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- PDB-3u4b: CH04H/CH02L Fab P4 -

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Basic information

Entry
Database: PDB / ID: 3u4b
TitleCH04H/CH02L Fab P4
Components
  • CH02 Light chain
  • CH04 Heavy chain
KeywordsIMMUNE SYSTEM / IGG / Immunoglobulin / HIV-1 / V1V2-directed
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.893 Å
AuthorsPancera, M. / Louder, R. / Mclellan, J.S. / KWong, P.D.
CitationJournal: Nature / Year: 2011
Title: Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9.
Authors: McLellan, J.S. / Pancera, M. / Carrico, C. / Gorman, J. / Julien, J.P. / Khayat, R. / Louder, R. / Pejchal, R. / Sastry, M. / Dai, K. / O'Dell, S. / Patel, N. / Shahzad-Ul-Hussan, S. / Yang, ...Authors: McLellan, J.S. / Pancera, M. / Carrico, C. / Gorman, J. / Julien, J.P. / Khayat, R. / Louder, R. / Pejchal, R. / Sastry, M. / Dai, K. / O'Dell, S. / Patel, N. / Shahzad-Ul-Hussan, S. / Yang, Y. / Zhang, B. / Zhou, T. / Zhu, J. / Boyington, J.C. / Chuang, G.Y. / Diwanji, D. / Georgiev, I. / Do Kwon, Y. / Lee, D. / Louder, M.K. / Moquin, S. / Schmidt, S.D. / Yang, Z.Y. / Bonsignori, M. / Crump, J.A. / Kapiga, S.H. / Sam, N.E. / Haynes, B.F. / Burton, D.R. / Koff, W.C. / Walker, L.M. / Phogat, S. / Wyatt, R. / Orwenyo, J. / Wang, L.X. / Arthos, J. / Bewley, C.A. / Mascola, J.R. / Nabel, G.J. / Schief, W.R. / Ward, A.B. / Wilson, I.A. / Kwong, P.D.
History
DepositionOct 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
H: CH04 Heavy chain
L: CH02 Light chain


Theoretical massNumber of molelcules
Total (without water)49,2212
Polymers49,2212
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-24 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.196, 86.196, 185.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody CH04 Heavy chain


Mass: 25546.404 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 CH02 Light chain


Mass: 23674.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.5 Å3/Da / Density % sol: 64.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 3350, 9% 2-Methyl-2,4-pentanediol, 0.1M Li2SO4, 0.1M Imidazole pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 15, 2011
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 29046 / Num. obs: 16038
Reflection shellResolution: 2.9→3 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.893→30.475 Å / SU ML: 0.83 / σ(F): 1.33 / Phase error: 28.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 811 5.08 %
Rwork0.2214 --
obs0.2237 15976 97.86 %
all-16038 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.387 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.5086 Å20 Å2-0 Å2
2--4.5086 Å2-0 Å2
3----9.0172 Å2
Refinement stepCycle: LAST / Resolution: 2.893→30.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 0 38 3419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033482
X-RAY DIFFRACTIONf_angle_d0.7224727
X-RAY DIFFRACTIONf_dihedral_angle_d11.3961245
X-RAY DIFFRACTIONf_chiral_restr0.048512
X-RAY DIFFRACTIONf_plane_restr0.004616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.893-3.07410.34971350.292331X-RAY DIFFRACTION93
3.0741-3.31120.27221300.26242522X-RAY DIFFRACTION99
3.3112-3.64390.28261390.23122512X-RAY DIFFRACTION99
3.6439-4.17010.25041400.21192529X-RAY DIFFRACTION99
4.1701-5.24950.2221170.17752577X-RAY DIFFRACTION98
5.2495-30.47660.28371500.23252694X-RAY DIFFRACTION98
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)
12.89210.9892-1.75292.2397-0.15644.46990.2584-0.36560.26350.4346-0.2398-0.1915-0.51750.39540.00790.4469-0.134-0.02490.4855-0.00630.316415.314227.1028-25.6212
21.33460.2737-0.63347.61551.70492.8898-0.2541-0.2069-0.07350.17340.391-0.13960.35280.0518-0.08480.45250.098-0.0350.50980.02790.3643-5.26911.0016-13.5926
32.98173.08760.14545.65970.28431.7973-0.08870.2107-0.1344-0.03520.0815-0.2022-0.04430.30840.01730.37590.0120.02570.4068-0.01320.259916.045218.7733-45.81
40.36010.8-0.07181.8365-0.02360.4971-0.1068-0.14090.1677-0.25680.09330.23990.0449-0.323-0.00010.42350.0722-0.03260.6173-0.03220.5156-13.64283.7583-27.7743
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain L and resid 1:110
2X-RAY DIFFRACTION2chain L and resid 111:214
3X-RAY DIFFRACTION3chain H and resid 1:134
4X-RAY DIFFRACTION4chain H and resid 135:233

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