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- PDB-1za6: The structure of an antitumor CH2-domain-deleted humanized antibody -

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Basic information

Entry
Database: PDB / ID: 1za6
TitleThe structure of an antitumor CH2-domain-deleted humanized antibody
Components
  • IGG Heavy chain
  • IGG Light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / CH2-domain-deletion
Function / homology
Function and homology information


: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLarson, S.B. / Day, J.S. / Glaser, S. / Braslawsky, G. / McPherson, A.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: The Structure of an Antitumor C(H)2-domain-deleted Humanized Antibody.
Authors: Larson, S.B. / Day, J.S. / Glaser, S. / Braslawsky, G. / McPherson, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Combined use of AFM and X-ray diffraction to analyze crystals of an engineered, domain-deleted antibody
Authors: Larson, S.B. / Kuznetsov, Y.G. / Day, J. / Zhou, J. / Glaser, S. / Braslawsky, G. / McPherson, A.
History
DepositionApr 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE There was no suitable sequence database match at time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IGG Light chain
B: IGG Heavy chain
C: IGG Light chain
D: IGG Heavy chain
E: IGG Light chain
F: IGG Heavy chain
G: IGG Light chain
H: IGG Heavy chain


Theoretical massNumber of molelcules
Total (without water)244,6368
Polymers244,6368
Non-polymers00
Water00
1
A: IGG Light chain
B: IGG Heavy chain
C: IGG Light chain
D: IGG Heavy chain


Theoretical massNumber of molelcules
Total (without water)122,3184
Polymers122,3184
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint-65 kcal/mol
Surface area48510 Å2
MethodPISA
2
E: IGG Light chain
F: IGG Heavy chain
G: IGG Light chain
H: IGG Heavy chain


Theoretical massNumber of molelcules
Total (without water)122,3184
Polymers122,3184
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10570 Å2
ΔGint-59 kcal/mol
Surface area48180 Å2
MethodPISA
3
A: IGG Light chain
B: IGG Heavy chain
C: IGG Light chain
D: IGG Heavy chain
E: IGG Light chain
F: IGG Heavy chain
G: IGG Light chain
H: IGG Heavy chain

A: IGG Light chain
B: IGG Heavy chain
C: IGG Light chain
D: IGG Heavy chain
E: IGG Light chain
F: IGG Heavy chain
G: IGG Light chain
H: IGG Heavy chain


Theoretical massNumber of molelcules
Total (without water)489,27216
Polymers489,27216
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area62170 Å2
ΔGint-263 kcal/mol
Surface area172860 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23910 Å2
ΔGint-137 kcal/mol
Surface area93610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.540, 224.200, 166.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
/ NCS ensembles :
ID
1
2
3
4
5
6
7
8
DetailsChains A, B, C, D are the presumed biological unit / Chains E, F, G, H are the presumed biological unit

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Components

#1: Antibody
IGG Light chain


Mass: 24206.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q6GMV9
#2: Antibody
IGG Heavy chain


Mass: 36952.125 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q6GMX6
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: 3.29 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 4 M sodium formate, 1.5 mM Triton X-100 detergent, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9194
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 2003
RadiationMonochromator: DOUBLE CRYSTAL, SI(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9194 Å / Relative weight: 1
ReflectionResolution: 2.8→45.13 Å / Num. obs: 76662 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9.06 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.152 / Net I/σ(I): 10.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.62 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 5 / % possible all: 98

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Processing

Software
NameVersionClassification
CNS1.1refinement
d*TREKV. 9.0data reduction
d*TREKV. 9.0data scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BBJ; PDB ENTRY 1FC1

1bbj

1fc1


Resolution: 2.8→45.13 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 38542.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: ENGH & HUBER / Details: USED NCS RESTRAINTS FOR EQUIVALENT CHAINS
RfactorNum. reflection% reflectionSelection details
Rfree0.296 5924 7.7 %RANDOM
Rwork0.246 ---
obs0.246 76662 99.5 %-
all-76929 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.13 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 41.4 Å2
Baniso -1Baniso -2Baniso -3
1-16.32 Å20 Å20 Å2
2---3.31 Å20 Å2
3----13.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.8 Å0.72 Å
Refinement stepCycle: LAST / Resolution: 2.8→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16740 0 0 0 16740
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.88
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.32
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.422
X-RAY DIFFRACTIONc_scbond_it1.522
X-RAY DIFFRACTIONc_scangle_it2.392.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight Biso Weight position
11RESTRAINEDX-RAY DIFFRACTION0.0876210
22X-RAY DIFFRACTION0.14812150
33X-RAY DIFFRACTION0.0856210
44X-RAY DIFFRACTION0.0936210
55X-RAY DIFFRACTION0.10912150
66X-RAY DIFFRACTION0.1112150
77X-RAY DIFFRACTION0.1096210
88X-RAY DIFFRACTION0.1366210
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.405 452 6.1 %
Rwork0.383 6992 -
obs--98 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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