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- PDB-1kdq: Crystal Structure Analysis of the Mutant S189D Rat Chymotrypsin -

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Basic information

Entry
Database: PDB / ID: 1kdq
TitleCrystal Structure Analysis of the Mutant S189D Rat Chymotrypsin
Components
  • CHYMOTRYPSIN B, B CHAIN
  • CHYMOTRYPSIN B, C CHAIN
KeywordsHYDROLASE / BETA BARREL
Function / homology
Function and homology information


Activation of Matrix Metalloproteinases / chymotrypsin / response to food / digestion / serine-type peptidase activity / response to nutrient / response to cytokine / protein catabolic process / response to peptide hormone / response to toxic substance ...Activation of Matrix Metalloproteinases / chymotrypsin / response to food / digestion / serine-type peptidase activity / response to nutrient / response to cytokine / protein catabolic process / response to peptide hormone / response to toxic substance / peptidase activity / positive regulation of apoptotic process / serine-type endopeptidase activity / proteolysis / extracellular region
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 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.55 Å
AuthorsSzabo, E. / Bocskei, Z. / Naray-Szabo, G. / Graf, L. / Venekei, I.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Three Dimensional Structures of S189D Chymotrypsin and D189S Trypsin Mutants: The Effect of Polarity at Site 189 on a Protease-specific Stabilization of the Substrate-binding Site
Authors: Szabo, E. / Venekei, I. / Bocskei, Z. / Naray-Szabo, G. / Graf, L.
History
DepositionNov 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHYMOTRYPSIN B, B CHAIN
B: CHYMOTRYPSIN B, C CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4993
Polymers24,4592
Non-polymers401
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-51 kcal/mol
Surface area10200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.589, 76.707, 83.478
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CHYMOTRYPSIN B, B CHAIN


Mass: 14190.851 Da / Num. of mol.: 1 / Mutation: C122S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pMP51 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): GRF182 / References: UniProt: P07338, chymotrypsin
#2: Protein CHYMOTRYPSIN B, C CHAIN


Mass: 10267.728 Da / Num. of mol.: 1 / Mutation: S189D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pMP51 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): GRF182 / References: UniProt: P07338, chymotrypsin
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.44 Å3/Da / Density % sol: 36.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG MME 2000, calcium chloride, ammonium sulphate, Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11 mM1dropHCl
210 mM1dropCaCl2
313 mg/mlprotein1drop
40.1 MHEPES1reservoirpH7.0
534 %(w/v)PEG2000MME1reservoir
60.1 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 31, 1998 / Details: NORMAL FOCUS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→32.903 Å / Num. all: 7974 / Num. obs: 7974 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 47.996 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 5.1
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.4 / % possible all: 97.3
Reflection
*PLUS
Highest resolution: 2.55 Å / Lowest resolution: 32.969 Å / Num. measured all: 34261

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
X-PLOR3.851refinement
CCP4(SCALA)data scaling
RefinementResolution: 2.55→32.969 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used torsion angle SA procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 367 4.6 %RANDOM
Rwork0.221 ---
all0.221 7965 --
obs0.221 7965 98.6 %-
Displacement parametersBiso mean: 35.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4331 Å0.3136 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4855 Å0.277 Å
Refinement stepCycle: LAST / Resolution: 2.55→32.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 1 16 1680
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.206
X-RAY DIFFRACTIONx_bond_d0.023
X-RAY DIFFRACTIONx_dihedral_angle_d29.984
X-RAY DIFFRACTIONx_improper_angle_d0.678
LS refinement shellResolution: 2.55→2.67 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3899 56 5.9 %
Rwork0.2567 902 -
obs--97.06 %
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.2749 / Rfactor Rwork: 0.2168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.152
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.984
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.678

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