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- PDB-4wuk: Crystal structure of apo CH65 Fab -

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Basic information

Entry
Database: PDB / ID: 4wuk
TitleCrystal structure of apo CH65 Fab
Components
  • CH65 heavy chain
  • CH65 light chain
KeywordsIMMUNE SYSTEM / immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLee, P.S. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI099275 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of the apo anti-influenza CH65 Fab.
Authors: Lee, P.S. / Arnell, A.J. / Wilson, I.A.
History
DepositionNov 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Other
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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

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Assembly

Deposited unit
H: CH65 heavy chain
L: CH65 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5414
Polymers48,1262
Non-polymers4152
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-10 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.095, 67.024, 130.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody CH65 heavy chain


Mass: 25406.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#2: Antibody CH65 light chain


Mass: 22720.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10 / Details: 1.8 M ammonium sulfate, 0.1 M CHES

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2012
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 55829 / % possible obs: 99.6 % / Redundancy: 7 % / Rsym value: 0.08 / Net I/σ(I): 14.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.5 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3sm5

3sm5
PDB Unreleased entry


Resolution: 1.7→46.763 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2073 2802 5.06 %
Rwork0.1805 --
obs0.1819 55419 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→46.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 26 348 3645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093444
X-RAY DIFFRACTIONf_angle_d1.2094720
X-RAY DIFFRACTIONf_dihedral_angle_d13.9191241
X-RAY DIFFRACTIONf_chiral_restr0.053536
X-RAY DIFFRACTIONf_plane_restr0.006603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6993-1.72860.34881350.28152421X-RAY DIFFRACTION93
1.7286-1.760.2521250.23052629X-RAY DIFFRACTION100
1.76-1.79390.26891460.19692623X-RAY DIFFRACTION100
1.7939-1.83050.23131460.18892611X-RAY DIFFRACTION100
1.8305-1.87030.2251420.19362617X-RAY DIFFRACTION100
1.8703-1.91380.30551420.26352566X-RAY DIFFRACTION97
1.9138-1.96170.38731330.3362485X-RAY DIFFRACTION95
1.9617-2.01470.19131430.19042612X-RAY DIFFRACTION100
2.0147-2.0740.23061660.21352598X-RAY DIFFRACTION99
2.074-2.14090.23251380.20262633X-RAY DIFFRACTION99
2.1409-2.21740.20071390.17182639X-RAY DIFFRACTION100
2.2174-2.30620.271410.26082553X-RAY DIFFRACTION96
2.3062-2.41120.21231340.17562636X-RAY DIFFRACTION100
2.4112-2.53830.21471310.18662664X-RAY DIFFRACTION100
2.5383-2.69730.23671370.19262671X-RAY DIFFRACTION100
2.6973-2.90550.22871430.19912669X-RAY DIFFRACTION100
2.9055-3.19790.19141390.17932688X-RAY DIFFRACTION100
3.1979-3.66050.18961340.15962714X-RAY DIFFRACTION100
3.6605-4.61120.15541410.12562726X-RAY DIFFRACTION100
4.6112-46.78040.14271470.14182862X-RAY DIFFRACTION100
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)
11.53780.5481-0.68281.5922-1.01442.17350.0128-0.0243-0.01560.01870.0315-0.0321-0.03050.032-0.03880.13520.01890.01360.1265-0.00610.077820.923-17.707-65.38
22.4694-1.0155-0.57534.49821.53522.09110.0422-0.09760.16050.0694-0.04830.2357-0.0227-0.08460.00610.20290.00480.00030.13020.00660.1219-5.375-15.886-35.027
33.7099-2.6556-1.22972.4310.7772.03190.00440.01950.59990.12220.1075-0.1963-0.4407-0.0379-0.07450.3050.00650.05190.15130.02040.252117.0093.256-64.057
41.6431-0.70640.98273.5412-1.79423.22840.0659-0.04060.01150.0879-0.1454-0.18310.02290.10410.0980.211-0.0030.03780.1176-0.01910.13547.579-5.789-34.451
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain H and resid 1:113H1 - 113
2X-RAY DIFFRACTION2chain H and resid 114:300H114 - 300
3X-RAY DIFFRACTION3chain L and resid 1:107L1 - 107
4X-RAY DIFFRACTION4chain L and resid 108:300L108 - 300

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