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- PDB-6b6r: Orthorhombic trypsin cryocooled to 100 K with 50% mpd as cryoprot... -

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Basic information

Entry
Database: PDB / ID: 6b6r
TitleOrthorhombic trypsin cryocooled to 100 K with 50% mpd as cryoprotectant
ComponentsCationic trypsin
KeywordsHYDROLASE
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
: / 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 family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / 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 family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BENZAMIDINE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.00005867689 Å
AuthorsJuers, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R15GM090248 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order.
Authors: Juers, D.H. / Farley, C.A. / Saxby, C.P. / Cotter, R.A. / Cahn, J.K.B. / Holton-Burke, R.C. / Harrison, K. / Wu, Z.
History
DepositionOct 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0098
Polymers23,3241
Non-polymers6857
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-42 kcal/mol
Surface area8880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.115, 58.195, 66.495
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Bos taurus (cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 5 types, 252 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Well: 25% PEG 8K, 0.2 M AmSO4, 0.1 M benzamidine Hal, 0.1 M Tris buffer pH 8.0 Protein: 40 mg/mL in water

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Apr 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→13.9 Å / Num. obs: 14445 / % possible obs: 98.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 8.24741653858 Å2 / CC1/2: 1 / Net I/σ(I): 29
Reflection shellResolution: 2→2.11 Å / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2046 / CC1/2: 1

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Processing

Software
NameVersionClassification
CrysalisPro1.10.1_2155data reduction
SCALAdata scaling
Cootmodel building
PHENIXrefinement
RefinementResolution: 2.00005867689→12.9147117001 Å / SU ML: 0.13599423797 / Cross valid method: FREE R-VALUE / σ(F): 1.37417677585 / Phase error: 15.446677673
RfactorNum. reflection% reflection
Rfree0.171912669493 753 5.22445014917 %
Rwork0.119646545354 --
obs0.122356255693 14413 98.3822525597 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 11.0583514945 Å2
Refinement stepCycle: LAST / Resolution: 2.00005867689→12.9147117001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 41 245 1915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006592676678391738
X-RAY DIFFRACTIONf_angle_d0.8594634607412371
X-RAY DIFFRACTIONf_chiral_restr0.0551245209768262
X-RAY DIFFRACTIONf_plane_restr0.0051575478298301
X-RAY DIFFRACTIONf_dihedral_angle_d10.35366047911036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.15380.1965262416431460.111485902142689X-RAY DIFFRACTION97.8936464088
2.1538-2.36940.1801461217671370.1097831423652718X-RAY DIFFRACTION99.8251748252
2.3694-2.70950.1631651413871700.1150532609172728X-RAY DIFFRACTION100
2.7095-3.40330.1883737803961290.1268470232872800X-RAY DIFFRACTION99.6258503401
3.4033-12.9150.1546833722721710.1260424265032725X-RAY DIFFRACTION94.7643979058

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