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- PDB-6o1f: Complex between soybean trypsin inhibitor beta1-tryptase and a hu... -

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Basic information

Entry
Database: PDB / ID: 6o1f
TitleComplex between soybean trypsin inhibitor beta1-tryptase and a humanized fab
Components
  • Heavy Chain hu31A.v11
  • Light Chain hu31A.v11
  • Trypsin inhibitor A
  • Tryptase alpha/beta-1
KeywordsIMMUNE SYSTEM/HYDROLASE / Antibody / fab / tryptase / inhibitor / IMMUNE SYSTEM / IMMUNE SYSTEM-HYDROLASE complex
Function / homology
Function and homology information


tryptase / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / serine-type peptidase activity / serine-type endopeptidase inhibitor activity / defense response / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site ...Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Trypsin inhibitor A / Tryptase alpha/beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Glycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsUltsch, M.H. / Yi, T.
CitationJournal: Cell / Year: 2019
Title: An Allosteric Anti-tryptase Antibody for the Treatment of Mast Cell-Mediated Severe Asthma.
Authors: Maun, H.R. / Jackman, J.K. / Choy, D.F. / Loyet, K.M. / Staton, T.L. / Jia, G. / Dressen, A. / Hackney, J.A. / Bremer, M. / Walters, B.T. / Vij, R. / Chen, X. / Trivedi, N.N. / Morando, A. / ...Authors: Maun, H.R. / Jackman, J.K. / Choy, D.F. / Loyet, K.M. / Staton, T.L. / Jia, G. / Dressen, A. / Hackney, J.A. / Bremer, M. / Walters, B.T. / Vij, R. / Chen, X. / Trivedi, N.N. / Morando, A. / Lipari, M.T. / Franke, Y. / Wu, X. / Zhang, J. / Liu, J. / Wu, P. / Chang, D. / Orozco, L.D. / Christensen, E. / Wong, M. / Corpuz, R. / Hang, J.Q. / Lutman, J. / Sukumaran, S. / Wu, Y. / Ubhayakar, S. / Liang, X. / Schwartz, L.B. / Babina, M. / Woodruff, P.G. / Fahy, J.V. / Ahuja, R. / Caughey, G.H. / Kusi, A. / Dennis, M.S. / Eigenbrot, C. / Kirchhofer, D. / Austin, C.D. / Wu, L.C. / Koerber, J.T. / Lee, W.P. / Yaspan, B.L. / Alatsis, K.R. / Arron, J.R. / Lazarus, R.A. / Yi, T.
History
DepositionFeb 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Tryptase alpha/beta-1
H: Heavy Chain hu31A.v11
I: Trypsin inhibitor A
L: Light Chain hu31A.v11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4766
Polymers98,3524
Non-polymers1242
Water7,945441
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8240 Å2
ΔGint-32 kcal/mol
Surface area36720 Å2
Unit cell
Length a, b, c (Å)128.520, 128.520, 245.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

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Components

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Protein , 2 types, 2 molecules AI

#1: Protein Tryptase alpha/beta-1 / Tryptase-1 / Tryptase I / Tryptase alpha-1


Mass: 29211.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPSAB1, TPS1, TPS2, TPSB1 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q15661, tryptase
#3: Protein Trypsin inhibitor A / Kunitz-type trypsin inhibitor A


Mass: 21328.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: KTI3 / Production host: Escherichia coli (E. coli) / References: UniProt: P01070

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Antibody , 2 types, 2 molecules HL

#2: Antibody Heavy Chain hu31A.v11


Mass: 24361.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Antibody Light Chain hu31A.v11


Mass: 23451.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 443 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 441 / 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

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 5% PEG 4000 0.1M lithium sulfate 0.1M Tris pH 7.5 / PH range: 6.8-7.5

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2015 / Details: Liquid Nitrogen cooled Dual Crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97395 Å / Relative weight: 1
ReflectionResolution: 2.15→31.48 Å / Num. obs: 65608 / % possible obs: 99.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.2
Reflection shellResolution: 2.15→2.226 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.681 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6404 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fvc,4a6l,1avu

1fvc

4a6l

1avu


Resolution: 2.15→31.48 Å / Cor.coef. Fo:Fc: 0.9504 / Cor.coef. Fo:Fc free: 0.9287 / SU R Cruickshank DPI: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.185 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.164
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1996 3.04 %RANDOM
Rwork0.1898 ---
obs0.1911 65608 99.72 %-
Displacement parametersBiso mean: 45.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.2372 Å20 Å20 Å2
2---1.2372 Å20 Å2
3---2.4744 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: 1 / Resolution: 2.15→31.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6608 0 8 441 7057
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016815HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.139303HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2246SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes156HARMONIC2
X-RAY DIFFRACTIONt_gen_planes990HARMONIC5
X-RAY DIFFRACTIONt_it6815HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.83
X-RAY DIFFRACTIONt_other_torsion17.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion871SEMIHARMONIC5
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_contact7839SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2632 146 3.07 %
Rwork0.2136 4614 -
all0.2152 4760 -
obs--99.72 %
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)
11.6331-0.4530.03681.3465-0.04780.7498-0.06820.02590.20080.08210.0048-0.2971-0.10040.11850.0634-0.0928-0.0688-0.0491-0.00150.0045-0.050468.265161.232638.7907
21.4480.2563-0.46840.96850.01780.5992-0.08580.1053-0.1881-0.0050.0477-0.02760.10710.0020.0381-0.0667-0.0372-0.00170.028-0.0384-0.073539.644339.240527.5735
32.46680.2177-1.11662.17560.58123.0118-0.27960.489-0.4031-0.03040.11230.21760.5177-0.32960.1673-0.0872-0.16660.0604-0.1007-0.1016-0.063114.954415.597619.673
40.87520.1165-0.27831.5527-0.55583.7253-0.1163-0.0968-0.02180.29370.03290.0235-0.2396-0.24850.0834-0.0323-0.0329-0.0496-0.0265-0.0011-0.131557.548554.122566.1349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|16 - A|400}
2X-RAY DIFFRACTION2{L|1 - L|108 H|1 - H|114}
3X-RAY DIFFRACTION3{L|109 - L|213 H|115 - H|216}
4X-RAY DIFFRACTION4{I|1 - I|177}

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