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- PDB-5x5x: Crystal structure of the Fab fragment of anti-osteocalcin C-termi... -

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Basic information

Entry
Database: PDB / ID: 5x5x
TitleCrystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219
Components
  • Fd chain of anti-osteocalcin antibody KTM219
  • L chain of anti-osteocalcin antibody KTM219
KeywordsIMMUNE SYSTEM / Quenchbody (Q-body) / Immunoglobulin fold / Osteocalcin / Open Sandwich Immunoassay (OS-IA)
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / FORMIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsKomatsu, M. / Dong, J. / Ueda, H. / Arai, R.
Funding support Japan, 7items
OrganizationGrant numberCountry
Cooperative Research Program of Network Joint Research Center for Materials and Devices20161175 Japan
Japan Society for the Promotion of ScienceJP15H04191 Japan
Japan Society for the Promotion of ScienceJP24780097 Japan
Japan Society for the Promotion of ScienceJP16H00761 Japan
Japan Society for the Promotion of ScienceJP16K05841 Japan
Japan Society for the Promotion of ScienceJP26420793 Japan
Japan Society for the Promotion of ScienceJP24360336 Japan
Citation
Journal: To be published
Title: Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219
Authors: Arai, R. / Komatsu, M. / Dong, J. / Ueda, H.
#1: Journal: Anal. Chem. / Year: 2007
Title: Noncompetitive detection of low molecular weight peptides by open sandwich immunoassay.
Authors: Lim, S.L. / Ichinose, H. / Shinoda, T. / Ueda, H.
History
DepositionFeb 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fd chain of anti-osteocalcin antibody KTM219
L: L chain of anti-osteocalcin antibody KTM219
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,71413
Polymers51,4632
Non-polymers1,25111
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-10 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.800, 71.472, 96.882
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11H-401-

HOH

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Fd chain of anti-osteocalcin antibody KTM219


Mass: 26202.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: Hybridoma KTM-219 / Plasmid: pET-Fab / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express lysY
#2: Antibody L chain of anti-osteocalcin antibody KTM219


Mass: 25259.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: Hybridoma KTM-219 / Plasmid: pET-Fab / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express lysY

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Non-polymers , 5 types, 250 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.6 M sodium formate, 29% PEG 3350

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2014
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 35733 / % possible obs: 98.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.3 Å2 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Rsym value: 0.066 / Χ2: 1.015 / Net I/av σ(I): 26.6 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
1.9-1.976.84.2334620.9180.1940.5220.4841.03397.5
1.97-2.056.86.0834680.950.1370.3690.3421.03797.3
2.05-2.146.88.2834610.9730.0980.2640.2451.03497.6
2.14-2.256.810.5735220.9830.0750.2030.1881.02598.5
2.25-2.396.812.8735590.9880.0620.1660.1541.02999.3
2.39-2.586.915.835840.9930.0480.130.121.02399.7
2.58-2.847.123.2336240.9970.0330.0880.0810.97299.9
2.84-3.257.129.0336310.9980.0250.0670.0620.999100
3.25-4.096.530.1735920.9980.0210.0550.0511.00998.5
4.09-506.547.0238300.9990.0130.0330.030.99499.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å40.1 Å
Translation3 Å40.1 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
PHASER2.5.5phasing
Cootmodel building
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KUZ

4kuz


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.128 / SU ML: 0.093 / SU R Cruickshank DPI: 0.1516 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.142
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 1786 5 %RANDOM
Rwork0.1806 ---
obs0.1828 33891 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.85 Å2 / Biso mean: 31.038 Å2 / Biso min: 13.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å2-
2--0.3 Å20 Å2
3---0.66 Å2
Refinement stepCycle: final / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 83 239 3593
Biso mean--44.73 40.06 -
Num. residues----433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023460
X-RAY DIFFRACTIONr_bond_other_d0.0060.023193
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.964678
X-RAY DIFFRACTIONr_angle_other_deg0.91437428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7795443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01125.118127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37715546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.487156
X-RAY DIFFRACTIONr_chiral_restr0.0820.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213855
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02749
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 113 -
Rwork0.206 2404 -
all-2517 -
obs--96.4 %

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