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- PDB-3s8k: Crystal structure of a papaya latex serine protease inhibitor (PP... -

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Basic information

Entry
Database: PDB / ID: 3s8k
TitleCrystal structure of a papaya latex serine protease inhibitor (PPI) at 1.7A resolution
ComponentsLatex serine proteinase inhibitor
KeywordsHYDROLASE INHIBITOR / Kunitz-STI fold / protease inhibitor
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular region
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
: / AMMONIUM ION / Latex serine proteinase inhibitor
Similarity search - Component
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGarcia-Pino, A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The plasticity of the beta-Trefoil fold constitutes an evolutionary platform for protease inhibition
Authors: Azarkan, M. / Martinez-Rodriguez, S. / Buts, L. / Baeyens-Volant, D. / Garcia-Pino, A.
History
DepositionMay 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Nov 20, 2019Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif
Item: _chem_comp.type / _struct_conn_type.id / _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Latex serine proteinase inhibitor
B: Latex serine proteinase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,72020
Polymers41,3662
Non-polymers2,35418
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-9 kcal/mol
Surface area16840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.262, 81.992, 140.891
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Latex serine proteinase inhibitor


Mass: 20682.906 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Carica papaya (papaya) / References: UniProt: P80691
#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 427 molecules

#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H4N
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8 M ammonium sulfate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.8073 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 4, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8073 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 51816 / Num. obs: 51816 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.15 % / Net I/σ(I): 17.3
Reflection shellResolution: 1.7→1.76 Å / % possible all: 90.5

