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- PDB-3s34: Structure of the 1121B Fab fragment -

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Basic information

Entry
Database: PDB / ID: 3s34
TitleStructure of the 1121B Fab fragment
Components
  • 1121B Fab heavy chain
  • 1121B Fab light chain
KeywordsIMMUNE SYSTEM / VEGF receptor domain 3
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFranklin, M.C.
CitationJournal: Structure / Year: 2011
Title: The Structural Basis for the Function of Two Anti-VEGF Receptor 2 Antibodies.
Authors: Franklin, M.C. / Navarro, E.C. / Wang, Y. / Patel, S. / Singh, P. / Zhang, Y. / Persaud, K. / Bari, A. / Griffith, H. / Shen, L. / Balderes, P. / Kussie, P.
History
DepositionMay 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_residues / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_residues / 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
Revision 1.3Oct 9, 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: 1121B Fab light chain
H: 1121B Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6653
Polymers46,5702
Non-polymers951
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-31 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.426, 66.426, 203.868
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Antibody 1121B Fab light chain


Mass: 23245.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): MAMMALIAN KIDNEY CELLS HEK293 / Production host: Homo sapiens (human)
#2: Antibody 1121B Fab heavy chain


Mass: 23324.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): MAMMALIAN KIDNEY CELLS HEK293 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Na/K phosphate, pH 5.5, 40% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 22, 2008
RadiationMonochromator: Rigaku VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→70 Å / Num. all: 27477 / Num. obs: 26790 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rsym value: 0.06 / Net I/σ(I): 20.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 4.5 / % possible all: 78.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YY9

1yy9


Resolution: 2.2→50.1 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.662 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22311 1345 5 %RANDOM
Rwork0.18313 ---
obs0.1852 25334 97.15 %-
all-27461 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.381 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.22 Å20 Å2
2--0.43 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3223 0 5 278 3506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223295
X-RAY DIFFRACTIONr_bond_other_d0.0020.022202
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9524482
X-RAY DIFFRACTIONr_angle_other_deg0.8713.0045377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.065423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70124.286126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0615523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1161513
X-RAY DIFFRACTIONr_chiral_restr0.080.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023673
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02653
X-RAY DIFFRACTIONr_nbd_refined0.1890.2470
X-RAY DIFFRACTIONr_nbd_other0.1990.22119
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21501
X-RAY DIFFRACTIONr_nbtor_other0.0840.21808
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.211
X-RAY DIFFRACTIONr_mcbond_it0.7271.52689
X-RAY DIFFRACTIONr_mcbond_other0.1271.5862
X-RAY DIFFRACTIONr_mcangle_it0.9223418
X-RAY DIFFRACTIONr_scbond_it1.56131414
X-RAY DIFFRACTIONr_scangle_it2.1524.51064
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 65 -
Rwork0.225 1362 -
obs--71.24 %
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)
15.8509-2.82575.163.1043-2.34955.75780.5257-0.1763-0.7325-0.14850.0650.49020.8907-0.3945-0.59070.0971-0.0416-0.0731-0.17960.0445-0.0313-35.78135.879410.5047
21.3747-0.5014-0.62383.76722.35694.82340.0469-0.23670.0089-0.11660.08320.0206-0.26130.1623-0.13-0.2009-0.02330.0194-0.13060.0259-0.1657-21.238519.988936.5129
32.6929-0.55912.27592.52730.71535.5005-0.0047-0.01620.22960.1108-0.0717-0.235-0.1236-0.0370.0764-0.17440.0413-0.0072-0.19160.0325-0.1405-35.363927.33412.588
44.06390.5845-0.49576.1219-0.58362.24810.0424-0.323-0.20270.3126-0.1-0.19190.06930.22020.0576-0.2099-0.0550.0169-0.1127-0.0186-0.1727-8.92425.367327.3488
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 109
2X-RAY DIFFRACTION2L110 - 214
3X-RAY DIFFRACTION3H1 - 116
4X-RAY DIFFRACTION4H117 - 219

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