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- PDB-5i1l: CRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV5-51/IGKV4-1 -

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Basic information

Entry
Database: PDB / ID: 5i1l
TitleCRYSTAL STRUCTURE OF HUMAN GERMLINE ANTIBODY IGHV5-51/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: 1.95 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 6, 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

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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)97,7336
Polymers97,5494
Non-polymers1842
Water8,017445
1
L: FAB LIGHT CHAIN
H: FAB HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8663
Polymers48,7742
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-27 kcal/mol
Surface area20580 Å2
MethodPISA
2
A: FAB LIGHT CHAIN
B: FAB HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8663
Polymers48,7742
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-25 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.970, 37.960, 112.340
Angle α, β, γ (deg.)90.00, 100.42, 90.00
Int Tables number4
Space group name H-MP1211

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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: 24544.506 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 24% PEG 3K, 0.2 M AMMONIUM ACETATE, 0.1 M TRIS PH 8.5
PH range: 8.5

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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 26, 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: 1.95→28 Å / Num. obs: 61554 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.7
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 3.1 / % possible all: 67.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.4 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.175
RfactorNum. reflection% reflectionSelection details
Rfree0.25807 1246 2 %RANDOM
Rwork0.19353 ---
obs0.19485 60181 92.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.912 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å2-0.76 Å2
2--1.79 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6700 0 12 445 7157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226905
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9549403
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3025876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61824.794267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.563151106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0421518
X-RAY DIFFRACTIONr_chiral_restr0.0810.21046
X-RAY DIFFRACTIONr_gen_planes_refined00.0215182
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_it3.00124379
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.20247088
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it10.71882526
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it11.195882315
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: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 63 -
Rwork0.243 3125 -
obs--67.1 %
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)
12.0363-0.61040.19281.09890.43971.29540.04910.1251-0.0207-0.1075-0.03290.0887-0.07430.1895-0.01630.0735-0.0443-0.00630.1073-0.00840.052877.11514.450165.1011
21.3801-0.75070.45260.98580.05442.9506-0.01710.02630.02-0.07370.00270.1265-0.0038-0.05020.01430.1041-0.02740.01610.0223-0.03010.10254.22033.046537.4612
33.77241.74580.97171.76250.47191.7522-0.17420.13790.455-0.01930.01480.2075-0.16330.07610.15930.1440.0095-0.02320.01290.01450.180930.997512.451910.9204
40.9281-0.15990.15110.7364-0.55292.3389-0.0228-0.0075-0.15330.0643-0.0842-0.02130.08940.07050.1070.076-0.040.00750.1142-0.00530.125815.5257-2.5098-16.9094
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 113
2X-RAY DIFFRACTION1H1 - 119
3X-RAY DIFFRACTION2L114 - 220
4X-RAY DIFFRACTION2H120 - 225
5X-RAY DIFFRACTION3A1 - 113
6X-RAY DIFFRACTION3B1 - 119
7X-RAY DIFFRACTION4A114 - 219
8X-RAY DIFFRACTION4B120 - 219

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