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- PDB-7t99: Crystal structure of engineered CYS-CYS fab dimer CL-205 (LC25) -

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Basic information

Entry
Database: PDB / ID: 7t99
TitleCrystal structure of engineered CYS-CYS fab dimer CL-205 (LC25)
Components
  • FAB Heavy Chain
  • FAB Light Chain
KeywordsIMMUNE SYSTEM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsHarris, S.F. / Boenig, G.D.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Comput Struct Biotechnol J / Year: 2022
Title: Antibody interfaces revealed through structural mining.
Authors: Yin, Y. / Romei, M.G. / Sankar, K. / Pal, L.R. / Hoi, K.H. / Yang, Y. / Leonard, B. / De Leon Boenig, G. / Kumar, N. / Matsumoto, M. / Payandeh, J. / Harris, S.F. / Moult, J. / Lazar, G.A.
History
DepositionDec 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAB Heavy Chain
B: FAB Light Chain
C: FAB Heavy Chain
D: FAB Light Chain
E: FAB Heavy Chain
F: FAB Light Chain
H: FAB Heavy Chain
L: FAB Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,49910
Polymers191,3098
Non-polymers1902
Water1,27971
1
A: FAB Heavy Chain
B: FAB Light Chain


Theoretical massNumber of molelcules
Total (without water)47,8272
Polymers47,8272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-23 kcal/mol
Surface area19430 Å2
MethodPISA
2
C: FAB Heavy Chain
D: FAB Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9223
Polymers47,8272
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-26 kcal/mol
Surface area19490 Å2
MethodPISA
3
E: FAB Heavy Chain
F: FAB Light Chain


Theoretical massNumber of molelcules
Total (without water)47,8272
Polymers47,8272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-24 kcal/mol
Surface area19470 Å2
MethodPISA
4
H: FAB Heavy Chain
L: FAB Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9223
Polymers47,8272
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-28 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.824, 62.451, 124.018
Angle α, β, γ (deg.)89.990, 98.370, 89.890
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
FAB Heavy Chain


Mass: 24329.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody
FAB Light Chain


Mass: 23498.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 3350, 100 mM sodium succinate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.631
11-H, K, -L20.369
ReflectionResolution: 2.65→62.45 Å / Num. obs: 37526 / % possible obs: 82.9 % / Redundancy: 1.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.029 / Rrim(I) all: 0.041 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.66-2.81.80.1541102359590.9780.1540.2182.390.2
8.4-62.4520.015254313020.9990.0150.02111.690.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→62.45 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.94 / SU B: 33.685 / SU ML: 0.351 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2649 1514 4 %RANDOM
Rwork0.1837 ---
obs0.1872 36011 82.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 144.24 Å2 / Biso mean: 63.732 Å2 / Biso min: 30.32 Å2
Baniso -1Baniso -2Baniso -3
1--37 Å2-2.81 Å23.72 Å2
2--46 Å21.21 Å2
3----9 Å2
Refinement stepCycle: final / Resolution: 2.65→62.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13132 0 10 71 13213
Biso mean--55.32 45.74 -
Num. residues----1728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01313547
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712376
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.64618486
X-RAY DIFFRACTIONr_angle_other_deg1.2121.57728636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.84651752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82422.69580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.507152132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2331556
X-RAY DIFFRACTIONr_chiral_restr0.070.21808
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217452
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023076
LS refinement shellResolution: 2.651→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 107 -
Rwork0.206 2727 -
all-2834 -
obs--82.91 %
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)
11.33410.14461.10570.02430.13051.0784-0.01580.2830.17-0.00760.00050.01380.1150.3160.01530.1890.1633-0.06780.2526-0.01520.1287-9.79-14.2-37.643
21.31470.28821.45170.33530.31772.2537-0.0242-0.12490.224-0.0183-0.120.0462-0.1355-0.25620.14420.15590.1741-0.04080.227-0.07430.1425-21.042-8.177-24.753
31.3455-0.04921.26280.49640.39111.78270.0631-0.24150.1269-0.0078-0.04830.07040.1587-0.1434-0.01480.14420.1938-0.04110.3509-0.08080.22469.413-45.43537.981
41.5056-0.43590.81130.2457-0.29721.2935-0.05270.19620.1790.0266-0.1105-0.0251-0.04230.18560.16320.17970.1547-0.070.25350.00310.113820.632-39.4125.004
50.5703-0.0270.20390.1404-0.02140.6435-0.05570.1571-0.0984-0.045-0.07490.02040.01440.25530.13070.16910.149-0.02630.298-0.08230.201816.531-45.732-38.704
60.2245-0.05380.00330.35130.58281.1955-0.1331-0.0438-0.19180.0123-0.10.1005-0.1578-0.24690.23310.18280.13910.00270.248-0.05880.28845.368-39.146-25.806
70.5802-0.17660.9180.59780.17461.92080.0226-0.1065-0.1186-0.00070.05590.02040.0666-0.1415-0.07850.12090.17380.00230.2954-0.01420.1974-16.926-14.4138.966
81.1374-0.29170.35330.4571-0.37020.8665-0.06990.1532-0.23960.0013-0.07790.056-0.06990.1740.14780.16660.1874-0.02960.3155-0.0210.1392-5.766-7.83926.042
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 214
2X-RAY DIFFRACTION2B1 - 212
3X-RAY DIFFRACTION3C2 - 214
4X-RAY DIFFRACTION4D1 - 212
5X-RAY DIFFRACTION5E2 - 214
6X-RAY DIFFRACTION6F1 - 212
7X-RAY DIFFRACTION7H2 - 214
8X-RAY DIFFRACTION8L1 - 212

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