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- PDB-1cq4: CI2 MUTANT WITH TETRAGLUTAMINE (MGQQQQGM) REPLACING MET59 -

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Basic information

Entry
Database: PDB / ID: 1cq4
TitleCI2 MUTANT WITH TETRAGLUTAMINE (MGQQQQGM) REPLACING MET59
Components(PROTEIN (SERINE PROTEINASE INHIBITOR 2)) x 2
KeywordsHYDROLASE INHIBITOR / SERINE PROTEASE INHIBITOR / POLYGLUTAMINE INSERTION MUTANT / SUBTILISIN- CHYMOTRYPSIN INHIBITOR-2 / IMMUNE SYSTEM
Function / homologyProteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / serine-type endopeptidase inhibitor activity / response to wounding / Subtilisin-chymotrypsin inhibitor-2A
Function and homology information
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChen, Y.W. / Stott, K.R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal structure of a dimeric chymotrypsin inhibitor 2 mutant containing an inserted glutamine repeat.
Authors: Chen, Y.W. / Stott, K. / Perutz, M.F.
#1: Journal: J.Mol.Biol. / Year: 1997
Title: Glutamine, Alanine or Glycine Repeats Inserted Into the Loop of a Protein Have Minimal Effects on Stability and Folding Rates
Authors: Ladurner, A.G. / Fersht, A.R.
#2: Journal: Fold.Des. / Year: 1996
Title: Towards the Complete Structural Characterization of a Protein Folding Pathway: The Structures of the Denatured, Transition and Native States for the Association/Folding of Two Complementary ...Title: Towards the Complete Structural Characterization of a Protein Folding Pathway: The Structures of the Denatured, Transition and Native States for the Association/Folding of Two Complementary Fragments of Cleaved Chymotrypsin Inhibitor 2. Direction Evidence for a Nucleation-Condensation Mechanism
Authors: Neira, J.L. / Davis, B. / Ladurner, A.G. / Buckle, A.M. / De Prat Gay, G. / Fersht, A.R.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Incorporation of Glutamine Repeats Makes Protein Oligomerize: Implications for Neurodegenerative Diseases
Authors: Stott, K. / Blackburn, J.M. / Butler, P.J.G. / Perutz, M.
#4: Journal: Biochemistry / Year: 1987
Title: Crystal and Molecular Structure of the Serine Proteinase Inhibitor Ci-2 from Barley Seeds
Authors: Mcphalen, C.A. / James, M.N.G.
#5: Journal: Protein Eng. / Year: 1987
Title: The Determination of the Three-Dimensional Structure of Barley Serine Proteinase Inhibitor 2 by Nuclear Magnetic Resonance, Distance Geometry and Restrained Molecular Dynamics
Authors: Clore, G.M. / Gronenborn, A.M. / Kjaer, M. / Poulsen, F.M.
History
DepositionNov 17, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (SERINE PROTEINASE INHIBITOR 2)
B: PROTEIN (SERINE PROTEINASE INHIBITOR 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1863
Polymers8,0892
Non-polymers961
Water99155
1
A: PROTEIN (SERINE PROTEINASE INHIBITOR 2)
B: PROTEIN (SERINE PROTEINASE INHIBITOR 2)
hetero molecules

A: PROTEIN (SERINE PROTEINASE INHIBITOR 2)
B: PROTEIN (SERINE PROTEINASE INHIBITOR 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3716
Polymers16,1794
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z1
2
A: PROTEIN (SERINE PROTEINASE INHIBITOR 2)
B: PROTEIN (SERINE PROTEINASE INHIBITOR 2)
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)49,11318
Polymers48,53712
Non-polymers5766
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area19290 Å2
ΔGint-226 kcal/mol
Surface area17310 Å2
MethodPISA
3
A: PROTEIN (SERINE PROTEINASE INHIBITOR 2)
B: PROTEIN (SERINE PROTEINASE INHIBITOR 2)
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)98,22636
Polymers97,07324
Non-polymers1,15312
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation9_556-x,-x+y,-z+11
crystal symmetry operation10_556-y,-x,-z+11
crystal symmetry operation11_556-x+y,y,-z+11
crystal symmetry operation12_556x,x-y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)68.267, 68.267, 60.833
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein/peptide PROTEIN (SERINE PROTEINASE INHIBITOR 2) / CHYMOTRYPSIN INHIBITOR 2 / CI2


Mass: 5212.127 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: EXISTS AS A1B2/A2B1 DOMAIN-SWAPPED DIMER / Source: (gene. exp.) Hordeum vulgare (barley) / Strain: HIPROLY / Plasmid: PCI2-Q4I / Production host: Escherichia coli (E. coli) / Variant (production host): NM554 / References: UniProt: P01053
#2: Protein/peptide PROTEIN (SERINE PROTEINASE INHIBITOR 2) / CHYMOTRYPSIN INHIBITOR 2 / CI2


Mass: 2877.325 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: EXISTS AS A1B2/A2B1 DOMAIN-SWAPPED DIMER / Source: (gene. exp.) Hordeum vulgare (barley) / Strain: HIPROLY / Plasmid: PCI2-Q4I / Production host: Escherichia coli (E. coli) / Variant (production host): NM554 / References: UniProt: P01053
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 7.5
Details: DROPS WERE PREPARED BY MIXING 2 MICROLITERS OF PURIFIED DIMER AT 25MG/ML WITH AN EQUAL VOLUME OF BUFFER (30% W/V PEG-400, 1.0 M LITHIUM SULPHATE, AND 1 MM CALCIUM CHLORIDE, IN 0.1 M TRIS-HCL ...Details: DROPS WERE PREPARED BY MIXING 2 MICROLITERS OF PURIFIED DIMER AT 25MG/ML WITH AN EQUAL VOLUME OF BUFFER (30% W/V PEG-400, 1.0 M LITHIUM SULPHATE, AND 1 MM CALCIUM CHLORIDE, IN 0.1 M TRIS-HCL AT PH 7.5), WHICH WAS ALSO USED AS THE WELL BUFFER (1 ML).
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
230 %(w/v)PEG4001reservoir
31.0 Mlithium sulfate1reservoir
41 mMcalcium chloride1reservoir
50.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.912
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 24, 1996 / Details: BENT MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 1.8→22.3 Å / Num. obs: 8153 / % possible obs: 99.7 % / Redundancy: 10.6 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.078 / Net I/σ(I): 3.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.325 / % possible all: 100
Reflection
*PLUS
Num. measured all: 86441 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.286

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CI2

2ci2


Resolution: 1.8→22 Å / SU B: 2.42 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.3 795 10 %RANDOM
Rwork0.24 ---
obs-7358 99.7 %-
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1--6.1 Å2-5.1 Å20 Å2
2---9 Å20 Å2
3---23.9 Å2
Refinement stepCycle: LAST / Resolution: 1.8→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms481 0 5 55 541
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.642
X-RAY DIFFRACTIONp_mcangle_it2.383
X-RAY DIFFRACTIONp_scbond_it2.572
X-RAY DIFFRACTIONp_scangle_it3.863
X-RAY DIFFRACTIONp_plane_restr0.0260.03
X-RAY DIFFRACTIONp_chiral_restr0.150.15
X-RAY DIFFRACTIONp_singtor_nbd0.190.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.090.3
X-RAY DIFFRACTIONp_planar_tor4.77
X-RAY DIFFRACTIONp_staggered_tor16.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor8.820
X-RAY DIFFRACTIONp_special_tor15

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