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- PDB-4kuz: Crystal structure of anti-emmprin antibody 4A5 Fab in trigonal form -

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Basic information

Entry
Database: PDB / ID: 4kuz
TitleCrystal structure of anti-emmprin antibody 4A5 Fab in trigonal form
Components
  • antibody 4A5 heavy chain
  • antibody 4A5 light chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTeplyakov, A. / Obmolova, G. / Gilliland, G.L.
CitationJournal: Proteins / Year: 2014
Title: Structural evidence for a constrained conformation of short CDR-L3 in antibodies.
Authors: Teplyakov, A. / Obmolova, G. / Malia, T.J. / Luo, J. / Gilliland, G.L.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 20, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: antibody 4A5 light chain
H: antibody 4A5 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0796
Polymers48,6952
Non-polymers3844
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-64 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.430, 126.430, 97.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody antibody 4A5 light chain


Mass: 24103.822 Da / Num. of mol.: 1
Fragment: Fab (mouse variable domain, human constant domain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): HEK293E / Production host: Homo sapiens (human)
#2: Antibody antibody 4A5 heavy chain


Mass: 24591.381 Da / Num. of mol.: 1
Fragment: Fab (mouse variable domain, human constant domain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): HEK293E / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 4.6 Å3/Da / Density % sol: 73.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.1 M CHES, pH 9.5, 2.0 M ammonium sulfate, 5% isopropanol, cryoprotectant: mother liquor + 25% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 24, 2008 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 24553 / Num. obs: 24553 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 20.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 4 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
AMoREphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1IL1 AND 1IGJ

1il1

1igj


Resolution: 2.7→29.2 Å / Cor.coef. Fo:Fc: 0.832 / Cor.coef. Fo:Fc free: 0.764 / σ(F): 1.34 / Phase error: 33.96 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.2684 2014 8.2 %
Rwork0.2302 --
obs0.2332 24553 99.38 %
all-23389 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20.71 Å20 Å2
2--1.42 Å20 Å2
3----2.13 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 20 61 3402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093418
X-RAY DIFFRACTIONf_angle_d1.2234641
X-RAY DIFFRACTIONf_dihedral_angle_d16.9371221
X-RAY DIFFRACTIONf_chiral_restr0.076516
X-RAY DIFFRACTIONf_plane_restr0.006586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7128-2.78060.33281340.27011540X-RAY DIFFRACTION89
2.7806-2.85570.36881410.26421600X-RAY DIFFRACTION92
2.8557-2.93970.3071460.22971593X-RAY DIFFRACTION91
2.9397-3.03450.27731430.23821570X-RAY DIFFRACTION91
3.0345-3.14280.30871400.23411624X-RAY DIFFRACTION92
3.1428-3.26850.28461390.21951577X-RAY DIFFRACTION92
3.2685-3.4170.26851410.22331632X-RAY DIFFRACTION92
3.417-3.59690.23461440.22191588X-RAY DIFFRACTION92
3.5969-3.82170.25751470.21161599X-RAY DIFFRACTION91
3.8217-4.11610.26121430.21481608X-RAY DIFFRACTION92
4.1161-4.52890.24181450.20571619X-RAY DIFFRACTION91
4.5289-5.1810.23811470.2191615X-RAY DIFFRACTION92
5.181-6.51520.24661470.23931656X-RAY DIFFRACTION92
6.5152-28.98610.30161530.2791708X-RAY DIFFRACTION92

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