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- PDB-4ecc: Chimeric GST Containing Inserts of Kininogen Peptides -

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Basic information

Entry
Database: PDB / ID: 4ecc
TitleChimeric GST Containing Inserts of Kininogen Peptides
Componentschimeric protein between GSHKT10 and domain 5 of kininogen-1Chimera
KeywordsTRANSFERASE / PROTEIN BINDING / GST / domain 5 of human high molecular weight kininogen / Biosynthetic Protein
Function / homology
Function and homology information


negative regulation of blood coagulation / negative regulation of cell adhesion / cysteine-type endopeptidase inhibitor activity / glutathione transferase / glutathione transferase activity / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / platelet alpha granule lumen / Post-translational protein phosphorylation / negative regulation of proteolysis ...negative regulation of blood coagulation / negative regulation of cell adhesion / cysteine-type endopeptidase inhibitor activity / glutathione transferase / glutathione transferase activity / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / platelet alpha granule lumen / Post-translational protein phosphorylation / negative regulation of proteolysis / hormone activity / vasodilation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / heparin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / inflammatory response / positive regulation of apoptotic process / endoplasmic reticulum lumen / signaling receptor binding / extracellular space / extracellular exosome / zinc ion binding / extracellular region / plasma membrane
Similarity search - Function
HMW kininogen / Kininogen-type cystatin domain / Kininogen-type cystatin domain profile. / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Cystatin superfamily / Glutathione S-transferase, C-terminal domain ...HMW kininogen / Kininogen-type cystatin domain / Kininogen-type cystatin domain profile. / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Cystatin superfamily / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Kininogen-1 / Glutathione S-transferase class-mu 26 kDa isozyme
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAmber, A.B. / Sergei, M.M. / Yi, P. / Rita, R. / Xiaoping, Q. / Marianne, P.-C. / William, C.M. / Vivien, Y. / Keith, R.M. / Anton, A.K.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Chimeric glutathione S-transferases containing inserts of kininogen peptides: potential novel protein therapeutics.
Authors: Bentley, A.A. / Merkulov, S.M. / Peng, Y. / Rozmarynowycz, R. / Qi, X. / Pusztai-Carey, M. / Merrick, W.C. / Yee, V.C. / McCrae, K.R. / Komar, A.A.
History
DepositionMar 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chimeric protein between GSHKT10 and domain 5 of kininogen-1


Theoretical massNumber of molelcules
Total (without water)26,9461
Polymers26,9461
Non-polymers00
Water1,27971
1
A: chimeric protein between GSHKT10 and domain 5 of kininogen-1

A: chimeric protein between GSHKT10 and domain 5 of kininogen-1


Theoretical massNumber of molelcules
Total (without water)53,8932
Polymers53,8932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area2640 Å2
ΔGint-21 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.520, 92.520, 58.087
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-371-

HOH

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Components

#1: Protein chimeric protein between GSHKT10 and domain 5 of kininogen-1 / Chimera / Glutathione S-transferase class-mu 26 kDa isozyme / GST 26 / Sj26 antigen / SjGST/Alpha-2-thiol ...Glutathione S-transferase class-mu 26 kDa isozyme / GST 26 / Sj26 antigen / SjGST/Alpha-2-thiol proteinase inhibitor / Fitzgerald factor / High molecular weight / kininogen / domain 5 of human high molecular weight kininogen


Mass: 26946.346 Da / Num. of mol.: 1 / Fragment: unp residues 1-49, kinonogen 498-510, 50-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata), (gene. exp.) homo sapiens (human)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P08515, UniProt: P01042, glutathione transferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTALLIZED SEQUENCE REPRESENTS A CHIMERIC CONSTRUCT. GLUTATHIONE S-TRANSFERASE CONTAINS A ...THE CRYSTALLIZED SEQUENCE REPRESENTS A CHIMERIC CONSTRUCT. GLUTATHIONE S-TRANSFERASE CONTAINS A LINKER CORRESPONDING TO DOMAIN OF A HUMAN KININOGEN-1

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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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: (1)0.2 M Ammonium Sulfate, 0.1 M Hepes, 25% PEG 3350 (2)0.2 M Lithium Sulfate, 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2008
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 12806 / Num. obs: 12806 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.2-2.28197.8
2.28-2.37197.8
2.37-2.48197.7
2.48-2.61197
2.61-2.77196.5
2.77-2.99197.4
2.99-3.29195.9
3.29-3.76195.6
3.76-4.74194
4.74-50191

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1M99

1m99


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.113 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26892 626 4.9 %RANDOM
Rwork0.21998 ---
all0.22231 12784 --
obs0.22231 12158 96.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.887 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2---0.41 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1682 0 0 71 1753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221727
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9882333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4375204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72724.05179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95715312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.447158
X-RAY DIFFRACTIONr_chiral_restr0.0950.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211302
X-RAY DIFFRACTIONr_mcbond_it0.971.51027
X-RAY DIFFRACTIONr_mcangle_it1.8221656
X-RAY DIFFRACTIONr_scbond_it2.583700
X-RAY DIFFRACTIONr_scangle_it4.1354.5677
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 53 -
Rwork0.244 884 -
obs--97.3 %

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