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- PDB-7t97: Crystal structure of engineered CYS-CYS fab dimer CH1-207 (HC4) -

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Basic information

Entry
Database: PDB / ID: 7t97
TitleCrystal structure of engineered CYS-CYS fab dimer CH1-207 (HC4)
Components
  • FAB Heavy chain
  • FAB Light Chain
KeywordsIMMUNE SYSTEM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.144 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 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)191,4308
Polymers191,4308
Non-polymers00
Water13,331740
1
A: FAB Heavy chain
B: FAB Light Chain


Theoretical massNumber of molelcules
Total (without water)47,8572
Polymers47,8572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-26 kcal/mol
Surface area18930 Å2
MethodPISA
2
C: FAB Heavy chain
D: FAB Light Chain


Theoretical massNumber of molelcules
Total (without water)47,8572
Polymers47,8572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-25 kcal/mol
Surface area18980 Å2
MethodPISA
3
E: FAB Heavy chain
F: FAB Light Chain


Theoretical massNumber of molelcules
Total (without water)47,8572
Polymers47,8572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-26 kcal/mol
Surface area19050 Å2
MethodPISA
4
H: FAB Heavy chain
L: FAB Light Chain


Theoretical massNumber of molelcules
Total (without water)47,8572
Polymers47,8572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-24 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.377, 141.075, 118.605
Angle α, β, γ (deg.)90.000, 90.320, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody
FAB Heavy chain


Mass: 24391.359 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: 23466.031 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / Source method: isolated from a natural source / Formula: H2O
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: 3.31 Å3/Da / Density % sol: 62.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.8 M sodium succinate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.144→75.69 Å / Num. obs: 90661 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 36.61 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.07 / Rrim(I) all: 0.131 / Net I/σ(I): 9.2
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
2.65-2.83.60.60737405104690.7580.3740.7142.499.9
8.39-75.693.50.033806723310.9990.0210.0392299.3

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
BUSTER2.11.7 (20-MAY-2020)refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.144→75.69 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.908 / SU R Cruickshank DPI: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.299 / SU Rfree Blow DPI: 0.215 / SU Rfree Cruickshank DPI: 0.218
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 4656 5.14 %RANDOM
Rwork0.1941 ---
obs0.1957 90661 66.6 %-
Displacement parametersBiso max: 217.71 Å2 / Biso mean: 35.98 Å2 / Biso min: 15.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.6805 Å20 Å20.151 Å2
2--1.7318 Å20 Å2
3----1.0513 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.144→75.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13149 0 0 740 13889
Biso mean---39.81 -
Num. residues----1729
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4466SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2274HARMONIC5
X-RAY DIFFRACTIONt_it13548HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1811SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11002SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13548HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg18484HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion18.01
LS refinement shellResolution: 2.144→2.22 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.252 110 6.06 %
Rwork0.2125 1704 -
obs--12.89 %

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