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- PDB-3naa: Crystal structure of Fab15 Mut5 -

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Basic information

Entry
Database: PDB / ID: 3naa
TitleCrystal structure of Fab15 Mut5
Components
  • Fab15 Mut5 heavy chain
  • Fab15 Mut5 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: 1.7 Å
AuthorsLuo, J. / Feng, Y. / Gilliland, G.L.
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: Advisory / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_conn_angle ...entity_src_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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 Mut5 light chain
H: Fab15 Mut5 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1488
Polymers47,7412
Non-polymers4066
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-115 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.534, 74.784, 65.198
Angle α, β, γ (deg.)90.00, 103.50, 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 Mut5 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 Mut5 heavy chain


Mass: 24501.354 Da / Num. of mol.: 1 / Mutation: V34I, G35S, 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, 495 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 54.58 %

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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: 1.7→30.559 Å / Num. all: 55410 / Num. obs: 55410 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.61 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.01 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 1.8 / Num. unique all: 5481 / % possible all: 98.3

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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: 1.7→30.559 Å / SU ML: 0.21 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.07 / σ(I): -3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 2788 5.08 %RANDOM
Rwork0.178 ---
obs0.1791 54885 97.97 %-
all-54886 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.574 Å2 / ksol: 0.397 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.9187 Å2-0 Å2-4.0868 Å2
2--3.2956 Å20 Å2
3---0.6231 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 17 489 3862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063494
X-RAY DIFFRACTIONf_angle_d1.0944753
X-RAY DIFFRACTIONf_dihedral_angle_d13.0891252
X-RAY DIFFRACTIONf_chiral_restr0.078532
X-RAY DIFFRACTIONf_plane_restr0.004606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72930.27621430.26412402X-RAY DIFFRACTION92
1.7293-1.76080.27531310.25122583X-RAY DIFFRACTION97
1.7608-1.79460.24761270.23952570X-RAY DIFFRACTION98
1.7946-1.83120.26611220.22422614X-RAY DIFFRACTION98
1.8312-1.87110.25771450.21912625X-RAY DIFFRACTION99
1.8711-1.91460.22341390.21532637X-RAY DIFFRACTION99
1.9146-1.96240.22671470.2042611X-RAY DIFFRACTION99
1.9624-2.01550.21841350.18872643X-RAY DIFFRACTION99
2.0155-2.07480.18791600.17652597X-RAY DIFFRACTION100
2.0748-2.14170.22911450.17072635X-RAY DIFFRACTION99
2.1417-2.21830.18581300.16942630X-RAY DIFFRACTION100
2.2183-2.30710.20561620.17112663X-RAY DIFFRACTION100
2.3071-2.4120.21041660.17522640X-RAY DIFFRACTION100
2.412-2.53910.22361200.16972658X-RAY DIFFRACTION100
2.5391-2.69810.20071420.16962668X-RAY DIFFRACTION100
2.6981-2.90630.20841380.17292660X-RAY DIFFRACTION100
2.9063-3.19850.16961400.16322681X-RAY DIFFRACTION100
3.1985-3.66070.17031400.14722666X-RAY DIFFRACTION100
3.6607-4.60950.14171420.14272585X-RAY DIFFRACTION97
4.6095-30.56360.21241140.1882329X-RAY DIFFRACTION85
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)
11.78680.2076-0.24610.7649-0.76311.6397-0.0058-0.26360.09980.2618-0.0085-0.0993-0.1167-0.0028-00.2303-0.0054-0.01660.2042-0.00840.198336.42835.440924.3594
21.8663-0.5630.33061.0467-0.48180.6939-0.07310.06080.1628-0.02310.03740.0034-0.03490.106900.1497-0.00390.00910.12480.00450.15649.0368.91320.3307
32.41051.11120.90470.51810.35111.17650.1592-0.7145-0.33290.2482-0.0608-0.12940.2393-0.210200.3063-0.0261-0.00920.41990.10740.240922.5773-6.963836.3886
42.44090.3066-0.10722.33940.09141.06590.01280.23-0.1278-0.28550.02960.04910.0606-0.0475-00.0908-0.0046-0.0060.041-0.01270.10317.5481-6.29961.1594
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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