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- PDB-2rdl: Hamster Chymase 2 -

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Basic information

Entry
Database: PDB / ID: 2rdl
TitleHamster Chymase 2
Components
  • Chymase 2
  • METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYLKETONE INHIBITOR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CHYMASE 2 / SERINE PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


serine-type endopeptidase activity
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 domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
methoxysuccinyl-alanyl-alanyl-prolyl-alanine chloromethyl ketone / Chymase 2
Similarity search - Component
Biological speciesMesocricetus auratus (golden hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsSpurlino, J. / Abad, M. / Kervinen, J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural basis for elastolytic substrate specificity in rodent alpha-chymases.
Authors: Kervinen, J. / Abad, M. / Crysler, C. / Kolpak, M. / Mahan, A.D. / Masucci, J.A. / Bayoumy, S. / Cummings, M.D. / Yao, X. / Olson, M. / de Garavilla, L. / Kuo, L. / Deckman, I. / Spurlino, J.
History
DepositionSep 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Dec 12, 2012Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chymase 2
B: Chymase 2
I: METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYLKETONE INHIBITOR
J: METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0478
Polymers51,6634
Non-polymers3844
Water2,288127
1
A: Chymase 2
I: METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYLKETONE INHIBITOR
hetero molecules

B: Chymase 2
J: METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0478
Polymers51,6634
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3670 Å2
MethodPISA
2
A: Chymase 2
I: METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0244
Polymers25,8312
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
MethodPISA
3
B: Chymase 2
J: METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYLKETONE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0244
Polymers25,8312
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.272, 71.272, 198.575
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Chymase 2 /


Mass: 25354.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Production host: unidentified baculovirus / References: UniProt: O70164
#2: Protein/peptide METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYLKETONE INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 476.952 Da / Num. of mol.: 2 / Source method: obtained synthetically
References: methoxysuccinyl-alanyl-alanyl-prolyl-alanine chloromethyl ketone
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE UNBOUND FORM OF THE INHIBITOR (CHAINS I,J) IS METHOXYSUCCINYL-ALA-ALA-PRO-ALA- ...THE UNBOUND FORM OF THE INHIBITOR (CHAINS I,J) IS METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A COVALENT BOND TO SER 195 FORMING A HEMIKETAL ALV AND 2) A COVALENT BOND TO NE2 OF HIS 57

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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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 3350, 0.1 M Tris-HCl, pH 8.5, and 0.2 M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 21, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→35 Å / Num. obs: 18529 / Biso Wilson estimate: 25.661 Å2

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.5→35 Å / FOM work R set: 0.847 / Stereochemistry target values: ml
RfactorNum. reflection% reflection
Rfree0.253 948 5.12 %
Rwork0.186 --
obs-18529 99.96 %
Solvent computationBsol: 34.569 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso max: 89.85 Å2 / Biso mean: 22.2 Å2 / Biso min: 6.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.119 Å20 Å2-0 Å2
2--0.119 Å20 Å2
3----0.239 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 20 127 3767
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.7081
X-RAY DIFFRACTIONf_bond_d0.0041
X-RAY DIFFRACTIONf_chiral_restr0.0511
X-RAY DIFFRACTIONf_dihedral_angle_d12.4061
X-RAY DIFFRACTIONf_plane_restr0.0031
X-RAY DIFFRACTIONf_nbd_refined4.0921
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
2.5-2.5240.196494X-RAY DIFFRACTION3594
2.524-2.550.183485X-RAY DIFFRACTION3594
2.55-2.5760.189486X-RAY DIFFRACTION3594
2.576-2.6030.177473X-RAY DIFFRACTION3595
2.603-2.6320.206493X-RAY DIFFRACTION3594
2.632-2.6620.202486X-RAY DIFFRACTION3593
2.662-2.6930.197476X-RAY DIFFRACTION3597
2.693-2.7260.202505X-RAY DIFFRACTION3595
2.726-2.7610.211481X-RAY DIFFRACTION3594
2.761-2.7970.195497X-RAY DIFFRACTION3594
2.797-2.8350.216485X-RAY DIFFRACTION3595
2.835-2.8760.219495X-RAY DIFFRACTION3595
2.876-2.9190.219479X-RAY DIFFRACTION3594
2.919-2.9640.198507X-RAY DIFFRACTION3594
2.964-3.0130.191487X-RAY DIFFRACTION3595
3.013-3.0650.203498X-RAY DIFFRACTION3594
3.065-3.120.209486X-RAY DIFFRACTION3595
3.12-3.180.192492X-RAY DIFFRACTION3595
3.18-3.2450.194519X-RAY DIFFRACTION3597
3.245-3.3160.177476X-RAY DIFFRACTION3593
3.316-3.3930.185519X-RAY DIFFRACTION3596
3.393-3.4770.171498X-RAY DIFFRACTION3596
3.477-3.5720.158497X-RAY DIFFRACTION3594
3.572-3.6770.169481X-RAY DIFFRACTION3594
3.677-3.7950.157510X-RAY DIFFRACTION3596
3.795-3.9310.152502X-RAY DIFFRACTION3595
3.931-4.0880.162511X-RAY DIFFRACTION3596
4.088-4.2730.147506X-RAY DIFFRACTION3595
4.273-4.4980.148516X-RAY DIFFRACTION3595
4.498-4.7790.147512X-RAY DIFFRACTION3595
4.779-5.1470.167530X-RAY DIFFRACTION3596
5.147-5.6630.168521X-RAY DIFFRACTION3596
5.663-6.4790.201542X-RAY DIFFRACTION3596
6.479-8.1460.223538X-RAY DIFFRACTION3595
8.146-35.370.235598X-RAY DIFFRACTION3595

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