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- PDB-2ci2: CRYSTAL AND MOLECULAR STRUCTURE OF THE SERINE PROTEINASE INHIBITO... -

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Basic information

Entry
Database: PDB / ID: 2ci2
TitleCRYSTAL AND MOLECULAR STRUCTURE OF THE SERINE PROTEINASE INHIBITOR CI-2 FROM BARLEY SEEDS
ComponentsCHYMOTRYPSIN INHIBITOR 2
KeywordsPROTEINASE INHIBITOR (CHYMOTRYPSIN)
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / response to wounding
Similarity search - Function
Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Subtilisin-chymotrypsin inhibitor-2A
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsMcphalen, C.A. / James, M.N.G.
Citation
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.
#1: Journal: Protein Eng. / Year: 1987
Title: Comparison of the Solution and X-Ray Structures of Barley Serine Proteinase Inhibitor 2
Authors: Clore, G.M. / Gronenborn, A.M. / James, M.N.G. / Kjaer, M. / Mcphalen, C.A. / Poulsen, F.M.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1985
Title: Crystal and Molecular Structure of Chymotrypsin Inhibitor 2 from Barley Seeds in Complex with Subtilisin Novo
Authors: Mcphalen, C.A. / Svendsen, I. / Jonassen, I. / James, M.N.G.
#3: Journal: J.Mol.Biol. / Year: 1983
Title: Preliminary Crystallographic Data for the Serine Protease Inhibitor Ci-2 from Barley Seeds
Authors: Mcphalen, C.A. / Evans, C. / Hayakawa, K. / Jonassen, I. / Svendsen, I. / James, M.N.G.
History
DepositionSep 5, 1988Processing site: BNL
SupersessionSep 7, 1988ID: 1CI2
Revision 1.0Sep 7, 1988Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 700SHEET THE SHEET SPECIFIED BELOW IS AN IRREGULAR SHEET. ALL BUT ONE HYDROGEN BOND BETWEEN STRANDS 2 ...SHEET THE SHEET SPECIFIED BELOW IS AN IRREGULAR SHEET. ALL BUT ONE HYDROGEN BOND BETWEEN STRANDS 2 AND 3 ARE PROVIDED BY BRIDGING WATER MOLECULES. SEE THE REFERENCE CITED ON THE *JRNL* RECORDS ABOVE FOR DETAILS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: CHYMOTRYPSIN INHIBITOR 2


Theoretical massNumber of molelcules
Total (without water)9,2651
Polymers9,2651
Non-polymers00
Water1,15364
1
I: CHYMOTRYPSIN INHIBITOR 2
x 6


Theoretical massNumber of molelcules
Total (without water)55,5886
Polymers55,5886
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation4_555-x,-y,z1
Unit cell
Length a, b, c (Å)69.015, 69.015, 52.890
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 CHYMOTRYPSIN INHIBITOR 2


Mass: 9264.659 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / References: UniProt: P01053
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ORDER OF THE FIRST FOUR RESIDUES PRESENTED ON THE *SEQRES* RECORDS BELOW IS UNKNOWN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.29 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 %(w/v)1reservoir(NH4)2SO4
250 mMTris-HCl1reservoir

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Data collection

Reflection
*PLUS
Reflection shell
*PLUS

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→8 Å / Rfactor obs: 0.198 / σ(I): 0
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms521 0 0 64 585
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.008
X-RAY DIFFRACTIONp_angle_d0.0290.016
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0210.016
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.9562
X-RAY DIFFRACTIONp_mcangle_it2.9092
X-RAY DIFFRACTIONp_scbond_it3.6113
X-RAY DIFFRACTIONp_scangle_it5.2853
X-RAY DIFFRACTIONp_plane_restr0.0140.012
X-RAY DIFFRACTIONp_chiral_restr0.1230.08
X-RAY DIFFRACTIONp_singtor_nbd0.2970.4
X-RAY DIFFRACTIONp_multtor_nbd0.2760.4
X-RAY DIFFRACTIONp_xhyhbond_nbd0.240.4
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor32.8
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
σ(I): 1 / Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. reflection obs: 4471 / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS

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