28.3276-4.10412.29077.16390.56636.52330.1066-1.4095-0.40430.01610.83520.3601-0.0037-1.5973-0.92571.1976-0.0359-0.00291.43780.41961.139130.822146.718153.9409
39.2056-5.45873.85986.74534.36672.2262-1.9803-0.13772.1152-0.53990.1863-0.112-1.6302-0.40791.8674.0698-0.0062-0.24962.5246-0.28512.4675126.1853184.4327165.0708
46.5177-4.61782.86557.1229-0.9060.14510.09930.5983-0.3202-0.20640.24090.2867-0.17180.14-0.38381.6486-0.0491-0.0291.54820.10111.0226139.4724151.2285135.4806
53.0253-2.5205-2.05695.8269-0.70311.05260.3307-0.9978-0.00620.03920.0844-0.36550.71960.3748-0.54961.4650.075-0.37461.56910.14591.153116.1593179.8157136.4187
62.36144.8564-0.79769.45234.53412.5252-0.51311.1486-0.41040.4074-0.0285-0.4445-0.3727-2.16340.33173.36890.5290.27012.9692-0.07272.08137.5284174.753173.0239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 2 through 126 )L2 - 126
2X-RAY DIFFRACTION2chain 'L' and (resid 127 through 227 )L127 - 227
3X-RAY DIFFRACTION3chain 'L' and (resid 228 through 337 )L228 - 337
4X-RAY DIFFRACTION4chain 'H' and (resid 1 through 139 )H1 - 139
5X-RAY DIFFRACTION5chain 'H' and (resid 140 through 307 )H140 - 307
6X-RAY DIFFRACTION6chain 'H' and (resid 308 through 384 )H308 - 384

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