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- PDB-3dif: Crystal structure of FabOX117 -

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Basic information

Entry
Database: PDB / ID: 3dif
TitleCrystal structure of FabOX117
Components
  • FabOX117 Heavy Chain Fragment
  • FabOX117 Light Chain Fragment
KeywordsIMMUNE SYSTEM / Antibody fragments / Fabs / Transient expression / Structural Genomics / Oxford Protein Production Facility / OPPF / Immunoglobulin domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNettleship, J.E. / Ren, J. / Owens, R.J. / Oxford Protein Production Facility (OPPF)
CitationJournal: Protein Expr.Purif. / Year: 2008
Title: A pipeline for the production of antibody fragments for structural studies using transient expression in HEK 293T cells.
Authors: Nettleship, J.E. / Ren, J. / Rahman, N. / Berrow, N.S. / Hatherley, D. / Barclay, A.N. / Owens, R.J.
History
DepositionJun 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 31, 2021Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FabOX117 Light Chain Fragment
B: FabOX117 Heavy Chain Fragment
C: FabOX117 Light Chain Fragment
D: FabOX117 Heavy Chain Fragment


Theoretical massNumber of molelcules
Total (without water)96,8664
Polymers96,8664
Non-polymers00
Water5,603311
1
A: FabOX117 Light Chain Fragment
B: FabOX117 Heavy Chain Fragment


Theoretical massNumber of molelcules
Total (without water)48,4332
Polymers48,4332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-23.5 kcal/mol
Surface area19250 Å2
MethodPISA
2
C: FabOX117 Light Chain Fragment
D: FabOX117 Heavy Chain Fragment


Theoretical massNumber of molelcules
Total (without water)48,4332
Polymers48,4332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-24.1 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.206, 70.602, 87.849
Angle α, β, γ (deg.)101.50, 102.94, 98.32
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31A
41C
12B
22D
32B
42D
52B
62D

NCS domain segments:

Refine code: 3

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPALAALAAA1 - 1961 - 196
211ASPASPALAALACC1 - 1961 - 196
321PROPROASNASNAA204 - 210204 - 210
421PROPROASNASNCC204 - 210204 - 210
112GLUGLUPROPROBB1 - 531 - 53
212GLUGLUPROPRODD1 - 531 - 53
322GLYGLYTHRTHRBB56 - 15956 - 159
422GLYGLYTHRTHRDD56 - 15956 - 159
532THRTHRLYSLYSBB171 - 215171 - 215
632THRTHRLYSLYSDD171 - 215171 - 215

NCS ensembles :
ID
1
2

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Components

#1: Antibody FabOX117 Light Chain Fragment


Mass: 23660.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pOPINVL / Cell line (production host): HEK293T / Organ (production host): Human embryonic kidney cells / Production host: Homo sapiens (human)
#2: Antibody FabOX117 Heavy Chain Fragment


Mass: 24772.779 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pOPINVH / Cell line (production host): HEK293T / Organ (production host): Human embryonic kidney cells / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF ENTITIES 1 AND 2 WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) ...THE SEQUENCE OF ENTITIES 1 AND 2 WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 85% of 0.2M Ammonium sulfate, 30% w/v PEG 4000 in 15% water - with 10 microliters of 1M NaOH per 1ml crystallization solution, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 35860 / % possible obs: 97.7 % / Observed criterion σ(I): -1.5 / Redundancy: 3.4 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 1.4 / Num. unique all: 3531 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345CCDdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DGG

3dgg


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.874 / SU B: 15.374 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.565 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28632 1774 5 %RANDOM
Rwork0.21856 ---
obs0.22204 33630 97.72 %-
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: 44.74 Å2
Baniso -1Baniso -2Baniso -3
1--4.98 Å20.96 Å2-0.87 Å2
2--3.55 Å22.08 Å2
3---2.14 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6543 0 0 311 6854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226727
X-RAY DIFFRACTIONr_bond_other_d0.0020.024474
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.9399175
X-RAY DIFFRACTIONr_angle_other_deg0.8263.00310931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3185845
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83624.131259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.749151050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8431521
X-RAY DIFFRACTIONr_chiral_restr0.0610.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027448
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021351
X-RAY DIFFRACTIONr_nbd_refined0.1630.2990
X-RAY DIFFRACTIONr_nbd_other0.1980.24379
X-RAY DIFFRACTIONr_nbtor_refined0.1760.23031
X-RAY DIFFRACTIONr_nbtor_other0.0810.23682
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2268
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.214
X-RAY DIFFRACTIONr_mcbond_it3.14245413
X-RAY DIFFRACTIONr_mcbond_other0.89541707
X-RAY DIFFRACTIONr_mcangle_it4.05366897
X-RAY DIFFRACTIONr_scbond_it4.80563060
X-RAY DIFFRACTIONr_scangle_it6.367102278
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1194tight positional0.030.05
2B1142tight positional0.040.05
1A1462loose positional0.545
2B1371loose positional0.475
1A1194tight thermal2.1710
2B1142tight thermal1.9410
1A1462loose thermal3.5230
2B1371loose thermal2.8230
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 115 -
Rwork0.286 2456 -
obs--95.86 %

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