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- PDB-5r43: Crystal Structure of deuterated gamma-Chymotrypsin at pH 7.5, cry... -

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Basic information

Entry
Database: PDB / ID: 5r43
TitleCrystal Structure of deuterated gamma-Chymotrypsin at pH 7.5, cryo temperature
Components
  • (Chymotrypsinogen ...) x 3
  • peptide SWPW
  • peptide TPGVY
KeywordsHYDROLASE / serine protease / hydrolase-peptide complex
Function / homology
Function and homology information


chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase activity / proteolysis / extracellular region
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
IODIDE ION / MALONIC ACID / Chymotrypsinogen A
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1 Å
AuthorsKreinbring, C.A. / Wilson, M.A. / Kovalevsky, A.Y. / Blakeley, M.P. / Fisher, S.Z. / Lazar, L.M. / Moulin, A.G. / Novak, W.R. / Petsko, G.A. / Ringe, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM32415 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM26788 United States
CitationJournal: To be published
Title: Effect of Temperature and pH on Ionizable Residues in gamma-Chymotrypsin: a X-ray and Neutron Crystallography Study
Authors: Kreinbring, C.A. / Wilson, M.A. / Kovalevsky, A.Y. / Blakeley, M.P. / Fisher, S.Z. / Lazar, L.M. / Moulin, A.G. / Novak, W.R. / Petsko, G.A. / Ringe, D.
History
DepositionFeb 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Chymotrypsinogen A
B: Chymotrypsinogen A
C: Chymotrypsinogen A
D: peptide SWPW
E: peptide TPGVY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6047
Polymers26,3735
Non-polymers2312
Water6,918384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.859, 68.859, 96.489
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-201-

IOD

21B-440-

HOH

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Components

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Chymotrypsinogen ... , 3 types, 3 molecules ABC

#1: Protein/peptide Chymotrypsinogen A


Mass: 1253.511 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#2: Protein Chymotrypsinogen A


Mass: 13934.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#3: Protein Chymotrypsinogen A


Mass: 10074.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin

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Protein/peptide , 2 types, 2 molecules DE

#4: Protein/peptide peptide SWPW


Mass: 574.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
#5: Protein/peptide peptide TPGVY


Mass: 535.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)

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Non-polymers , 3 types, 386 molecules

#6: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#7: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 45% saturated ammonium sulfate, 0.75% saturated cetyltrimethylammonium bromide, 100 mM sodium iodide; sodium malonate
PH range: 10 mM sodium cacodylate pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 118425 / % possible obs: 94.5 % / Redundancy: 16.1 % / Rmerge(I) obs: 0.07 / Χ2: 1.421 / Net I/σ(I): 18.8 / Num. measured all: 1906448
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1-1.042.50.46573531.008159.5
1.04-1.084.50.314106960.993186.4
1.08-1.136.70.223121590.99198.6
1.13-1.1911.90.216124410.9991100
1.19-1.2619.30.283124292.0541100
1.26-1.3622.20.235124542.4211100
1.36-1.4922.50.158124841.5231100
1.49-1.7122.70.095125770.9931100
1.71-2.1522.80.07126900.9971100
2.15-5018.10.047131421.002199.8

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1GCT

1gct


Resolution: 1→56.05 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.482 / SU ML: 0.011 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.019 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1319 5925 5 %RANDOM
Rwork0.1147 ---
obs0.1155 111803 94.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.85 Å2 / Biso mean: 13.976 Å2 / Biso min: 6.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.22 Å2
Refinement stepCycle: final / Resolution: 1→56.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 8 391 2229
Biso mean--16.11 31.72 -
Num. residues----247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021989
X-RAY DIFFRACTIONr_bond_other_d0.0020.021806
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9422744
X-RAY DIFFRACTIONr_angle_other_deg1.0073.0014229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0845.036279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14225.60666
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.76715308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.604153
X-RAY DIFFRACTIONr_chiral_restr0.0950.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212246
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02377
X-RAY DIFFRACTIONr_rigid_bond_restr1.92833791
X-RAY DIFFRACTIONr_sphericity_free29.645219
X-RAY DIFFRACTIONr_sphericity_bonded9.92953906
LS refinement shellResolution: 1→1.026 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 271 -
Rwork0.311 4760 -
all-5031 -
obs--55.09 %

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