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- PDB-5i1d: CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV3-23/IGKV4-1 -

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Basic information

Entry
Database: PDB / ID: 5i1d
TitleCRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV3-23/IGKV4-1
Components
  • FAB HEAVY CHAIN
  • FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / MONOCLONAL ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTeplyakov, A. / Obmolova, G. / Malia, T. / Luo, J. / Gilliland, G.
Citation
Journal: Mabs / Year: 2016
Title: Structural diversity in a human antibody germline library.
Authors: Teplyakov, A. / Obmolova, G. / Malia, T.J. / Luo, J. / Muzammil, S. / Sweet, R. / Almagro, J.C. / Gilliland, G.L.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Protein crystallization with microseed matrix screening: application to human germline antibody Fabs.
Authors: Obmolova, G. / Malia, T.J. / Teplyakov, A. / Sweet, R.W. / Gilliland, G.L.
History
DepositionFeb 5, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 24, 2016ID: 3QOS
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jun 29, 2016Group: Database references
Revision 1.3Aug 3, 2016Group: Database references
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: FAB LIGHT CHAIN
H: FAB HEAVY CHAIN
A: FAB LIGHT CHAIN
B: FAB HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0587
Polymers96,7704
Non-polymers2883
Water11,440635
1
L: FAB LIGHT CHAIN
H: FAB HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4813
Polymers48,3852
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-39 kcal/mol
Surface area19750 Å2
MethodPISA
2
A: FAB LIGHT CHAIN
B: FAB HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5774
Polymers48,3852
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-43 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.710, 111.000, 159.990
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 FAB LIGHT CHAIN


Mass: 24229.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody FAB HEAVY CHAIN


Mass: 24154.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.87 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0 M AMMONIUM SULFATE, 2% PEG 400, 0.1 M HEPES PH 7.5
PH range: 7.5

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 23, 2008 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 75540 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 11.6 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 21.6
Reflection shellResolution: 2→2.06 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 5 / % possible all: 96.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B2X,1LVE

2b2x

1lve


Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.449 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.158
RfactorNum. reflection% reflectionSelection details
Rfree0.25132 1109 1.5 %RANDOM
Rwork0.21578 ---
obs0.21632 74238 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 46.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2---0.23 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6548 0 15 635 7198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226729
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.9589159
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8975859
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34524.715263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55151072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.871522
X-RAY DIFFRACTIONr_chiral_restr0.0710.21028
X-RAY DIFFRACTIONr_gen_planes_refined00.0215050
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.81224295
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.75246934
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it23.763882434
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it24.83882225
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.004→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 80 -
Rwork0.263 5173 -
obs--96.9 %

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