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.682 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1993 2632 5.08 %
Rwork0.1812 --
obs0.1822 51816 90.46 %
all-51816 -
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.588 Å2 / ksol: 0.473 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.6296 Å20 Å2-0 Å2
2--19.7026 Å20 Å2
3----15.073 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 140 411 3404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153103
X-RAY DIFFRACTIONf_angle_d1.5414220
X-RAY DIFFRACTIONf_dihedral_angle_d12.5911126
X-RAY DIFFRACTIONf_chiral_restr0.092467
X-RAY DIFFRACTIONf_plane_restr0.006525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73090.27241190.25992307X-RAY DIFFRACTION83
1.7309-1.76420.23211270.22992300X-RAY DIFFRACTION81
1.7642-1.80020.26611100.21742333X-RAY DIFFRACTION83
1.8002-1.83930.25121280.21532312X-RAY DIFFRACTION82
1.8393-1.8820.21611190.19922307X-RAY DIFFRACTION82
1.882-1.92910.19691330.18952333X-RAY DIFFRACTION82
1.9291-1.98120.191280.1822405X-RAY DIFFRACTION85
1.9812-2.03940.20831220.16872428X-RAY DIFFRACTION86
2.0394-2.10520.20861420.18712619X-RAY DIFFRACTION92
2.1052-2.18030.20571490.17622621X-RAY DIFFRACTION94
2.1803-2.26750.20691410.16522696X-RAY DIFFRACTION94
2.2675-2.37050.18561490.16442705X-RAY DIFFRACTION96
2.3705-2.49530.19551550.15952780X-RAY DIFFRACTION97
2.4953-2.65130.18451540.15872839X-RAY DIFFRACTION99
2.6513-2.85540.17791390.15712877X-RAY DIFFRACTION99
2.8554-3.14170.19191450.16352881X-RAY DIFFRACTION99
3.1417-3.59390.1711580.16772824X-RAY DIFFRACTION98
3.5939-4.51890.18331540.16852769X-RAY DIFFRACTION94
4.5189-19.6830.23311600.2312848X-RAY DIFFRACTION93
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.7796-0.96060.23432.05010.2511.52830.07840.0258-0.04530.1219-0.0381-0.01320.16140.2596-0.01940.2317-0.0063-0.00990.29670.00590.222523.088638.056327.2408
25.2811-0.5253-1.32663.38490.68353.89320.188-0.31220.60420.3488-0.36320.9331-0.2921-0.67250.12230.27410.09090.03880.7119-0.1070.37472.473953.033524.8922
31.04180.16260.03360.75-0.24991.2950.02030.1503-0.1736-0.1521-0.03450.07020.1610.06860.00590.21430.0269-0.00840.2482-0.02350.191621.49738.812920.1998
41.2991-0.48620.2411.9290.2221.17770.10440.04670.0072-0.1511-0.13680.286-0.0923-0.37310.01670.21760.0208-0.00680.3206-0.02920.222411.438348.111118.5947
51.2224-0.4238-1.67710.5970.95364.55880.00460.499-0.02160.03090.06280.09960.351-0.228-0.10120.26580.0056-0.02650.2933-0.02130.213714.95146.809210.7965
61.4992-0.58241.92241.0536-1.1673.83780.09110.41940.0332-0.0283-0.122-0.0642-0.20420.6740.05210.25930.02660.00030.3248-0.00110.218425.701946.178818.3369
71.4515-0.16110.26010.88440.15722.97720.15770.20370.145-0.0969-0.0783-0.0422-0.37850.2652-0.0730.26660.01650.02930.33340.01570.241124.67653.60729.9115
82.2996-0.0323-1.54860.69170.03591.81810.2604-0.13320.22290.0415-0.05060.0285-0.4763-0.0506-0.14270.26470.01250.02260.2908-0.00140.253116.336955.521629.0821
93.01830.49450.22062.8863-0.48753.04210.0664-0.2157-0.3370.0952-0.0438-0.09620.2863-0.08490.03750.2187-0.0169-0.03240.27740.02650.198223.822740.28628.8999
101.68940.04730.51472.3659-0.51832.01270.1039-0.1994-0.0358-0.1720.0180.0940.2409-0.2721-0.07370.2208-0.0169-0.01170.24480.01910.227537.872830.822543.5508
111.3787-0.01340.49451.21370.12171.9991-0.10870.50370.1728-0.14910.0655-0.0731-0.33790.47090.08370.2536-0.0721-0.00970.3550.05160.219653.043746.786342.5321
120.66280.29560.00360.68520.0090.83340.0601-0.0387-0.08840.0915-0.012-0.05470.0352-0.1444-0.03520.2199-0.0098-0.01290.25990.0330.247642.870533.891848.228
130.28940.05930.26630.9379-0.10392.35480.0181-0.0871-0.01140.11310.0137-0.0479-0.20220.048-0.02820.17830.0009-0.00280.24110.00310.183845.528341.233955.4892
141.60430.50650.17291.3825-0.05192.01240.01860.10.17260.05340.04870.0184-0.32250.0224-0.05450.25490.0135-0.00360.24010.01090.221144.60547.816444.6716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:37)
2X-RAY DIFFRACTION2chain 'A' and (resseq 38:47)
3X-RAY DIFFRACTION3chain 'A' and (resseq 48:78)
4X-RAY DIFFRACTION4chain 'A' and (resseq 79:106)
5X-RAY DIFFRACTION5chain 'A' and (resseq 107:118)
6X-RAY DIFFRACTION6chain 'A' and (resseq 119:140)
7X-RAY DIFFRACTION7chain 'A' and (resseq 141:154)
8X-RAY DIFFRACTION8chain 'A' and (resseq 155:171)
9X-RAY DIFFRACTION9chain 'A' and (resseq 172:184)
10X-RAY DIFFRACTION10chain 'B' and (resseq 2:24)
11X-RAY DIFFRACTION11chain 'B' and (resseq 25:47)
12X-RAY DIFFRACTION12chain 'B' and (resseq 48:78)
13X-RAY DIFFRACTION13chain 'B' and (resseq 79:154)
14X-RAY DIFFRACTION14chain 'B' and (resseq 155:183)

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