[English] 日本語
Yorodumi
- PDB-7h68: THE 1.25 A CRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH (2R... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7h68
TitleTHE 1.25 A CRYSTAL STRUCTURE OF HUMAN CHYMASE IN COMPLEX WITH (2R)-2-benzyl-4-[(R)-(5-fluoro-3-methyl-1H-indol-2-yl)-phenylmethyl]-3-hydroxy-2H-furan-5-one
ComponentsChymase
KeywordsHYDROLASE / HUMAN CHYMASE / SERINE PROTEINASE
Function / homology
Function and homology information


chymase / basement membrane disassembly / cytokine precursor processing / peptide metabolic process / Activation of Matrix Metalloproteinases / midbrain development / extracellular matrix disassembly / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / serine-type peptidase activity ...chymase / basement membrane disassembly / cytokine precursor processing / peptide metabolic process / Activation of Matrix Metalloproteinases / midbrain development / extracellular matrix disassembly / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / serine-type peptidase activity / peptide binding / secretory granule / protein maturation / cellular response to glucose stimulus / protein catabolic process / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsBanner, D.W. / Benz, J.M. / Joseph, C. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chymase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8168
Polymers25,0331
Non-polymers7837
Water5,693316
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.600, 73.600, 48.484
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 25032.910 Da / Num. of mol.: 1 / Mutation: YES
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

-
Non-polymers , 5 types, 323 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-A1AO4 / (5R)-5-benzyl-3-[(R)-(5-fluoro-3-methyl-1H-indol-2-yl)(phenyl)methyl]-4-hydroxyfuran-2(5H)-one


Mass: 427.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H22FNO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.21 %
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.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.22→32.91 Å / Num. obs: 67565 / % possible obs: 86.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rrim(I) all: 0.036 / Net I/σ(I): 19.65 / Num. measured all: 213822
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Rmerge(I) obsNum. measured obsNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs
1.22-1.2532.50.457243418720.6120.6111.38
1.25-1.2853.90.34447130170.7490.4571.83
1.28-1.3266.20.291628536070.8140.3852.4
1.32-1.3676.40.242832540410.8790.3113.3
1.36-1.489.70.1991094245780.9220.2494.36
1.4-1.4598.40.1691481548940.950.2046.09
1.45-1.5199.50.1381734947920.9750.1628.58
1.51-1.5799.20.1091674945790.9850.12711.03
1.57-1.6499.60.0841613843970.9920.09814.17
1.64-1.7299.80.0681551542240.9940.0817.26
1.72-1.8199.70.0541473340020.9960.06321.64
1.81-1.9299.80.0431408538270.9970.0526.43
1.92-2.0599.80.0341322635930.9980.03932.64
2.05-2.2299.80.0291224233260.9990.03436.83
2.22-2.4399.60.0261131030680.9990.03140.84
2.43-2.7299.60.0251023427910.9990.02943.58
2.72-3.1499.40.023903124620.9990.02747.66
3.14-3.8499.30.019758720850.9990.02351.11
3.84-5.4497.40.017562915870.9990.0251.81
5.44-32.9188.30.0227228230.9990.02449.47

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→32.91 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.079 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1481 3309 5.2 %RANDOM
Rwork0.12483 ---
obs0.12605 60896 89.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.312 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0 Å2
2---0.05 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.25→32.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 48 316 2119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191910
X-RAY DIFFRACTIONr_bond_other_d0.0010.021830
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9862605
X-RAY DIFFRACTIONr_angle_other_deg0.7743.0034219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1355245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63322.78579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.53215322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3041515
X-RAY DIFFRACTIONr_chiral_restr0.0930.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212149
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02440
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.38133740
X-RAY DIFFRACTIONr_sphericity_free21.605576
X-RAY DIFFRACTIONr_sphericity_bonded5.353932
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 136 -
Rwork0.236 2412 -
obs--48.39 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more