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- PDB-5i1k: CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV5-51/IGKV3-20 -

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Basic information

Entry
Database: PDB / ID: 5i1k
TitleCRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV5-51/IGKV3-20
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: 1.65 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
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,97412
Polymers47,9182
Non-polymers1,05610
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-23 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.760, 74.090, 102.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody FAB LIGHT CHAIN


Mass: 23373.900 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 FAB HEAVY CHAIN


Mass: 24544.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 537 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.54 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 1.0 M AMMONIUM SULFATE, 0.1 M CHES PH 9.5 / PH range: 9.5

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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: Mar 18, 2009 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→28.2 Å / Num. obs: 53058 / % possible obs: 89.8 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 27.5
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 5.8 / % possible all: 49.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.717 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.092
RfactorNum. reflection% reflectionSelection details
Rfree0.19748 1090 2.1 %RANDOM
Rwork0.17245 ---
obs0.17298 51882 89.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0 Å20 Å2
2---0.34 Å2-0 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 62 527 3799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.023359
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.271.9734568
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9695422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2424.228123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.65215528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1861512
X-RAY DIFFRACTIONr_chiral_restr0.1110.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212474
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_it2.6262.1031697
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.7954.6892116
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.5842.5621662
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.2675520
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: 1.653→1.695 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 43 -
Rwork0.25 2072 -
obs--49.6 %

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