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- PDB-7h6b: THE 2.17 A CRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH met... -

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Basic information

Entry
Database: PDB / ID: 7h6b
TitleTHE 2.17 A CRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH methyl 4-[(5-fluoro-3-methyl-1-benzothiophen-2-yl)sulfonylamino]-3-methylsulfonylbenzoate (TOA EIYO INHIBITOR)
ComponentsChymase
KeywordsHYDROLASE / HUMAN CHYMASE / SERINE PROTEINASE
Function / homology
Function and homology information


chymase / basement membrane disassembly / cytokine precursor processing / peptide metabolic process / midbrain development / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / serine-type peptidase activity ...chymase / basement membrane disassembly / cytokine precursor processing / peptide metabolic process / midbrain development / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / serine-type peptidase activity / protein maturation / peptide binding / secretory granule / protein catabolic process / cellular response to glucose stimulus / Signaling by SCF-KIT / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / regulation of inflammatory response / : / endopeptidase activity / serine-type endopeptidase activity / extracellular space / extracellular region / cytosol
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsBanner, D.W. / Benz, J.M. / Schlatter, D. / Hilpert, H.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Not funded Switzerland
CitationJournal: To be published
Title: Crystal structures of human Chymase and Cathepsin G
Authors: Markus, R. / Tosstorff, A.
History
DepositionApr 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chymase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5082
Polymers25,0511
Non-polymers4581
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.580, 53.520, 65.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chymase / Alpha-chymase / Mast cell protease I


Mass: 25050.904 Da / Num. of mol.: 1 / Mutation: C28S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CMA1, CYH, CYM / Production host: Escherichia coli (E. coli) / References: UniProt: P23946, chymase
#2: Chemical ChemComp-A1AO9 / methyl 4-(5-fluoro-3-methyl-1-benzothiophene-2-sulfonamido)-3-(methanesulfonyl)benzoate


Mass: 457.516 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16FNO6S3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
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: 1.66 Å3/Da / Density % sol: 25.96 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: Sample of human Chymase in 50 mM MES/NaOH pH 5.5, 150mM NaCl, 1mM TCEP, 10% Glycerol) at a concentration of 11mg/ml to 14mg/ml.Add [2-[(4-methylpyridin-2-yl)amino]-2-oxoethyl] 2- ...Details: Sample of human Chymase in 50 mM MES/NaOH pH 5.5, 150mM NaCl, 1mM TCEP, 10% Glycerol) at a concentration of 11mg/ml to 14mg/ml.Add [2-[(4-methylpyridin-2-yl)amino]-2-oxoethyl] 2-methylquinoline-4-carboxylate at 10x molar ratio. The compound helps to obtain crystals but is not visible in the structures. Add 0.5 mM ZnCl2. Add inhibitor, incubate for 16h on ice. Crystallize using microbatch setups with Al's oil (Hampton Research), with total drop size 1ul with 50% protein sample, using crystallization reagent of 0.1M Tris/HCl pH 8.5, 0.2M NaCl, 25% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.18→18.96 Å / Num. obs: 8882 / % possible obs: 96.3 % / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.088 / Net I/σ(I): 13.69 / Num. measured all: 36488
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Rmerge(I) obsNum. measured obsNum. unique obsRrim(I) allNet I/σ(I) obs
2.18-2.3182.60.404439511610.4653.6
2.31-2.4799.60.336593613430.3794.98
2.47-2.6699.80.241529512040.2726.63
2.66-2.9199.30.166503611500.1878.91
2.91-3.2499.60.089446410290.10114.46
3.24-3.7299.60.05140199320.05722.49
3.72-4.5199.30.04433697970.0526.23
4.51-6.299.10.03626636480.04230.21
6.2-18.9687.40.02813113890.03333.57

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→18.96 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 27.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2389 423 4.76 %
Rwork0.2 --
obs0.2019 8880 98.25 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.17→18.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 29 65 1815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021796
X-RAY DIFFRACTIONf_angle_d0.5132436
X-RAY DIFFRACTIONf_dihedral_angle_d13.898675
X-RAY DIFFRACTIONf_chiral_restr0.044261
X-RAY DIFFRACTIONf_plane_restr0.004311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.480.29731380.23692666X-RAY DIFFRACTION95
2.48-3.130.25161450.22232834X-RAY DIFFRACTION100
3.13-18.960.21381400.17812957X-RAY DIFFRACTION100
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)
11.60691.23880.30653.11610.58080.1646-0.03250.3626-0.1783-0.21490.2992-0.6234-0.05140.0937-0.01630.2347-0.01690.01610.2044-0.03270.185733.8902-2.517524.9256
22.41670.74490.32750.41380.40050.5341-0.07980.39320.2366-0.1057-0.21280.0977-0.1252-0.0724-0.32210.30480.04580.01980.1452-0.04470.108517.2349-1.186823.2697
31.7037-0.3851-0.43451.2680.46760.9305-0.08310.11460.01140.02090.02750.15480.2203-0.2380.04640.2125-0.01510.00730.125-0.01230.122315.9417-3.617425.2769
40.7885-0.1245-0.48180.4393-0.04990.3323-0.0658-0.2345-0.15650.2103-0.0262-0.1220.20170.1385-0.09470.30090.0093-0.03920.15160.03460.172625.424-4.310629.7912
51.6012-0.9194-0.63891.0535-0.43111.4684-0.0065-0.5264-0.27930.21220.08580.08240.04850.1656-0.00150.3133-0.0194-0.05630.3631-0.02150.210725.16287.884642.7239
61.67920.3603-0.12192.27070.01771.7058-0.0291-0.3929-0.04750.1001-0.1146-0.194-0.09540.3050.01910.21130.01480.00830.16720.0170.135723.69612.217937.1409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 103 )
4X-RAY DIFFRACTION4chain 'A' and (resid 104 through 155 )
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 179 )
6X-RAY DIFFRACTION6chain 'A' and (resid 180 through 242 )

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