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- PDB-1w7z: Crystal structure of the free (uncomplexed) Ecballium elaterium t... -

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Basic information

Entry
Database: PDB / ID: 1w7z
TitleCrystal structure of the free (uncomplexed) Ecballium elaterium trypsin inhibitor (EETI-II)
ComponentsTRYPSIN INHIBITOR II
KeywordsPROTEASE INHIBITOR / SQUASH SEED INHIBITOR / CYSTEIN KNOT / ECBALLIUM ELATERIUM / TRYPSIN
Function / homologyPlant trypsin inhibitors / Proteinase inhibitor I7, squash / Squash family serine protease inhibitor / Squash family of serine protease inhibitors signature. / Proteinase/amylase inhibitor domain superfamily / serine-type endopeptidase inhibitor activity / extracellular region / FORMIC ACID / Trypsin inhibitor 2
Function and homology information
Biological speciesECBALLIUM ELATERIUM (jumping cucumber)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsKraetzner, R. / Debreczeni, J.E. / Pape, T. / Kolmar, H. / Schneider, T.R. / Uson, I. / Scheldrick, G.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of Ecballium Elaterium Trypsin Inhibitor II (Eeti-II): A Rigid Molecular Scaffold
Authors: Kraetzner, R. / Debreczeni, J.E. / Pape, T. / Schneider, T.R. / Wentzel, A. / Kolmar, H. / Scheldrick, G.M. / Uson, I.
History
DepositionSep 14, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPSIN INHIBITOR II
B: TRYPSIN INHIBITOR II
C: TRYPSIN INHIBITOR II
D: TRYPSIN INHIBITOR II
E: TRYPSIN INHIBITOR II
F: TRYPSIN INHIBITOR II
G: TRYPSIN INHIBITOR II
H: TRYPSIN INHIBITOR II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,36514
Polymers25,1588
Non-polymers2076
Water2,342130
1
A: TRYPSIN INHIBITOR II
B: TRYPSIN INHIBITOR II
C: TRYPSIN INHIBITOR II
D: TRYPSIN INHIBITOR II
E: TRYPSIN INHIBITOR II
F: TRYPSIN INHIBITOR II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,07512
Polymers18,8686
Non-polymers2076
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
G: TRYPSIN INHIBITOR II


Theoretical massNumber of molelcules
Total (without water)3,1451
Polymers3,1451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
H: TRYPSIN INHIBITOR II


Theoretical massNumber of molelcules
Total (without water)3,1451
Polymers3,1451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.160, 82.340, 62.930
Angle α, β, γ (deg.)90.00, 118.80, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.46618, 0.11675, -0.87695), (0.12906, -0.98962, -0.06314), (-0.87522, -0.08374, -0.47641)15.75949, 11.51061, 28.55935
2given(-0.46815, -0.0702, -0.88086), (-0.12596, 0.99196, -0.01211), (0.87463, 0.10529, -0.4732)33.69431, 2.2104, -3.94623
3given(-0.99966, 0.00089, -0.02594), (-9.0E-5, -0.99952, -0.03111), (-0.02596, -0.0311, 0.99918)35.63662, 13.93484, 0.42877
4given(-0.52223, -0.10698, 0.84607), (0.85274, 0.07774), (-0.516521, 0.99122, 0.13182)20.87148, -1.51129, 27.61448
5given(0.54517, 0.07613, 0.83486), (0.07249, -0.99642, 0.04352), (0.83519, 0.0368, -0.54873)0.58361, 11.65154, -2.06494
6given(-0.55647, 0.39253, 0.7323), (-0.45287, -0.88223, 0.12876), (0.6966, -0.25999, 0.6687)16.74032, 30.82043, -1.78582
7given(-0.74484, -0.3314, -0.57913), (-0.35553, 0.93158, -0.07583), (0.56463, 0.14942, -0.8117)39.00362, -20.38629, -12.19298
DetailsTHE QUATERNARY STRUCTURE OF THE PROTEIN IS BELIEVED TOBE HEXAMERIC. CHAINS A TO F FORM THE HEXAMER, WHEREASCHAINS G AND H DO NOT OBEY ANY NON-CRYSTALLOGRAPHICSYMMETRY.

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Components

#1: Protein/peptide
TRYPSIN INHIBITOR II / / EETI-II


Mass: 3144.696 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ECBALLIUM ELATERIUM (jumping cucumber) / Plasmid: PLZPWB-ETI-II / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3110 / References: UniProt: P12071
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.58 Å3/Da / Density % sol: 48 %
Crystal growpH: 4.6 / Details: 2M NA-FORMATE 0.1 M NA-ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 16, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.68→55.13 Å / Num. obs: 35516 / % possible obs: 96 % / Observed criterion σ(I): 3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14
Reflection shellResolution: 1.68→1.8 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H9H

1h9h


Resolution: 1.67→55.13 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.394 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1779 5 %RANDOM
Rwork0.194 ---
obs0.197 33780 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20.31 Å2
2---0.13 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 1.67→55.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 12 130 1808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221802
X-RAY DIFFRACTIONr_bond_other_d0.0060.021632
X-RAY DIFFRACTIONr_angle_refined_deg1.8142.0022434
X-RAY DIFFRACTIONr_angle_other_deg1.03533838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2565240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65222.58162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3815281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1791519
X-RAY DIFFRACTIONr_chiral_restr0.1380.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02331
X-RAY DIFFRACTIONr_nbd_refined0.2470.2387
X-RAY DIFFRACTIONr_nbd_other0.2140.21635
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2864
X-RAY DIFFRACTIONr_nbtor_other0.130.21163
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3430.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5290.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8651.51232
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.95421951
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6363570
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5134.5480
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.72 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.262 95
Rwork0.231 1769

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