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- PDB-6hgu: Crystal Structure of an anti-APP-tag Fab -

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Basic information

Entry
Database: PDB / ID: 6hgu
TitleCrystal Structure of an anti-APP-tag Fab
Components
  • anti-APP-tag Fab heavy-chain
  • anti-APP-tag Fab light-chain
KeywordsIMMUNE SYSTEM / IgG / Fab fragment
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: 1.5 Å
AuthorsRondeau, J.M. / Goepfert, A.
CitationJournal: Immunity / Year: 2020
Title: Structural Analysis Reveals that the Cytokine IL-17F Forms a Homodimeric Complex with Receptor IL-17RC to Drive IL-17RA-Independent Signaling.
Authors: Goepfert, A. / Lehmann, S. / Blank, J. / Kolbinger, F. / Rondeau, J.M.
History
DepositionAug 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.2Jan 17, 2024Group: 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
Revision 2.3Oct 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
A: anti-APP-tag Fab heavy-chain
B: anti-APP-tag Fab light-chain
H: anti-APP-tag Fab heavy-chain
L: anti-APP-tag Fab light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5749
Polymers95,9674
Non-polymers6075
Water14,628812
1
A: anti-APP-tag Fab heavy-chain
B: anti-APP-tag Fab light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4986
Polymers47,9832
Non-polymers5154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-20 kcal/mol
Surface area19510 Å2
MethodPISA
2
H: anti-APP-tag Fab heavy-chain
L: anti-APP-tag Fab light-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0763
Polymers47,9832
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-25 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.240, 67.840, 77.860
Angle α, β, γ (deg.)109.760, 92.360, 115.300
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody anti-APP-tag Fab heavy-chain / 6E10A5 Fab


Mass: 23832.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)
#2: Antibody anti-APP-tag Fab light-chain / anti-APP Fab


Mass: 24150.826 Da / Num. of mol.: 2 / Fragment: anti-APP-tag Fab heavy-chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 812 / 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: 2.79 Å3/Da / Density % sol: 55.94 % / Mosaicity: 0.23 °
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, 20% isopropanol, 10% PEG 1,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9788 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 1, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.5→35.75 Å / Num. obs: 159668 / % possible obs: 96.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 24.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.018 / Rrim(I) all: 0.049 / Net I/σ(I): 14.3 / Num. measured all: 1150437 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.5-1.584.20.525229020.8930.2910.60194.5
4.75-35.7560.02249900.9990.010.02495.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.11.7refinement
XDSdata reduction
Aimless0.7.1data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IFL

3ifl


Resolution: 1.5→15.15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.07 / SU Rfree Blow DPI: 0.069 / SU Rfree Cruickshank DPI: 0.068
RfactorNum. reflection% reflectionSelection details
Rfree0.207 7948 4.98 %RANDOM
Rwork0.187 ---
obs0.188 159563 96.4 %-
Displacement parametersBiso max: 124.33 Å2 / Biso mean: 31.9 Å2 / Biso min: 14.62 Å2
Baniso -1Baniso -2Baniso -3
1--3.1219 Å23.9687 Å23.9884 Å2
2--4.2976 Å2-2.3678 Å2
3----1.1756 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: final / Resolution: 1.5→15.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6634 0 39 812 7485
Biso mean--35.71 42.01 -
Num. residues----864
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2258SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1128HARMONIC5
X-RAY DIFFRACTIONt_it6855HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion925SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8202SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6855HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9347HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion4.3
X-RAY DIFFRACTIONt_other_torsion13.79
LS refinement shellResolution: 1.5→1.54 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2325 549 4.73 %
Rwork0.2258 11054 -
all0.2261 11603 -
obs--93.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7478-0.79290.45771.6556-0.35390.8187-0.13890.10070.0164-0.110.0622-0.00740.0124-0.00360.0767-0.0332-0.0175-0.005-0.01960.0002-0.04183.787218.89174.3143
21.50660.01720.79482.18780.08231.5594-0.0786-0.02570.13210.0981-0.0352-0.1631-0.078-0.0130.1138-0.05380.0117-0.0165-0.05250.0111-0.032818.781916.283120.1644
34.71873.9780.30013.99460.13320.5062-0.3170.3713-0.1097-0.40210.3124-0.1001-0.0180.01480.0046-0.0304-0.04170.0159-0.0656-0.0213-0.042715.920153.12043.4197
41.8267-0.39460.08213.08190.45340.85540.081-0.0883-0.02320.459-0.0577-0.20220.1088-0.0715-0.02330.0176-0.0237-0.0256-0.09370.0176-0.03714.249952.620919.3852
50.54390.00960.50190.8054-0.19772.61870.0156-0.06640.0673-0.00540.02390.0656-0.0233-0.1093-0.0395-0.02510.00020.0035-0.02830.0127-0.03831.128936.5924-26.4491
61.37440.03940.43211.8343-0.17231.45870.0245-0.0536-0.02370.0663-0.0239-0.0620.0818-0.0201-0.0006-0.0469-0.0099-0.0231-0.01930.0298-0.062241.713325.6871-10.5203
72.10642.8776-0.6075.7934-1.69620.7757-0.20530.14140.243-0.44570.26570.4715-0.0335-0.0419-0.06030.0568-0.0703-0.0522-0.12950.0399-0.060214.3624.6616-32.0803
81.52780.42991.54181.95840.86454.13-0.05950.2114-0.205-0.12630.0559-0.38780.04460.30940.0036-0.0201-0.04150.0672-0.0703-0.0133-0.023429.5985-1.6357-30.9537
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1group10
2X-RAY DIFFRACTION2group20
3X-RAY DIFFRACTION3group30
4X-RAY DIFFRACTION4group40
5X-RAY DIFFRACTION5group50
6X-RAY DIFFRACTION6group60
7X-RAY DIFFRACTION7group70
8X-RAY DIFFRACTION8group80

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