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- PDB-2hkh: Crystal structure of the Fab M75 -

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Basic information

Entry
Database: PDB / ID: 2hkh
TitleCrystal structure of the Fab M75
Components
  • Immunoglobulin Heavy chain Fab fragment
  • Immunoglobulin Light chain Fab fragment
KeywordsIMMUNE SYSTEM / Immunoglobulin / Fab fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKral, V. / Mader, P. / Stouracova, R. / Fabry, M. / Sedlacek, J. / Brynda, J.
CitationJournal: Proteins / Year: 2008
Title: Stabilization of antibody structure upon association to a human carbonic anhydrase IX epitope studied by X-ray crystallography, microcalorimetry, and molecular dynamics simulations.
Authors: Kral, V. / Mader, P. / Collard, R. / Fabry, M. / Horejsi, M. / Rezacova, P. / Kozisek, M. / Zavada, J. / Sedlacek, J. / Rulisek, L. / Brynda, J.
History
DepositionJul 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE AT THE TIME OF PROCESSING, A UNP REFERENCE SEQUENCE WAS NOT AVAILABLE FOR IMMUNOGLOBULIN ...SEQUENCE AT THE TIME OF PROCESSING, A UNP REFERENCE SEQUENCE WAS NOT AVAILABLE FOR IMMUNOGLOBULIN LIGHT CHAIN FAB FRAGMENT OR IMMUNOGLOBULIN HEAVY CHAIN FAB FRAGMENT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Immunoglobulin Light chain Fab fragment
H: Immunoglobulin Heavy chain Fab fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6403
Polymers47,5482
Non-polymers921
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-31 kcal/mol
Surface area19850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)40.982, 43.154, 57.370
Angle α, β, γ (deg.)85.30, 88.45, 84.29
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Immunoglobulin Light chain Fab fragment


Mass: 24144.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: Hybridoma cells
#2: Antibody Immunoglobulin Heavy chain Fab fragment


Mass: 23403.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: Hybridoma cells
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 4000, 100 mM Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 10, 2001
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 57110 / Num. obs: 57110 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 39.4 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 6.5
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.304 / Num. unique all: 1573 / Rsym value: 0.304 / % possible all: 68.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1NBV

1nbv


Resolution: 2.1→20.46 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.903 / SU B: 14.744 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.633 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The Friedel pairs were used in phasing.
RfactorNum. reflection% reflectionSelection details
Rfree0.27292 1417 8.2 %RANDOM
Rwork0.21934 ---
obs0.22394 15795 75.84 %-
all-15795 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.073 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å2-0.52 Å20.2 Å2
2--0.28 Å2-0.22 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 6 96 3378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223365
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.954586
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.3565423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36224.328134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.83815533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0451513
X-RAY DIFFRACTIONr_chiral_restr0.1010.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022539
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.21506
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22227
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2180
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4971.52165
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.86123464
X-RAY DIFFRACTIONr_scbond_it1.32831367
X-RAY DIFFRACTIONr_scangle_it2.0014.51122
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 76 -
Rwork0.286 785 -
obs--50.83 %
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)
13.4806-1.55260.99732.4181-0.68442.01310.0771-0.0993-0.0187-0.0927-0.0198-0.06520.099-0.0594-0.0573-0.0924-0.01630.0096-0.08740.0003-0.0984.5168.1694-13.0047
22.00430.8533-2.05950.712-1.26333.76390.00220.1564-0.06340.0264-0.0111-0.0720.0641-0.13070.0088-0.0994-0.0048-0.0306-0.10680.01-0.03367.514-13.416916.0498
32.3385-1.51291.66382.9806-1.21543.70680.01220.22310.1592-0.1312-0.071-0.1613-0.2420.08480.0587-0.1053-0.01690.0267-0.0098-0.0204-0.0315-6.66321.71050.4005
44.5835-2.2759-0.36023.43120.35562.5233-0.1576-0.05670.03130.24080.1662-0.22450.01190.1208-0.0086-0.116-0.0695-0.0479-0.08060.0082-0.041112.9371-0.387423.5027
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LA1 - 1121 - 112
2X-RAY DIFFRACTION2LA113 - 219113 - 219
3X-RAY DIFFRACTION3HB2 - 1182 - 118
4X-RAY DIFFRACTION4HB119 - 218119 - 218

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