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- PDB-2cj5: Crystal Structure of a Cell Wall Invertase Inhibitor from Tobacco... -

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Basic information

Entry
Database: PDB / ID: 2cj5
TitleCrystal Structure of a Cell Wall Invertase Inhibitor from Tobacco (pH 5.0)
ComponentsINVERTASE INHIBITOR
KeywordsINHIBITOR / PROTEIN BINDING / FOUR-HELIX BUNDLE / HELICAL HAIRPIN
Function / homology
Function and homology information


plant-type cell wall modification / plant-type cell wall / enzyme inhibitor activity / hydrolase activity
Similarity search - Function
Cell wall/vacuolar inhibitor of fructosidase / Invertase/pectin methylesterase inhibitor family protein / Pectinesterase inhibitor domain / Invertase/pectin methylesterase inhibitor domain superfamily / Plant invertase/pectin methylesterase inhibitor / Plant invertase/pectin methylesterase inhibitor / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Cell wall / vacuolar inhibitor of fructosidase 1
Similarity search - Component
Biological speciesNICOTIANA TABACUM (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsHothorn, M. / Scheffzek, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Multiple Crystal Forms of the Cell-Wall Invertase Inhibitor from Tobacco Support High Conformational Rigidity Over a Broad Ph-Range
Authors: Hothorn, M. / Scheffzek, K.
History
DepositionMar 29, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INVERTASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4016
Polymers16,0311
Non-polymers3695
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)131.840, 131.840, 47.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-2010-

HOH

21A-2042-

HOH

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Components

#1: Protein INVERTASE INHIBITOR


Mass: 16031.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NICOTIANA TABACUM (common tobacco) / Tissue: CELL WALL / Plasmid: PETM20 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI DE3 / References: UniProt: O49908
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
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: 3.7 Å3/Da / Density % sol: 66.8 %
Crystal growpH: 5 / Details: 19% PEG 4000, 0.1 M NAOAC PH 5.0, 0.2 M LI2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.84→43.94 Å / Num. obs: 21167 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.4
Reflection shellResolution: 1.84→1.95 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.1 / % possible all: 83.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RJ1

1rj1


Resolution: 1.84→43.94 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.297 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1059 5 %RANDOM
Rwork0.18 ---
obs0.182 20107 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å20 Å2
2--0.42 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.84→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 22 158 1283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221139
X-RAY DIFFRACTIONr_bond_other_d0.0010.021046
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9931542
X-RAY DIFFRACTIONr_angle_other_deg0.873.0012441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7145146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69325.6141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88315200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.435154
X-RAY DIFFRACTIONr_chiral_restr0.0830.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021243
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02196
X-RAY DIFFRACTIONr_nbd_refined0.2270.2297
X-RAY DIFFRACTIONr_nbd_other0.1640.21021
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2576
X-RAY DIFFRACTIONr_nbtor_other0.0850.2628
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2126
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4080.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1510.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2061.5960
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3121184
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8533451
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.14.5358
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: 1.84→1.88 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.256 52
Rwork0.232 977
Refinement TLS params.Method: refined / Origin x: 13.821 Å / Origin y: 52.938 Å / Origin z: 11.747 Å
111213212223313233
T-0.189 Å20.0351 Å2-0.0016 Å2--0.0454 Å20.0124 Å2---0.1618 Å2
L1.6561 °2-0.2071 °2-0.2072 °2-0.8424 °20.2052 °2--1.8714 °2
S-0.0215 Å °-0.1645 Å °-0.0802 Å °0.04 Å °-0.0215 Å °0.0862 Å °0.0326 Å °-0.2489 Å °0.043 Å °

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