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- PDB-6w5a: Crystal Structure of the Fab fragment of humanized 5c8 antibody c... -

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Basic information

Entry
Database: PDB / ID: 6w5a
TitleCrystal Structure of the Fab fragment of humanized 5c8 antibody containing the fluorescent non-canonical amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine at pH 9.7
Components
  • Antibody 5c8* Fab Heavy Chain
  • Antibody 5c8* Fab Light Chain
KeywordsIMMUNE SYSTEM / immunoglobulin / Fab / L-(7-hydroxycoumarin-4-yl)ethylglycine
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsHenderson, J.N. / Simmons, C.R. / Mills, J.H.
CitationJournal: Biochemistry / Year: 2020
Title: Structural Insights into How Protein Environments Tune the Spectroscopic Properties of a Noncanonical Amino Acid Fluorophore.
Authors: Henderson, J.N. / Simmons, C.R. / Fahmi, N.E. / Jeffs, J.W. / Borges, C.R. / Mills, J.H.
History
DepositionMar 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Revision 1.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Antibody 5c8* Fab Heavy Chain
L: Antibody 5c8* Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)48,0752
Polymers48,0752
Non-polymers00
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-25 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.861, 60.182, 73.258
Angle α, β, γ (deg.)90.000, 98.940, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-412-

HOH

21L-426-

HOH

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Components

#1: Antibody Antibody 5c8* Fab Heavy Chain


Mass: 24061.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Antibody 5c8* Fab Light Chain


Mass: 24013.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 3350, 0.1 M Citric Acid/Sodium Citrate pH 3.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91976 Å / Relative weight: 1
ReflectionResolution: 1.75→72.37 Å / Num. obs: 39519 / % possible obs: 99 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.082 / Rrim(I) all: 0.175 / Χ2: 1.325 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.783.70.69419850.6620.40.8040.60799.5
1.78-1.813.80.6419320.7150.3630.7390.62499.1
1.81-1.853.80.54519530.7770.3110.6310.70699.2
1.85-1.893.90.55520000.1490.3180.6430.8899.2
1.89-1.933.80.45219200.8380.2570.5220.91397.7
1.93-1.9740.419670.840.2210.4591.09398.6
1.97-2.024.30.37819870.8640.20.4291.38399.4
2.02-2.074.40.35319750.8950.1840.3991.4399.5
2.07-2.144.40.30819660.910.1610.3491.68999.7
2.14-2.24.40.28919940.9180.1520.3281.96699.2
2.2-2.284.30.26119490.9180.1380.2971.76498.8
2.28-2.3840.24319420.9310.1330.2781.80797.2
2.38-2.484.60.22419860.9340.1150.2531.78699.7
2.48-2.614.50.20219910.9460.1050.2291.57799.7
2.61-2.784.40.17319700.9590.0910.1961.48299.6
2.78-2.994.30.15919790.9560.0830.181.46298.8
2.99-3.294.40.13619820.9710.0720.1551.25498.4
3.29-3.774.60.12219990.9710.0640.1381.27399.8
3.77-4.754.30.10919880.970.060.1251.19698.4
4.75-504.40.12520540.9610.0670.1421.10899

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.79 Å45.37 Å
Translation6.79 Å45.37 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASER2.6.1phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6bjz

6bjz


Resolution: 1.75→72.37 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.413 / SU ML: 0.103 / SU R Cruickshank DPI: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.132
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 1955 4.9 %RANDOM
Rwork0.1925 ---
obs0.1949 37564 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 62.92 Å2 / Biso mean: 29.291 Å2 / Biso min: 14.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20.65 Å2
2---0.01 Å20 Å2
3----0.94 Å2
Refinement stepCycle: final / Resolution: 1.75→72.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 0 271 3481
Biso mean---33.05 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023329
X-RAY DIFFRACTIONr_bond_other_d0.0020.022967
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.9484550
X-RAY DIFFRACTIONr_angle_other_deg0.97336885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4445444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.39325.21119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15215502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.195156
X-RAY DIFFRACTIONr_chiral_restr0.1010.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213814
X-RAY DIFFRACTIONr_gen_planes_other00.02716
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.284 127 -
Rwork0.265 2684 -
obs--96.23 %
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)
10.9781-0.19910.29211.4733-0.46982.3289-0.02-0.14370.02110.34260.02730.2713-0.0305-0.1605-0.00730.08710.01280.06990.07970.00240.0576-39.58712.97824.752
21.2298-1.0021-0.41412.0790.51240.59880.03770.1082-0.0739-0.1106-0.09360.15530.0051-0.09360.05590.01610.0012-0.0310.0579-0.00650.093-30.1744.985-2.756
31.3434-0.4536-0.90560.4320.5492.111-0.1222-0.33750.09230.22830.1532-0.07340.22950.2056-0.0310.17660.0546-0.01460.1767-0.02850.0298-17.4929.20628.355
41.4207-0.38930.64311.3151-0.62151.87610.01760.13820.0436-0.1729-0.02520.05030.03430.05320.00770.03420.0127-0.00920.0511-0.00630.0483-17.63612.095-9.744
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 117
2X-RAY DIFFRACTION2H118 - 219
3X-RAY DIFFRACTION3L2 - 114
4X-RAY DIFFRACTION4L115 - 216

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