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- PDB-5b4m: Crystal structure of an Fab against human influenza A -

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Basic information

Entry
Database: PDB / ID: 5b4m
TitleCrystal structure of an Fab against human influenza A
Components
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / Human Influenza A / non-structure 1 / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsYuan, Y.A.
CitationJournal: To Be Published
Title: Crystal structure of an Fab against human influenza A
Authors: Yuan, Y.A.
History
DepositionApr 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab heavy chain
L: Fab light chain
C: Fab heavy chain
D: Fab light chain


Theoretical massNumber of molelcules
Total (without water)95,8484
Polymers95,8484
Non-polymers00
Water00
1
H: Fab heavy chain
L: Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,9242
Polymers47,9242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-22 kcal/mol
Surface area19800 Å2
MethodPISA
2
C: Fab heavy chain
D: Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,9242
Polymers47,9242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-22 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.592, 90.940, 81.442
Angle α, β, γ (deg.)90.00, 92.21, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11H
21C
12L
22D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGHA1 - 2211 - 221
21ARGARGCC1 - 2211 - 221
12CYSCYSLB1 - 2181 - 218
22CYSCYSDD1 - 2181 - 218

NCS ensembles :
ID
1
2

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Components

#1: Antibody Fab heavy chain


Mass: 23993.029 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab light chain


Mass: 23931.182 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
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: 1.99 Å3/Da / Density % sol: 38.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 3350, NaCl, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Date: Jul 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→81.38 Å / Num. obs: 27507 / % possible obs: 98.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.1
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.2 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.4→81.38 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.844 / SU B: 40.151 / SU ML: 0.412 / Cross valid method: THROUGHOUT / ESU R: 1.2 / ESU R Free: 0.412 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33796 1477 5.1 %RANDOM
Rwork0.28508 ---
obs0.28785 27507 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.122 Å2
Baniso -1Baniso -2Baniso -3
1-5.64 Å20 Å2-0.37 Å2
2---2.83 Å20 Å2
3----2.78 Å2
Refinement stepCycle: 1 / Resolution: 2.4→81.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6738 0 0 0 6738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.026910
X-RAY DIFFRACTIONr_bond_other_d0.0040.026276
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9519428
X-RAY DIFFRACTIONr_angle_other_deg1.022314534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9145874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7424.357280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.514151090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3751528
X-RAY DIFFRACTIONr_chiral_restr0.0820.21064
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217844
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021544
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1380.2293508
X-RAY DIFFRACTIONr_mcbond_other0.1370.2283507
X-RAY DIFFRACTIONr_mcangle_it0.260.3424378
X-RAY DIFFRACTIONr_mcangle_other0.260.3424379
X-RAY DIFFRACTIONr_scbond_it0.0650.2313402
X-RAY DIFFRACTIONr_scbond_other0.0640.2313402
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.1380.3455051
X-RAY DIFFRACTIONr_long_range_B_refined1.1781.8587642
X-RAY DIFFRACTIONr_long_range_B_other1.1781.8597643
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11H118850.1
12C118850.1
21L113210.12
22D113210.12
LS refinement shellResolution: 2.402→2.465 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 115 -
Rwork0.346 1820 -
obs--88.52 %
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)
10.7993-0.3771-0.18992.05061.07121.34460.0314-0.0696-0.0279-0.0025-0.04110.0311-0.0985-0.02080.00980.1409-0.044-0.01920.50570.03140.473813.3957-1.922921.5759
22.3318-0.7733-1.10291.10160.72591.5033-0.0394-0.15010.02930.00660.0477-0.01480.0290.0144-0.00840.0023-0.0208-0.01730.54470.04130.49323.88133.413935.3431
31.39890.98590.88722.70051.70231.9358-0.03930.03030.0767-0.03990.00830.0442-0.0450.02110.0310.14280.03460.09650.49610.03620.49214.650227.978418.0319
42.53150.33291.2920.32870.33331.9068-0.06510.09250.07210.03440.0282-0.0287-0.09070.17880.0370.11210.02530.04980.49020.01680.54125.926821.7175.2839
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 221
2X-RAY DIFFRACTION2L1 - 218
3X-RAY DIFFRACTION3C1 - 221
4X-RAY DIFFRACTION4D1 - 218

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