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- PDB-3nab: Crystal Structure of fab15 Mut6 -

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Basic information

Entry
Database: PDB / ID: 3nab
TitleCrystal Structure of fab15 Mut6
Components
  • Fab15 Mut6 heavy chain
  • Fab15 Mut6 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: 2.32 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_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 Mut6 light chain
H: Fab15 Mut6 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6157
Polymers47,2952
Non-polymers3215
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-143 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.618, 75.197, 67.226
Angle α, β, γ (deg.)90.00, 108.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab15 Mut6 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 Mut6 heavy chain


Mass: 24054.867 Da / Num. of mol.: 1 / Mutation: V34I, G35S, F50R, A60S, Q66H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo Sapiens (human)
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate, 12% PEG MME 5000, 0.2 M Zn acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

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: 2.32→42.6 Å / Num. all: 22257 / Num. obs: 22257 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.64 % / Biso Wilson estimate: 52.5 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.6
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2224 / % possible all: 100

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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: 2.32→34.935 Å / SU ML: 0.43 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): -3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 1130 5.08 %RANDOM
Rwork0.2035 ---
obs0.2064 22228 99.26 %-
all-22228 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.168 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.4432 Å2-0 Å2-1.7374 Å2
2--2.5539 Å20 Å2
3---2.8893 Å2
Refinement stepCycle: LAST / Resolution: 2.32→34.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 8 184 3475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083366
X-RAY DIFFRACTIONf_angle_d1.0824567
X-RAY DIFFRACTIONf_dihedral_angle_d15.7511199
X-RAY DIFFRACTIONf_chiral_restr0.072514
X-RAY DIFFRACTIONf_plane_restr0.005580
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.32-2.42560.32211240.244526352635100
2.4256-2.55350.29911420.232226412641100
2.5535-2.71340.30761570.226926272627100
2.7134-2.92280.32881610.229426302630100
2.9228-3.21680.29031430.198326702670100
3.2168-3.68180.20191310.17226352635100
3.6818-4.6370.20041410.14672651265199
4.637-34.93870.20771310.1732609260996
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)
14.18251.0606-1.24860.8506-1.98172.00430.3724-1.22890.15890.2894-0.3116-0.0581-0.41790.37730.00190.3309-0.1051-0.01420.592-0.01590.30136.0435.017924.5431
23.6605-1.16630.46021.64330.08040.4899-0.1469-0.12360.2479-0.07760.05320.0028-0.08460.098-0.00010.2317-0.01450.00940.14160.0010.26679.00068.89570.7776
32.19071.38040.11.9849-0.07461.49890.2908-1.5068-0.61030.3786-0.3773-0.29420.03520.4128-0.19990.4093-0.04680.00191.0610.31350.30922.1275-7.691236.1794
42.17590.36890.03160.9351-0.30441.3103-0.00070.0881-0.1267-0.17040.03220.1658-0.0925-0.101600.22630.0052-0.01260.1364-0.01860.29788.3117-7.132.5589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain L and resid 1:109
2X-RAY DIFFRACTION2chain L and resid 110:214
3X-RAY DIFFRACTION3chain H and resid 1:112
4X-RAY DIFFRACTION4chain H and resid 113:222

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