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- PDB-3bx7: Engineered Human Lipocalin 2 (LCN2) in Complex with the Extracell... -

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Basic information

Entry
Database: PDB / ID: 3bx7
TitleEngineered Human Lipocalin 2 (LCN2) in Complex with the Extracellular Domain of Human CTLA-4
Components
  • CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED ANTIGEN 4
  • ENGINEERED HUMAN LIPOCALIN 2
KeywordsDE NOVO PROTEIN / PROTEIN BINDING / PROTEIN DESIGN / PROTEIN-PROTEIN COMPLEX / GLYCOPROTEIN / IMMUNOGLOBULIN DOMAIN / POLYMORPHISM / TRANSMEMBRANE PROTEIN
Function / homology
Function and homology information


protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CTLA4 inhibitory signaling / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / adaptive immune response ...protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CTLA4 inhibitory signaling / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / adaptive immune response / immune response / positive regulation of apoptotic process / external side of plasma membrane / DNA damage response / perinuclear region of cytoplasm / Golgi apparatus / plasma membrane
Similarity search - Function
Cytotoxic T-lymphocyte antigen 4 / Cytotoxic T-lymphocyte protein 4/CD28 / Calycin beta-barrel core domain / Lipocalin / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily ...Cytotoxic T-lymphocyte antigen 4 / Cytotoxic T-lymphocyte protein 4/CD28 / Calycin beta-barrel core domain / Lipocalin / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cytotoxic T-lymphocyte protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchonfeld, D.L. / Chatwell, L. / Skerra, A.
CitationJournal: To be Published
Title: High affinity molecular recognition and functional blockade of CTLA-4 by an engineered human lipocalin
Authors: Schonfeld, D.L. / Matschiner, G. / Chatwell, L. / Trentmann, S. / Schlehuber, S. / Hohlbaum, A. / Skerra, A.
History
DepositionJan 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED ANTIGEN 4
A: ENGINEERED HUMAN LIPOCALIN 2


Theoretical massNumber of molelcules
Total (without water)33,5032
Polymers33,5032
Non-polymers00
Water3,351186
1
C: CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED ANTIGEN 4
A: ENGINEERED HUMAN LIPOCALIN 2

C: CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED ANTIGEN 4
A: ENGINEERED HUMAN LIPOCALIN 2


Theoretical massNumber of molelcules
Total (without water)67,0064
Polymers67,0064
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area5580 Å2
ΔGint-34.5 kcal/mol
Surface area27280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.706, 120.706, 82.957
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED ANTIGEN 4 / CTLA-4 / CD152 / CYTOTOXIC T-LYMPHOCYTE PROTEIN 4


Mass: 13310.083 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTLA4, CD152 / Plasmid: pCTLA4-8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P16410
#2: Protein ENGINEERED HUMAN LIPOCALIN 2 / ENGINEERED LCN2 / ENGINEERED NEUTROPHIL-GELATINASE ASSOCIATED LIPOCALIN / ENGINEERED SIDEROCALIN


Mass: 20192.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pNGAL62 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 1.4 M Na-malonate, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.95373 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 31, 2006 / Details: mirror
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 40987 / % possible obs: 98.9 % / Redundancy: 8.6 % / Rsym value: 4.9 / Net I/σ(I): 30
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 3.3 / Rsym value: 41.9 / % possible all: 96.8

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I85 chain C, PDB ENTRY 1DFV chain B

1i85

1dfv


Resolution: 2.1→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.226 2036 5 %
Rwork0.209 --
obs-40457 98.8 %
Solvent computationBsol: 48.786 Å2
Displacement parametersBiso mean: 39.06 Å2
Baniso -1Baniso -2Baniso -3
1-5.048 Å20.47 Å20 Å2
2--5.048 Å20 Å2
3----10.097 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2287 0 0 186 2473
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3991.5
X-RAY DIFFRACTIONc_scbond_it2.0982
X-RAY DIFFRACTIONc_mcangle_it2.2512
X-RAY DIFFRACTIONc_scangle_it3.1442.5
LS refinement shellResolution: 2.1→2.18 Å /
Rfactor% reflection
Rfree0.32 -
Rwork0.291 -
obs-96.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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