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- PDB-2v7n: Unusual twinning in crystals of the CitS binding antibody Fab fra... -

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Basic information

Entry
Database: PDB / ID: 2v7n
TitleUnusual twinning in crystals of the CitS binding antibody Fab fragment f3p4
Components
  • IMMUNOGLOBULIN HEAVY CHAIN
  • IMMUNOGLOBULIN LIGHT CHAIN
KeywordsIMMUNE SYSTEM / BINDING PROTEIN / RECOMBINANT FAB FRAGMENT / SYNTHETIC ANTIBODY LIBRARY (HUCAL) / PHAGE DISPLAY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsFrey, D. / Huber, T. / Plueckthun, A. / Gruetter, M.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structure of the Recombinant Antibody Fab Fragment F3P4.
Authors: Frey, D. / Huber, T. / Plueckthun, A. / Gruetter, M.G.
History
DepositionJul 31, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMMUNOGLOBULIN LIGHT CHAIN
B: IMMUNOGLOBULIN HEAVY CHAIN
C: IMMUNOGLOBULIN LIGHT CHAIN
D: IMMUNOGLOBULIN HEAVY CHAIN
E: IMMUNOGLOBULIN LIGHT CHAIN
F: IMMUNOGLOBULIN HEAVY CHAIN
G: IMMUNOGLOBULIN LIGHT CHAIN
H: IMMUNOGLOBULIN HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)191,7018
Polymers191,7018
Non-polymers00
Water9,728540
1
A: IMMUNOGLOBULIN LIGHT CHAIN
B: IMMUNOGLOBULIN HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)47,9252
Polymers47,9252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-23.4 kcal/mol
Surface area19170 Å2
MethodPISA
2
C: IMMUNOGLOBULIN LIGHT CHAIN
D: IMMUNOGLOBULIN HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)47,9252
Polymers47,9252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-25.2 kcal/mol
Surface area18840 Å2
MethodPISA
3
E: IMMUNOGLOBULIN LIGHT CHAIN
F: IMMUNOGLOBULIN HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)47,9252
Polymers47,9252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-25.2 kcal/mol
Surface area18820 Å2
MethodPISA
4
G: IMMUNOGLOBULIN LIGHT CHAIN
H: IMMUNOGLOBULIN HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)47,9252
Polymers47,9252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-25.5 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.790, 185.920, 102.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody
IMMUNOGLOBULIN LIGHT CHAIN / VK3


Mass: 23382.799 Da / Num. of mol.: 4 / Fragment: FAB FRAGMENT, RESIDUES 1-255
Source method: isolated from a genetically manipulated source
Details: SYNTHETIC GENE, DERIVED FROM PHAGE DISPLAY OF THE HUMAN COMBINATORIAL ANTIBODY LIBRARY (HUCAL)
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PMX9 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SB356
#2: Antibody
IMMUNOGLOBULIN HEAVY CHAIN / FRAGMENT VH3 C1


Mass: 24542.365 Da / Num. of mol.: 4 / Fragment: FAB FRAGMENT, RESIDUES 1-259
Source method: isolated from a genetically manipulated source
Details: SYNTHETIC GENE, DERIVED FROM PHAGE DISPLAY OF THE HUMAN COMBINATORIAL ANTIBODY LIBRARY (HUCAL)
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PMX9 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SB356
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsC-TERMINAL HISTIDINE TAG AT HEAVY CHAIN

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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: 2.3 Å3/Da / Density % sol: 46.6 % / Description: NONE
Crystal growpH: 6.5
Details: 23% PEG4000, 50 MM LI2SO4, 50 MM NA2SO4, 50 MM N-(2ACETAMIDO) IMINODIACETIC ACID (ADA), PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 16, 2006 / Details: BENT MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→31 Å / Num. obs: 151552 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.2
Reflection shellResolution: 1.9→1.92 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.5 / % possible all: 83.3

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Processing

Software
NameVersionClassification
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
PHASER1.3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→15 Å / Num. parameters: 53672 / Num. restraintsaints: 100475 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2017 4240 3 %RANDOM
all0.1553 143072 --
obs0.1552 -95.1 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 13417
Refinement stepCycle: LAST / Resolution: 1.92→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12877 0 0 540 13417
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0.064
X-RAY DIFFRACTIONs_from_restr_planes0.0287
X-RAY DIFFRACTIONs_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.044
X-RAY DIFFRACTIONs_approx_iso_adps0

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