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- PDB-6dzr: Crystal structure of h38C2 K99R mutation -

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Basic information

Entry
Database: PDB / ID: 6dzr
TitleCrystal structure of h38C2 K99R mutation
Components
  • h38c2 heavy chain
  • h38c2 light chain
KeywordsIMMUNE SYSTEM / Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CITRATE ANION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPark, H. / Rader, C.
CitationJournal: Cell Chem Biol / Year: 2019
Title: Site-Selective Antibody Functionalization via Orthogonally Reactive Arginine and Lysine Residues.
Authors: Hwang, D. / Nilchan, N. / Nanna, A.R. / Li, X. / Cameron, M.D. / Roush, W.R. / Park, H. / Rader, C.
History
DepositionJul 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 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
H: h38c2 heavy chain
L: h38c2 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0484
Polymers47,7632
Non-polymers2852
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-41 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.699, 91.699, 109.011
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Antibody h38c2 heavy chain


Mass: 23886.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody h38c2 light chain


Mass: 23876.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 200 mM Ammonium Acetate, 40 mM Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→35.1 Å / Num. obs: 20372 / % possible obs: 95 % / Redundancy: 20 % / Net I/σ(I): 41
Reflection shellResolution: 2.4→2.48 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AXT

1axt


Resolution: 2.4→35.087 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.88
RfactorNum. reflection% reflection
Rfree0.2277 994 4.88 %
Rwork0.1816 --
obs0.1838 20368 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→35.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 18 139 3513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123458
X-RAY DIFFRACTIONf_angle_d1.2594705
X-RAY DIFFRACTIONf_dihedral_angle_d17.0012051
X-RAY DIFFRACTIONf_chiral_restr0.057521
X-RAY DIFFRACTIONf_plane_restr0.007600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4003-2.52690.33421500.26552759X-RAY DIFFRACTION100
2.5269-2.68510.25741780.24342717X-RAY DIFFRACTION100
2.6851-2.89230.26861400.23912756X-RAY DIFFRACTION100
2.8923-3.18320.26651390.21542757X-RAY DIFFRACTION100
3.1832-3.64340.24051540.18542760X-RAY DIFFRACTION100
3.6434-4.58870.18191210.14152802X-RAY DIFFRACTION100
4.5887-35.09040.17981120.14682823X-RAY DIFFRACTION100
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)
15.61974.6233-1.71397.8755-2.0031.6768-0.1458-0.3464-0.56080.1815-0.0978-0.84420.23070.38560.20410.36160.0246-0.08180.2857-0.00970.282583.502461.83919.0649
23.03912.5721.15166.0730.82082.01530.106-0.16830.20250.5457-0.17010.17890.0107-0.12860.08260.2749-0.00490.01290.25380.01140.200776.046366.648120.6779
30.195-0.5096-0.23575.1304-2.23312.4094-0.0368-0.2519-0.21150.0181-0.3363-0.43240.14090.30390.49640.3002-0.03330.03210.31770.0480.253576.71856.533415.7245
43.5951.007-0.03862.271-1.45236.7014-0.16210.49280.0034-0.09720.09490.10660.7289-0.0056-0.84580.92020.06090.29730.39230.0810.327170.26224.47872.9098
51.6701-1.2158-2.36183.68782.55686.2836-0.2561-0.168-0.22920.3424-0.03140.10360.53820.31910.2280.420.0450.05140.34630.02930.301574.833134.20878.0529
64.34993.82172.38884.83642.8981.7345-0.4505-0.9193-0.57140.0599-0.0273-0.51630.6311-0.21-0.41880.8590.19640.14320.47710.07670.430678.902125.878511.4064
73.8042-0.4765-0.95772.6221.36542.7593-0.13520.17570.2889-0.4846-0.62681.3648-0.2568-0.30980.28160.38350.062-0.10160.4045-0.09490.557762.042370.0339-0.5988
82.58480.7362-0.46444.47951.90215.1818-0.05320.08360.0434-0.5436-0.07760.2463-0.2207-0.10160.07920.3010.0323-0.04630.26860.01670.2972.30167.3581-1.0906
91.49912.11221.40055.82753.21954.41870.10660.31020.1726-0.7741-0.4590.3949-0.3944-0.12460.1130.26190.0237-0.02530.3757-0.12540.380864.08948.1167-9.2357
102.89831.0471-0.86022.5984-2.83835.9154-0.16710.2332-0.37140.5569-0.27970.33760.4768-0.49120.13010.5523-0.11360.15580.3259-0.17340.49662.134130.27953.7228
112.94773.9558-2.0855.4838-2.81725.37030.16170.0984-0.07370.2381-0.30950.37370.022-0.36670.10960.2890.00990.05310.3381-0.13850.430761.087737.45951.5492
124.623.1376-2.96342.7304-3.14563.99210.1268-0.5162-0.34810.5676-0.57210.28070.1667-0.19020.07480.6194-0.16790.23150.4305-0.06850.494459.055727.87939.8673
133.98390.4961-0.87164.024-4.77316.6384-0.30740.5424-0.50830.2641-0.13090.62610.8313-0.3107-0.0220.6457-0.21270.16390.4472-0.19520.797156.565425.3133-1.4974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 33 )
2X-RAY DIFFRACTION2chain 'H' and (resid 34 through 101 )
3X-RAY DIFFRACTION3chain 'H' and (resid 102 through 124 )
4X-RAY DIFFRACTION4chain 'H' and (resid 125 through 139 )
5X-RAY DIFFRACTION5chain 'H' and (resid 140 through 208 )
6X-RAY DIFFRACTION6chain 'H' and (resid 209 through 220 )
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 33 )
8X-RAY DIFFRACTION8chain 'L' and (resid 34 through 106 )
9X-RAY DIFFRACTION9chain 'L' and (resid 107 through 118 )
10X-RAY DIFFRACTION10chain 'L' and (resid 119 through 155 )
11X-RAY DIFFRACTION11chain 'L' and (resid 156 through 177 )
12X-RAY DIFFRACTION12chain 'L' and (resid 178 through 193 )
13X-RAY DIFFRACTION13chain 'L' and (resid 194 through 218 )

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