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- PDB-5k8a: NIST FAB -

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Basic information

Entry
Database: PDB / ID: 5k8a
TitleNIST FAB
Components
  • Heavy chain
  • humanized Fab Lite chain
KeywordsIMMUNE SYSTEM / measurement standard / pseudo-tetragonal packing
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.999 Å
AuthorsGallagher, D.T. / Galvin, C.V. / Karageorgos, I. / Marino, J.P.
Citation
Journal: Data Brief / Year: 2018
Title: Data on crystal organization in the structure of the Fab fragment from the NIST reference antibody, RM 8671.
Authors: Gallagher, D.T. / Karageorgos, I. / Hudgens, J.W. / Galvin, C.V.
#1: Journal: Biologicals / Year: 2017
Title: Biophysical characterization and structure of the Fab fragment from the NIST reference antibody, RM 8671.
Authors: Karageorgos, I. / Gallagher, E.S. / Galvin, C. / Gallagher, D.T. / Hudgens, J.W.
History
DepositionMay 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 2.0Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Oct 23, 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
L: humanized Fab Lite chain
H: Heavy chain
M: humanized Fab Lite chain
V: Heavy chain
A: humanized Fab Lite chain
B: Heavy chain
E: humanized Fab Lite chain
F: Heavy chain


Theoretical massNumber of molelcules
Total (without water)190,7428
Polymers190,7428
Non-polymers00
Water6,575365
1
L: humanized Fab Lite chain
H: Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,6852
Polymers47,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-29 kcal/mol
Surface area19380 Å2
MethodPISA
2
M: humanized Fab Lite chain
V: Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,6852
Polymers47,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-31 kcal/mol
Surface area19760 Å2
MethodPISA
3
E: humanized Fab Lite chain
F: Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,6852
Polymers47,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-30 kcal/mol
Surface area19420 Å2
MethodPISA
4
A: humanized Fab Lite chain
B: Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,6852
Polymers47,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-30 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.156, 149.203, 195.032
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Antibody
humanized Fab Lite chain


Mass: 23150.730 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody
Heavy chain


Mass: 24534.699 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.87 Å3/Da / Density % sol: 57.2 % / Mosaicity: 1.233 ° / Mosaicity esd: 0.008 °
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25 mg/mL ptn, 1.9 M AmSO4, 200 mM LiSO4, 100 mM Histidine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.67
11K, H, -L20.33
ReflectionResolution: 1.999→20 Å / Num. obs: 147109 / % possible obs: 99.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.083 / Net I/av σ(I): 25.565 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.999-2.034.30.841196.1
2.03-2.074.90.755199.4
2.07-2.115.70.676199.8
2.11-2.155.80.58199.8
2.15-2.25.80.503199.9
2.2-2.255.80.444199.8
2.25-2.315.90.402199.8
2.31-2.3760.346199.9
2.37-2.4460.298199.8
2.44-2.5260.259199.9
2.52-2.615.50.215199.8
2.61-2.715.80.1891100
2.71-2.846.60.1551100
2.84-2.996.50.1291100
2.99-3.176.40.105199.9
3.17-3.426.20.086199.9
3.42-3.765.70.072199.9
3.76-4.35.90.06199.9
4.3-5.396.20.0521100
5.39-205.80.045199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.07 Å29.77 Å
Translation7.07 Å29.77 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.7phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3qwo

3qwo


Resolution: 1.999→19.87 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.291 / SU ML: 0.07 / SU R Cruickshank DPI: 0.0286 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.026
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1892 7274 5 %RANDOM
Rwork0.1644 ---
obs0.1656 138161 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 136.6 Å2 / Biso mean: 44.992 Å2 / Biso min: 24.26 Å2
Baniso -1Baniso -2Baniso -3
1-21.36 Å20 Å20 Å2
2--0.57 Å2-0 Å2
3----21.93 Å2
Refinement stepCycle: final / Resolution: 1.999→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13264 0 0 367 13631
Biso mean---50.87 -
Num. residues----1744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213612
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.95118528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90651736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24824.32500
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.615152184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1331544
X-RAY DIFFRACTIONr_chiral_restr0.0990.22112
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110068
X-RAY DIFFRACTIONr_mcbond_it3.0134.3556968
X-RAY DIFFRACTIONr_mcangle_it4.0386.518696
X-RAY DIFFRACTIONr_scbond_it3.6454.5396643
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 448 -
Rwork0.215 9911 -
all-10359 -
obs--98.15 %

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