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- PDB-7h60: THE 1.875 A CRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH 3-... -

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Basic information

Entry
Database: PDB / ID: 7h60
TitleTHE 1.875 A CRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH 3-[[ethoxycarbonyl(methyl)amino]methyl]-5-fluoro-1-(naphthalen-1-ylmethyl)indole-2-carboxylic acid - ZN CRYSTAL FORM
ComponentsChymase
KeywordsHYDROLASE / HUMAN CHYMASE / SERINE PROTEINASE / HYDROLASE (SERINE PROTEASE)
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: 1.88 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)25,5333
Polymers25,0331
Non-polymers5002
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.960, 74.960, 49.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 25032.910 Da / Num. of mol.: 1 / Mutation: C28S, F135K
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1AOT / 3-{[(ethoxycarbonyl)(methyl)amino]methyl}-5-fluoro-1-[(naphthalen-1-yl)methyl]-1H-indole-2-carboxylic acid


Mass: 434.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H23FN2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.75 Å3/Da / Density % sol: 55.33 %
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 23, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→19.15 Å / Num. obs: 22233 / % possible obs: 97.9 % / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.083 / Net I/σ(I): 13.98 / Num. measured all: 72983
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Rmerge(I) obsNum. measured obsNum. unique obsRrim(I) allNet I/σ(I) obs
1.87-1.9992.20.2741104935280.3314.33
1.99-2.121000.2521042732380.3024.75
2.12-2.2999.80.1941033231820.2326.17
2.29-2.5199.80.124971029640.1479.3
2.51-2.7999.60.085846325560.10113.1
2.79-3.2299.40.054796123680.06419.46
3.22-3.9198.60.035660219410.04228.79
3.91-5.4297.40.025527815340.0338.44
5.42-19.1593.50.02331619220.02741.79

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→19.15 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.924 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22616 1137 5.1 %RANDOM
Rwork0.18571 ---
obs0.18777 21095 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.375 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.88→19.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1759 0 33 245 2037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121915
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161817
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.8252606
X-RAY DIFFRACTIONr_angle_other_deg0.5551.7844193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3885241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.495515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.90310322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022295
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02458
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6491.335943
X-RAY DIFFRACTIONr_mcbond_other0.6491.335943
X-RAY DIFFRACTIONr_mcangle_it1.1342.4021191
X-RAY DIFFRACTIONr_mcangle_other1.1342.4041192
X-RAY DIFFRACTIONr_scbond_it0.671.44972
X-RAY DIFFRACTIONr_scbond_other0.671.44973
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1652.6231416
X-RAY DIFFRACTIONr_long_range_B_refined4.51416.042045
X-RAY DIFFRACTIONr_long_range_B_other4.20714.281993
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.875→1.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 77 -
Rwork0.4 1455 -
obs--93.02 %
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)
10.11310.12970.05830.55-0.24411.2179-0.06860.01630.0015-0.03790.02560.0438-0.0399-0.07090.04290.0465-0.0088-0.00240.0272-0.00680.0544-32.321112.7567-2.8485
20.74230.0081-0.20730.66620.68170.82020.007-0.02760.02860.04870.0015-0.04780.05550.0528-0.00860.02930.00060.00780.04150.02130.061-26.2236.07324.0438
30.8630.56360.55030.87350.23480.82460.0291-0.0575-0.03170.0854-0.0517-0.00320.0652-0.05130.02260.020800.00930.0277-0.0050.0301-28.92567.44465.0053
40.90720.8613-0.18191.90790.71731.51710.0039-0.0013-0.1390.00030.0167-0.07360.09550.14-0.02070.02130.01940.00270.0221-0.00880.0684-26.7141-1.1206-1.3716
50.2273-0.0042-0.21071.21470.74290.6509-0.12690.0286-0.0855-0.22210.1721-0.1719-0.0210.0739-0.04520.1086-0.04940.07480.0377-0.01850.0962-12.485714.228-8.198
62.02571.10630.08471.55660.42270.4882-0.05160.00790.1215-0.2097-0.00250.1111-0.0742-0.00530.05410.03610.0004-0.01380.00330.00960.0424-26.213222.8569-5.4353
71.24510.34330.37761.5170.16970.4077-0.06730.0166-0.0141-0.09630.0545-0.069-0.03340.02070.01290.021-0.01690.00480.0178-0.00610.0391-17.512725.06-0.4228
80.73570.1352-0.09921.6350.53060.8705-0.01380.016-0.0077-0.01420.0298-0.02230.0375-0.0378-0.01610.024-0.0023-0.00070.0193-0.00980.0409-20.065119.7341-2.4293
90.62070.00860.28613.746-0.34570.4992-0.04240.0449-0.13560.11550.0883-0.1076-0.06930.1655-0.04590.022-0.0088-0.0090.0834-0.01760.0911-13.84756.65674.0523
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 39
2X-RAY DIFFRACTION2A40 - 61
3X-RAY DIFFRACTION3A63 - 103
4X-RAY DIFFRACTION4A104 - 123
5X-RAY DIFFRACTION5A124 - 140
6X-RAY DIFFRACTION6A141 - 168
7X-RAY DIFFRACTION7A169 - 196
8X-RAY DIFFRACTION8A197 - 225
9X-RAY DIFFRACTION9A226 - 245

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