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- PDB-2cj4: Crystal Structure of a Cell Wall Invertase Inhibitor from Tobacco... -

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Basic information

Entry
Database: PDB / ID: 2cj4
TitleCrystal Structure of a Cell Wall Invertase Inhibitor from Tobacco at pH 4.6
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: 1.63 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 1.3Dec 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 1.4Oct 9, 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
B: INVERTASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5879
Polymers32,0632
Non-polymers5247
Water6,125340
1
A: INVERTASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2464
Polymers16,0311
Non-polymers2143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: INVERTASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3425
Polymers16,0311
Non-polymers3104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)131.350, 47.180, 57.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2015-

HOH

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Components

#1: Protein INVERTASE INHIBITOR


Mass: 16031.401 Da / Num. of mol.: 2
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.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.8 Å3/Da / Density % sol: 55.4 %
Crystal growpH: 4.6 / Details: 17% PEG 4000, 0.1 M NAOAC PH 4.6, 0.2 M LI2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9774
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 6, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.63→19.65 Å / Num. obs: 43726 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.7
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.1 / % possible all: 81.5

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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: 1.63→19.65 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.878 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.189 2187 5 %RANDOM
Rwork0.151 ---
obs0.153 41534 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: 9.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.63→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 31 340 2569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222280
X-RAY DIFFRACTIONr_bond_other_d0.0010.022109
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9923089
X-RAY DIFFRACTIONr_angle_other_deg0.8443.0014938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7375297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07925.55681
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.49315411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.566158
X-RAY DIFFRACTIONr_chiral_restr0.090.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02394
X-RAY DIFFRACTIONr_nbd_refined0.2450.2577
X-RAY DIFFRACTIONr_nbd_other0.1820.21977
X-RAY DIFFRACTIONr_nbtor_refined0.180.21183
X-RAY DIFFRACTIONr_nbtor_other0.0830.21125
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2224
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3240.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.671.51926
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.92222374
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4993903
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7664.5712
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: 1.63→1.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.228 117
Rwork0.166 2217
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2203-0.3183-0.12611.64860.28230.7052-0.0279-0.0582-0.08680.01480.031-0.12750.03470.072-0.0031-0.122-0.0090.0001-0.13290.0129-0.112751.9780.0584.024
20.63950.4753-0.01371.7692-0.17320.6308-0.02060.07340.0055-0.09960.0098-0.0717-0.00380.04860.0109-0.10820.0111-0.0035-0.1368-0.0009-0.129238.695-0.457-18.845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 150
2X-RAY DIFFRACTION2B1 - 150

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