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- PDB-3gt3: Structure of proteinase K with the mad triangle B3C -

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Basic information

Entry
Database: PDB / ID: 3gt3
TitleStructure of proteinase K with the mad triangle B3C
ComponentsProteinase K
KeywordsHYDROLASE / PHASING TOOL / 5-AMINO-2 / 4 / 6-TRIIODOISOPHTHALIC ACID / I3C / MAGIC TRIANGLE / 6-TRIBROMOISOPHTHALIC ACID / B3C / MAD TRIANGLE / Disulfide bond / Metal-binding / Protease / Serine protease / Zymogen
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. ...Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BRV / Proteinase K
Similarity search - Component
Biological speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsBeck, T. / Gruene, T. / Sheldrick, G.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: The magic triangle goes MAD: experimental phasing with a bromine derivative
Authors: Beck, T. / Gruene, T. / Sheldrick, G.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: A magic triangle for experimental phasing of macromolecules
Authors: Beck, T. / Krasauskas, A. / Gruene, T. / Sheldrick, G.M.
History
DepositionMar 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8227
Polymers28,9591
Non-polymers1,8636
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.840, 67.840, 101.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-432-

HOH

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Components

#1: Protein Proteinase K / / Tritirachium alkaline proteinase / Endopeptidase K


Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Engyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical
ChemComp-BRV / 5-amino-2,4,6-tribromobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-tribromoisophthalic acid


Mass: 417.834 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H4Br3NO4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSO4 311, HOH 312-315, HOH 316 HAVE THE FOLLOWING SITUATION. WHEN ASN A 161 HAS ALTERNATE ...SO4 311, HOH 312-315, HOH 316 HAVE THE FOLLOWING SITUATION. WHEN ASN A 161 HAS ALTERNATE CONFORMATION B, THERE ARE TWO POSSIBLE CONFORMATION. ONE HAS SO4 311, HOH 312-315, THE OTHER HAS HOH 316. THE REFERENCE OF 5-AMINO-2,4,6-TRIBROMOISOPHTHALIC ACID WILL BE SUBMITTED TO ACTA CRYSTALLOGR.,SECT.C. THE REFERENCE OF I3C IS ACTA CRYSTALLOGRAPHICA SECTION E(2008) E64, O1286 TITLE: 5-AMINO-2,4,6-TRIIODOISOPHTHALIC ACID MONOHYDRATE AUTHOR: T. BECK AND G.M. SHELDRICK

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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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.1M TRIS, 1.28M ammonium sulfate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 106 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9129, 0.9197, 0.9202, 0.9204
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2008 / Details: double crystal Si(111) fixed-exit monochromator
RadiationMonochromator: double crystal Si(111) fixed-exit monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91291
20.91971
30.92021
40.92041
ReflectionResolution: 1.5→48 Å / Num. all: 38897 / Num. obs: 38897 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 24.9
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 8.3 / % possible all: 99.2

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
SADABSdata scaling
SHELXDphasing
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 1.5→48 Å / Num. parameters: 10095 / Num. restraintsaints: 9056 / Occupancy max: 1 / Occupancy min: 0.03 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1935 -RANDOM
Rwork0.143 ---
all0.145 38826 --
obs0.143 38826 99.8 %-
Displacement parametersBiso max: 86.94 Å2 / Biso mean: 14.02 Å2 / Biso min: 5.07 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 74 417 2492
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_approx_iso_adps0
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_from_restr_planes0.419
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.053
X-RAY DIFFRACTIONs_similar_dist0.007
X-RAY DIFFRACTIONs_zero_chiral_vol0.057
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.031

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