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- PDB-7sen: Crystal structure of Fab containing a fluorescent noncanonical am... -

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Basic information

Entry
Database: PDB / ID: 7sen
TitleCrystal structure of Fab containing a fluorescent noncanonical amino acid with blocked excited state proton transfer
Components
  • 5c8* Fab heavy chain
  • 5c8* Fab light chain
KeywordsIMMUNE SYSTEM / Fragment antigen binding (Fab) / noncanonical amino acid / 7-hydroxycoumarin
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsHenderson, J.N. / Mills, J.H. / Simmons, C.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM136996 United States
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structural Basis for Blocked Excited State Proton Transfer in a Fluorescent, Photoacidic Non-Canonical Amino Acid-Containing Antibody Fragment.
Authors: Henderson, J.N. / Simmons, C.R. / Mills, J.H.
History
DepositionSep 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: 5c8* Fab heavy chain
L: 5c8* Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,0022
Polymers48,0022
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-22 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.174, 59.811, 73.043
Angle α, β, γ (deg.)90.000, 96.090, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody 5c8* Fab heavy chain


Mass: 23988.801 Da / Num. of mol.: 1 / Mutation: W47L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: 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


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.71 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 27-33% PEG 3350, 0.1 M Citric acid/Sodium citrate pH 3.0-4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.09→72.63 Å / Num. obs: 21470 / % possible obs: 94.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.081 / Rrim(I) all: 0.156 / Χ2: 0.749 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.142.70.4117510.7820.2660.4920.56366.1
2.14-2.182.80.4127960.8170.2650.4910.58570.6
2.18-2.222.90.48650.8490.2590.4790.66976.9
2.22-2.2630.4519680.8280.2890.5380.56683.3
2.26-2.313.10.4099920.8550.2620.4870.5689.6
2.31-2.373.30.43811090.8520.2740.5180.55195.9
2.37-2.423.50.41111180.8750.2550.4840.51399.1
2.42-2.493.60.43511370.8580.2660.510.53699.7
2.49-2.563.70.36811330.8830.2230.4310.567100
2.56-2.653.80.34711200.9090.2080.4050.601100
2.65-2.743.70.28811200.9370.1730.3360.675100
2.74-2.853.80.23511740.9490.1410.2750.72100
2.85-2.983.70.20411170.9660.1230.2390.774100
2.98-3.143.70.16111400.9750.0970.1880.854100
3.14-3.333.70.12911440.9790.0780.150.979100
3.33-3.593.70.111390.9860.060.1171.034100
3.59-3.953.70.08611520.9890.0520.1011.011100
3.95-4.523.60.06411560.9940.0390.0750.94599.9
4.52-5.73.70.05211400.9960.0310.0610.756100
5.7-503.70.05711990.9950.0340.0671.071100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.6 Å49.76 Å
Translation6.6 Å49.76 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.6.1phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6bjz

6bjz


Resolution: 2.09→72.63 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.91 / SU B: 15.48 / SU ML: 0.196 / SU R Cruickshank DPI: 0.2888 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 1090 5.1 %RANDOM
Rwork0.1855 ---
obs0.189 20380 93.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.34 Å2 / Biso mean: 30.525 Å2 / Biso min: 15.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0.12 Å2
2--0.11 Å20 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 2.09→72.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3266 0 0 131 3397
Biso mean---28.45 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023375
X-RAY DIFFRACTIONr_bond_other_d0.0020.023020
X-RAY DIFFRACTIONr_angle_refined_deg1.8031.9564606
X-RAY DIFFRACTIONr_angle_other_deg1.0093.0017004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5555.023441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89425.2125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69315513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.465157
X-RAY DIFFRACTIONr_chiral_restr0.0990.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0213857
X-RAY DIFFRACTIONr_gen_planes_other00.02725
LS refinement shellResolution: 2.094→2.148 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 45 -
Rwork0.26 1021 -
all-1066 -
obs--62.82 %
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)
11.19240.86350.33891.8791.32561.6283-0.0133-0.01-0.0435-0.11250.0154-0.0809-0.07820.0422-0.00210.0773-0.00090.05080.00160.00180.037826.6406-2.324283.3478
20.06770.143-0.10110.8584-0.51381.10340.01880.0028-0.0030.0909-0.04210.011-0.03470.11730.02320.0414-0.00790.02220.0212-0.00410.015918.4179-10.5647112.1917
30.89020.0273-0.10120.5909-0.17621.6845-0.02460.12510.026-0.01350.02960.00430.1008-0.0142-0.0050.0779-0.01280.04520.0199-0.00220.03045.025-5.778480.1722
41.03860.46050.79240.81840.95711.29050.0181-0.00190.00820.1642-0.00470.04990.08410.0175-0.01340.1211-0.02150.07190.0063-0.01460.04915.6155-3.6922118.1874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 117
2X-RAY DIFFRACTION2H118 - 226
3X-RAY DIFFRACTION3L1 - 111
4X-RAY DIFFRACTION4L112 - 215

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