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- PDB-3nac: Crystal structure of Fab15 Mut7 -

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Basic information

Entry
Database: PDB / ID: 3nac
TitleCrystal structure of Fab15 Mut7
Components
  • Fab15 Mut7 heavy chain
  • Fab15 Mut7 light chain
KeywordsIMMUNE SYSTEM / antibody / antibody canonical structure / thermal stability / non-X-pro cis peptide bond / antibody engineering
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLuo, J.
CitationJournal: To be Published
Title: Co-evolution of antibody stability and Vk CDR-L3 canonical structure
Authors: Luo, J. / Feng, Y. / Gilliland, G.L.
History
DepositionJun 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 31, 2021Group: Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_conn_angle ...entity_src_gen / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab15 Mut7 light chain
H: Fab15 Mut7 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,57013
Polymers47,7772
Non-polymers79311
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-234 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.663, 74.437, 65.764
Angle α, β, γ (deg.)90.00, 104.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody Fab15 Mut7 light chain


Mass: 23239.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo Sapiens (human)
#2: Antibody Fab15 Mut7 heavy chain


Mass: 24537.393 Da / Num. of mol.: 1 / Mutation: V34I, G35S, F50R, A60S, Q66H, E95Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo Sapiens (human)

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Non-polymers , 4 types, 424 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M sodium acetate, 12% PEG MME 5000, 0.2 M zinc acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 17, 2010
RadiationMonochromator: Accel Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→46.8 Å / Num. obs: 46820 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 7.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4711 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NA9

3na9


Resolution: 1.8→36.56 Å / SU ML: 0.23 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 2453 5.24 %RANDOM
Rwork0.1845 ---
obs0.1859 46820 98.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.743 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.5024 Å2-0 Å2-5.0547 Å2
2--5.2666 Å2-0 Å2
3---0.2357 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 29 413 3800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073525
X-RAY DIFFRACTIONf_angle_d1.0944797
X-RAY DIFFRACTIONf_dihedral_angle_d13.5271278
X-RAY DIFFRACTIONf_chiral_restr0.078535
X-RAY DIFFRACTIONf_plane_restr0.004610
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8-1.83460.26921350.23452425242598
1.8346-1.87210.28491340.2342448244898
1.8721-1.91280.28041280.20962469246998
1.9128-1.95730.24551260.19742448244899
1.9573-2.00620.1951390.1892449244999
2.0062-2.06040.23991390.17742446244699
2.0604-2.12110.20461370.17222480248099
2.1211-2.18950.21061390.17322489248999
2.1895-2.26780.22471410.18224472447100
2.2678-2.35860.24411350.178624942494100
2.3586-2.46590.19531420.183824682468100
2.4659-2.59580.20861350.184324902490100
2.5958-2.75840.2291420.18925122512100
2.7584-2.97130.22061360.188724782478100
2.9713-3.27020.19491370.17392482248299
3.2702-3.7430.1841390.17242486248699
3.743-4.71420.18311350.15552479247998
4.7142-36.56710.21751340.18582377237793
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)
11.99430.1124-0.03910.3901-0.86981.9929-0.0599-0.23350.19620.2570.0219-0.152-0.16360.00380.00010.25580.0123-0.0250.1717-0.01660.210236.44675.636124.2537
22.5157-0.67110.41191.2668-0.38260.4683-0.02810.2730.3313-0.0628-0.00230.0416-0.04640.090200.15390.00610.0130.15360.0150.17549.13448.70310.4189
32.58811.01820.33030.60060.0591.68680.0642-0.8398-0.29640.2434-0.0068-0.10550.132-0.33740.00080.3326-0.0136-0.00230.44080.11330.219422.5403-6.192636.742
43.18350.28370.23631.23390.78060.81640.05480.2445-0.2434-0.1981-0.02010.15120.0202-0.016-00.0881-0.0025-0.0090.0105-0.01990.11347.6533-6.29051.361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain L and resseq 1:109
2X-RAY DIFFRACTION2chain L and resseq 110:214
3X-RAY DIFFRACTION3chain H and resseq 1:112
4X-RAY DIFFRACTION4chain H and resseq 113:225

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