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- PDB-4fq2: Crystal Structure of 10-1074 Fab -

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Basic information

Entry
Database: PDB / ID: 4fq2
TitleCrystal Structure of 10-1074 Fab
Components
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / IG FOLD / ANTI HIV / ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsScharf, L. / Bjorkman, P.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Complex-type N-glycan recognition by potent broadly neutralizing HIV antibodies.
Authors: Mouquet, H. / Scharf, L. / Euler, Z. / Liu, Y. / Eden, C. / Scheid, J.F. / Halper-Stromberg, A. / Gnanapragasam, P.N. / Spencer, D.I. / Seaman, M.S. / Schuitemaker, H. / Feizi, T. / ...Authors: Mouquet, H. / Scharf, L. / Euler, Z. / Liu, Y. / Eden, C. / Scheid, J.F. / Halper-Stromberg, A. / Gnanapragasam, P.N. / Spencer, D.I. / Seaman, M.S. / Schuitemaker, H. / Feizi, T. / Nussenzweig, M.C. / Bjorkman, P.J.
History
DepositionJun 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2May 19, 2021Group: Derived calculations / Source and taxonomy / Category: entity_src_gen / struct_site
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 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

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Assembly

Deposited unit
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9806
Polymers49,6712
Non-polymers3084
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-25 kcal/mol
Surface area20770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.383, 40.261, 84.460
Angle α, β, γ (deg.)90.00, 95.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab heavy chain


Mass: 26490.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
#2: Antibody Fab light chain


Mass: 23180.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-6E / Production host: homo sapiens (human)
#3: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: PEG 3350, Bis-Tris HCl, NaCl, pH 5.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2012
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.704→36.313 Å / Num. all: 42465 / Num. obs: 42465 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rsym value: 0.075 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.7-1.82.30.8490.90.849180.6
1.8-1.912.80.5581.40.558198
1.91-2.042.70.3282.40.328196.2
2.04-2.22.80.23.80.2197.8
2.2-2.412.80.155.10.15196.4
2.41-2.692.80.1017.40.101197
2.69-3.112.80.06511.10.065195.3
3.11-3.812.80.03917.60.039195.2
3.81-5.392.80.02920.70.029192.6
5.39-36.3132.80.02721.30.027192.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å36.31 Å
Translation2.5 Å36.31 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→36.313 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.23 / σ(F): 1.35 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 1479 4.72 %
Rwork0.1868 --
obs0.1885 31363 95.46 %
all-32856 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.373 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.1653 Å20 Å2-2.7781 Å2
2--2.1845 Å2-0 Å2
3---3.9808 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 20 305 3685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073466
X-RAY DIFFRACTIONf_angle_d1.2344715
X-RAY DIFFRACTIONf_dihedral_angle_d15.3791236
X-RAY DIFFRACTIONf_chiral_restr0.079529
X-RAY DIFFRACTIONf_plane_restr0.005601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96130.29161350.24142719X-RAY DIFFRACTION97
1.9613-2.03140.25221340.21832722X-RAY DIFFRACTION95
2.0314-2.11280.24061370.21062743X-RAY DIFFRACTION98
2.1128-2.20890.2361340.19582735X-RAY DIFFRACTION97
2.2089-2.32530.24291340.20332706X-RAY DIFFRACTION96
2.3253-2.4710.22091340.2052694X-RAY DIFFRACTION95
2.471-2.66170.26191370.20652776X-RAY DIFFRACTION97
2.6617-2.92950.27631340.19962701X-RAY DIFFRACTION95
2.9295-3.35310.21471320.18172685X-RAY DIFFRACTION94
3.3531-4.22360.20151340.16152699X-RAY DIFFRACTION94
4.2236-36.31980.17771340.16512704X-RAY DIFFRACTION91
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)
13.1711-0.84690.7593.8756-0.90163.4874-0.0041-0.3207-0.13240.2058-0.0224-0.0714-0.048-0.04610.0280.1046-0.03830.01840.17470.01790.152-10.9374.0689188.2397
21.87030.13571.0620.97070.17091.8914-0.0466-0.492-0.09080.07320.05480.0922-0.1729-0.3138-0.00220.148-0.02590.06460.1680.03670.1538-2.71937.139183.3925
34.71851.75660.54745.04450.56323.80690.0219-0.68870.17850.3916-0.06730.0621-0.3649-0.36080.01290.24730.0287-0.03810.35310.02440.152716.16478.3065200.9326
45.62141.0296-0.42342.3821-0.37070.6439-0.10440.1537-0.3107-0.1140.08080.05420.0894-0.03710.02020.12760.00790.01450.0833-0.01250.10960.48927.3113166.9493
51.65680.09130.48061.8251-1.11846.86740.084-0.3261-0.16320.2137-0.0264-0.0470.1056-0.14-0.04860.1253-0.0387-0.00220.14670.01950.161828.7559-0.5033193.1756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:90 )H1 - 90
2X-RAY DIFFRACTION2( CHAIN H AND RESID 91:138 )H91 - 138
3X-RAY DIFFRACTION3( CHAIN H AND RESID 139:216 )H139 - 216
4X-RAY DIFFRACTION4( CHAIN L AND RESID 8:105 )L8 - 105
5X-RAY DIFFRACTION5( CHAIN L AND RESID 106:210 )L106 - 210

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