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- PDB-2cj6: Crystal Structure of a Cell Wall Invertase Inhibitor from Tobacco... -

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Basic information

Entry
Database: PDB / ID: 2cj6
TitleCrystal Structure of a Cell Wall Invertase Inhibitor from Tobacco (pH 7.5)
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
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
IODIDE ION / Cell wall / vacuolar inhibitor of fructosidase 1
Similarity search - Component
Biological speciesNICOTIANA TABACUM (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 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 1.5Oct 23, 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)19,07725
Polymers16,0311
Non-polymers3,04624
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.830, 93.830, 36.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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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-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.9 Å3/Da / Density % sol: 57.4 %
Crystal growpH: 7.5 / Details: 18 % PEG 4000, 0.1 M BIS-TRIS PH 7.5, 0.2 M NAI

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.976
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 26, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2→46.93 Å / Num. obs: 12748 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.8
Reflection shellResolution: 2→2.12 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.5 / % possible all: 98.5

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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: 2→46.93 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.844 / SU B: 5.129 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.274 638 5 %RANDOM
Rwork0.217 ---
obs0.22 12109 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: 13.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.04 Å20 Å2
2---0.09 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1095 0 24 107 1226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221128
X-RAY DIFFRACTIONr_bond_other_d0.0020.021047
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9841531
X-RAY DIFFRACTIONr_angle_other_deg0.88732460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3565149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47125.6141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91615205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.024154
X-RAY DIFFRACTIONr_chiral_restr0.0880.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021238
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02197
X-RAY DIFFRACTIONr_nbd_refined0.2530.2313
X-RAY DIFFRACTIONr_nbd_other0.1810.2989
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2559
X-RAY DIFFRACTIONr_nbtor_other0.0850.2660
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3040.244
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3420.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8161.5743
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35921182
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1433416
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3354.5347
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: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 46
Rwork0.256 875

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