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- PDB-1nqb: TRIVALENT ANTIBODY FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 1nqb
TitleTRIVALENT ANTIBODY FRAGMENT
ComponentsSINGLE-CHAIN ANTIBODY FRAGMENT
KeywordsIMMUNOGLOBULIN / ANTIBODY FRAGMENT / MULTIVALENT ANTIBODY / DIABODY / DOMAIN SWAPPING
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWilliams, R.L. / Pei, X.Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: The 2.0-A resolution crystal structure of a trimeric antibody fragment with noncognate VH-VL domain pairs shows a rearrangement of VH CDR3.
Authors: Pei, X.Y. / Holliger, P. / Murzin, A.G. / Williams, R.L.
History
DepositionApr 4, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 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: SINGLE-CHAIN ANTIBODY FRAGMENT
C: SINGLE-CHAIN ANTIBODY FRAGMENT


Theoretical massNumber of molelcules
Total (without water)56,7552
Polymers56,7552
Non-polymers00
Water8,593477
1
A: SINGLE-CHAIN ANTIBODY FRAGMENT
C: SINGLE-CHAIN ANTIBODY FRAGMENT

A: SINGLE-CHAIN ANTIBODY FRAGMENT
C: SINGLE-CHAIN ANTIBODY FRAGMENT

A: SINGLE-CHAIN ANTIBODY FRAGMENT
C: SINGLE-CHAIN ANTIBODY FRAGMENT


Theoretical massNumber of molelcules
Total (without water)170,2656
Polymers170,2656
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
2
A: SINGLE-CHAIN ANTIBODY FRAGMENT

A: SINGLE-CHAIN ANTIBODY FRAGMENT

A: SINGLE-CHAIN ANTIBODY FRAGMENT


Theoretical massNumber of molelcules
Total (without water)85,1333
Polymers85,1333
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5060 Å2
ΔGint-38 kcal/mol
Surface area32120 Å2
MethodPISA
3
C: SINGLE-CHAIN ANTIBODY FRAGMENT

C: SINGLE-CHAIN ANTIBODY FRAGMENT

C: SINGLE-CHAIN ANTIBODY FRAGMENT


Theoretical massNumber of molelcules
Total (without water)85,1333
Polymers85,1333
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5280 Å2
ΔGint-36 kcal/mol
Surface area32050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.320, 136.320, 74.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (0.281213, 0.959633, -0.004829), (0.959644, -0.281202, 0.002888), (0.001414, -0.005446, -0.999984)
Vector: 0.2754, -0.0755, 45.3868)

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Components

#1: Antibody SINGLE-CHAIN ANTIBODY FRAGMENT / VARIABLE HEAVY (VH) DOMAIN / VARIABLE LIGHT (VL) DOMAIN


Mass: 28377.535 Da / Num. of mol.: 2
Fragment: VH DOMAIN RESIDUES 2 - 120, VL DOMAIN RESIDUES 121 - 233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Cell line: NQ11 MURINE-MURINE HYBRIDOMA, B1-8 MURINE-MURINE HYBRIDOMA
Gene: B1-8 VH DOMAIN FUSED TO NQ11 V / Plasmid: B18NQ11 / Cellular location (production host): SECRETED
Gene (production host): B1-8 VH DOMAIN FUSED TO NQ11 VL DOMAIN
Production host: Escherichia coli (E. coli) / Strain (production host): TG1TR / References: UniProt: P01751
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.5 Å3/Da / Density % sol: 45 %
Crystal growpH: 6.5
Details: 30% 2-PROPANOL, 0.2M NA CITRATE, 0.1M NA CACODYLATE PH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %2-propanol1reservoir
20.1 MNa cacodylate1reservoir
30.2 MNa citrate1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1994 / Details: MIRRORS
RadiationMonochromator: BENT CYLINDRICAL GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 33839 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 35.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 12 / Rsym value: 0.174 / % possible all: 98.1
Reflection
*PLUS
Num. measured all: 95579
Reflection shell
*PLUS
% possible obs: 98.1 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(SCALA)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JEL

1jel
PDB Unreleased entry


Resolution: 2→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: INDIVIDUAL ISOTROPIC B FA / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1649 5 %RANDOM
Rwork0.187 ---
obs0.187 33679 96.84 %-
Displacement parametersBiso mean: 12.9 Å2
Refine analyzeLuzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 0 477 4099
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.41
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.109
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.871.5
X-RAY DIFFRACTIONx_mcangle_it2.6362
X-RAY DIFFRACTIONx_scbond_it3.4392
X-RAY DIFFRACTIONx_scangle_it4.862.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Weight Biso : 1 / Weight position: 300

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)
11RESTRAINTS1.361.167
221.0521.4077
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2908 227 5.383 %
Rwork0.271 3903 -
obs--96.84 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 31030
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.109
LS refinement shell
*PLUS
Rfactor obs: 0.271

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