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- PDB-6ntt: X-ray Crystal Structure of Soybean Trypsin Inhibitor (Kunitz) Com... -

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Basic information

Entry
Database: PDB / ID: 6ntt
TitleX-ray Crystal Structure of Soybean Trypsin Inhibitor (Kunitz) Complexed with 1,5-Disulfonyl Naphthalene
ComponentsTrypsin inhibitor A
KeywordsPLANT PROTEIN / silver bullets / ligands / symmetry / oligomer / crystallization / buffer
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity
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 / Mainly Beta
Similarity search - Domain/homology
naphthalene-1,5-disulfonic acid / Trypsin inhibitor A
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMcPherson, A.
CitationJournal: Cryst.Growth Des. / Year: 2019
Title: Lattice Interactions in Crystals of Soybean Trypsin Inhibitor (Kunitz) Produced by Inclusion of 1,5-Disulfonylnaphthalene
Authors: McPherson, A. / Day, J. / Larson, S.B.
History
DepositionJan 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trypsin inhibitor A
B: Trypsin inhibitor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5138
Polymers48,0632
Non-polymers1,4516
Water4,053225
1
A: Trypsin inhibitor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5153
Polymers24,0311
Non-polymers4842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Trypsin inhibitor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9985
Polymers24,0311
Non-polymers9674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.880, 64.680, 69.080
Angle α, β, γ (deg.)90.00, 97.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 1 - 177 / Label seq-ID: 25 - 201

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Trypsin inhibitor A / Kunitz-type trypsin inhibitor A


Mass: 24031.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: KTI3 / Production host: Glycine max (soybean) / References: UniProt: P01070
#2: Chemical ChemComp-21D / naphthalene-1,5-disulfonic acid


Mass: 288.297 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H8O6S2
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.23 Å3/Da / Density % sol: 49 % / Description: thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Lyophilized protein dissolved in water to 25 mg/ml. Sitting drop vapor diffusion against reservoirs of 25% PEG 3350 with 0.10 M MES buffer ph 6.5. 3 ul drops composed of equal amounts of ...Details: Lyophilized protein dissolved in water to 25 mg/ml. Sitting drop vapor diffusion against reservoirs of 25% PEG 3350 with 0.10 M MES buffer ph 6.5. 3 ul drops composed of equal amounts of protein stock solution and reservoir supplemented with 0.10 M 1,5-Disulfonyl Naphthalene. Crystallization time about 2 weeks.
PH range: 6.3 - 6.7

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→32.61 Å / Num. obs: 13649 / % possible obs: 99 % / Redundancy: 4.7 % / Biso Wilson estimate: 83 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.122 / Rrim(I) all: 0.136 / Rsym value: 0.124 / Net I/av σ(I): 5.3 / Net I/σ(I): 4.7
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.2 / Rrim(I) all: 0.538 / % possible all: 85

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AVU

1avu


Resolution: 2.4→32.61 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.909 / SU B: 32.498 / SU ML: 0.391 / Cross valid method: THROUGHOUT / ESU R: 1.697 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30595 656 4.9 %RANDOM
Rwork0.20924 ---
obs0.21376 12813 93.2 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.999 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å2-2.2 Å2
2---1.71 Å20 Å2
3---3.46 Å2
Refinement stepCycle: 1 / Resolution: 2.4→32.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 90 225 3054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132971
X-RAY DIFFRACTIONr_bond_other_d00.0172680
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.6244053
X-RAY DIFFRACTIONr_angle_other_deg1.11.5996237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1915350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4623.161155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30415474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4781518
X-RAY DIFFRACTIONr_chiral_restr0.0490.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023658
X-RAY DIFFRACTIONr_gen_planes_other00.02608
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0743.9231403
X-RAY DIFFRACTIONr_mcbond_other2.0743.9221402
X-RAY DIFFRACTIONr_mcangle_it3.3025.8761746
X-RAY DIFFRACTIONr_mcangle_other3.3025.8771747
X-RAY DIFFRACTIONr_scbond_it2.2844.4421568
X-RAY DIFFRACTIONr_scbond_other2.2834.4261566
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7316.5872306
X-RAY DIFFRACTIONr_long_range_B_refined6.94674.6810703
X-RAY DIFFRACTIONr_long_range_B_other6.94674.69310704
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4513 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.18 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 57 -
Rwork0.298 943 -
obs--92.68 %
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)
12.052-0.95660.38954.55351.16684.87280.0393-0.0819-0.1890.1194-0.0080.07110.40360.0557-0.03120.3244-0.0369-0.01720.0164-0.02680.279312.73913.37144.071
25.4807-0.2567-0.80714.66452.56745.2568-0.0275-0.17910.8272-0.11650.0624-0.1266-0.5494-0.1011-0.03480.3634-0.0145-0.08160.0189-0.04490.321929.71143.03257.795
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 177
2X-RAY DIFFRACTION2B-8 - 177

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