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- PDB-1nn6: Human Pro-Chymase -

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Basic information

Entry
Database: PDB / ID: 1nn6
TitleHuman Pro-Chymase
ComponentsChymase
KeywordsHYDROLASE / Serine Protease / Zymogen / Chymase / Conformational change
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 / Trypsin-like serine proteases ...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 / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsReiling, K.K. / Krucinski, J. / Miercke, L.J.W. / Raymond, W.W. / Caughey, G.H. / Stroud, R.M.
Citation
Journal: Biochemistry / Year: 2003
Title: Structure of human pro-chymase: a model for the activating transition of granule-associated proteases.
Authors: Reiling, K.K. / Krucinski, J. / Miercke, L.J. / Raymond, W.W. / Caughey, G.H. / Stroud, R.M.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: The 2.2 A Crystal Structure of Human Chymase in Complex with Succinyl-Ala-Ala-Pro-Phe-chloromethylketone: Structural Explanation for its Dipeptidyl Carboxypeptidase Specificity
Authors: Pereira, P.J. / Wang, Z.M. / Rubin, H. / Huber, R. / Bode, W. / Schechter, N.M. / Strobl, S.
#3: Journal: Biochemistry / Year: 1977
Title: Structure of bovine trypsinogen at 1.9 A resolution.
Authors: Kossiakoff, A.A. / Chambers, J.L. / Kay, L.M. / Stroud, R.M.
#4: Journal: J.Biol.Chem. / Year: 1991
Title: Structure, chromosomal assignment, and deduced amino acid sequence of a human gene for mast cell chymase.
Authors: Caughey, G.H. / Zerweck, E.H. / Vanderslice, P.
History
DepositionJan 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)25,8993
Polymers25,2531
Non-polymers6462
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.688, 55.639, 88.686
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 / Mast cell protease I


Mass: 25253.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Human mast cell chymase gene / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): High Five (Trichoplusia ni) cells / References: UniProt: P23946, chymase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.35 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% Peg 4k, 150mM Na Formate, and 100 mM Tris , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1500 mM1dropNaCl
22 mMBis-Tris1droppH6.1
35.0 mg/mlprotein1drop
420 %PEG40001reservoir
5150 mMsodium formate1reservoir
6100 mMTris1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 30, 1999
RadiationMonochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.75→28.7 Å / Num. all: 225846 / Num. obs: 222007 / % possible obs: 98.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.8
Reflection shellResolution: 1.75→1.77 Å / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 1.7 / Num. unique all: 826 / % possible all: 97.5
Reflection
*PLUS
Num. obs: 27938 / Num. measured all: 222007
Reflection shell
*PLUS
% possible obs: 97.5 % / Rmerge(I) obs: 0.69

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KLT

1klt


Resolution: 1.75→47 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24524 1235 4.8 %RANDOM within shells
Rwork0.20304 ---
all0.20499 25836 --
obs0.20499 24317 98.39 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.285 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1691 0 42 153 1886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211791
X-RAY DIFFRACTIONr_bond_other_d0.0010.021605
X-RAY DIFFRACTIONr_angle_refined_deg1.8031.972433
X-RAY DIFFRACTIONr_angle_other_deg1.21833722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0183220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.04415307
X-RAY DIFFRACTIONr_chiral_restr0.1460.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021956
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02361
X-RAY DIFFRACTIONr_nbd_refined0.2460.3328
X-RAY DIFFRACTIONr_nbd_other0.2110.31483
X-RAY DIFFRACTIONr_nbtor_other0.6210.53
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.5173
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3770.312
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.324
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4560.511
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0231.51104
X-RAY DIFFRACTIONr_mcangle_it1.77621779
X-RAY DIFFRACTIONr_scbond_it2.6093687
X-RAY DIFFRACTIONr_scangle_it4.1444.5654
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.388 87
Rwork0.259 1767
Refinement
*PLUS
Lowest resolution: 28.7 Å / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.8

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