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- PDB-1klt: CRYSTAL STRUCTURE OF PMSF-TREATED HUMAN CHYMASE AT 1.9 ANGSTROMS ... -

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Basic information

Entry
Database: PDB / ID: 1klt
TitleCRYSTAL STRUCTURE OF PMSF-TREATED HUMAN CHYMASE AT 1.9 ANGSTROMS RESOLUTION
ComponentsCHYMASE
KeywordsSERINE PROTEASE / HYDROLASE / MAST CELL / ANGIOTENSIN / ALPHA TOLUENESULFONIC ACID
Function / homology
Function and homology information


chymase / basement membrane disassembly / cytokine precursor processing / midbrain development / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / serine-type peptidase activity / secretory granule ...chymase / basement membrane disassembly / cytokine precursor processing / midbrain development / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / serine-type peptidase activity / secretory granule / cellular response to glucose stimulus / peptide binding / protein catabolic process / Signaling by SCF-KIT / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / regulation of inflammatory response / collagen-containing extracellular matrix / endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / extracellular space / extracellular region / cytoplasm / cytosol
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
phenylmethanesulfonic acid / Chymase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMcgrath, M.E.
Citation
Journal: Biochemistry / Year: 1997
Title: Crystal structure of phenylmethanesulfonyl fluoride-treated human chymase at 1.9 A.
Authors: McGrath, M.E. / Mirzadegan, T. / Schmidt, B.F.
#1: Journal: FEBS Lett. / Year: 1997
Title: Production of Crystallizable Human Chymase from a Bacillus Subtilis System
Authors: Mcgrath, M.E. / Osawa, A.E. / Barnes, M.G. / Clark, J.M. / Mortara, K.D. / Schmidt, B.F.
History
DepositionOct 16, 1997Processing site: BNL
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / software / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHYMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2232
Polymers25,0511
Non-polymers1721
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.930, 58.160, 86.090
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


Mass: 25050.904 Da / Num. of mol.: 1 / Mutation: C22S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Bacillus subtilis (bacteria) / Strain (production host): WB751 / Variant (production host): PROTEASE DEFICIENT / References: UniProt: P23946, chymase
#2: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growpH: 5.6
Details: COMPLEX WAS CRYSTALLIZED FROM 20% PEG 2000, 20% ISOPROPANOL, 0.1M SODIUM CITRATE, PH 5.6.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
220 %PEG40001reservoir
320 %2-propanol1reservoir
40.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→39.1 Å / Num. obs: 14518 / % possible obs: 80.4 % / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 11
Reflection shellResolution: 1.9→2.1 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.344 / % possible all: 50.4
Reflection
*PLUS
Num. measured all: 31632
Reflection shell
*PLUS
% possible obs: 50.4 %

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Processing

Software
NameVersionClassification
bioteX(MSC)data collection
bioteX(MSC)data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
bioteXdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL

Resolution: 1.9→6 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1186 9.97 %RANDOM
Rwork0.183 ---
obs0.183 11899 80.4 %-
Displacement parametersBiso mean: 19.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 10 219 2366
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.27
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.84
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.98 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.284 45 9.6 %
Rwork0.321 426 -
obs--50.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.84
LS refinement shell
*PLUS
Rfactor obs: 0.321

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