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- PDB-1rj1: Crystal Structure of a Cell Wall Invertase Inhibitor from Tobacco -

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Basic information

Entry
Database: PDB / ID: 1rj1
TitleCrystal Structure of a Cell Wall Invertase Inhibitor from Tobacco
Componentsinvertase inhibitor
KeywordsPROTEIN BINDING / FOUR-HELIX BUNDLE / HELICAL HAIRPIN
Function / homology
Function and homology information


enzyme inhibitor activity / cell wall organization
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
Cell wall / vacuolar inhibitor of fructosidase 1-like
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsHothorn, M. / D'Angelo, I. / Marquez, J.A. / Greiner, S. / Scheffzek, K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The invertase inhibitor Nt-CIF from tobacco: a highly thermostable four-helix bundle with an unusual N-terminal extension
Authors: Hothorn, M. / D'Angelo, I. / Marquez, J.A. / Greiner, S. / Scheffzek, K.
History
DepositionNov 18, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: invertase inhibitor


Theoretical massNumber of molelcules
Total (without water)16,0881
Polymers16,0881
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.670, 106.400, 55.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a monomer in solution

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Components

#1: Protein invertase inhibitor


Mass: 16088.454 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Tissue: cell wall / Gene: NTINH1 / Plasmid: pETM20 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami (DE3) / References: UniProt: O49908
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4.0M sodium formate, 0.1M bis-Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop / Details: Hothorn, M., (2003) Acta Cryst., D59, 2279.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
24 Msodium formate1reservoir
30.1 MBis-Tris1reservoirpH7.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.87→19.25 Å / Num. all: 15311 / Num. obs: 15112 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 23.84
Reflection shellResolution: 1.87→1.99 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 8.92 / Num. unique all: 2210 / % possible all: 93.1
Reflection
*PLUS
Num. obs: 15167 / % possible obs: 97.8 %
Reflection shell
*PLUS
Lowest resolution: 2 Å / % possible obs: 88.2 % / Num. unique obs: 2455

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1RJ4

1rj4


Resolution: 1.87→19.25 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2543413.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 615 4.1 %RANDOM
Rwork0.194 ---
obs0.194 15112 98.7 %-
all-15311 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.2858 Å2 / ksol: 0.385833 e/Å3
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1-3.15 Å20 Å20 Å2
2---0.64 Å20 Å2
3----2.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å-0.01 Å
Refinement stepCycle: LAST / Resolution: 1.87→19.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1107 0 0 121 1228
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d17.8
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_mcbond_it2.751.5
X-RAY DIFFRACTIONc_mcangle_it3.562
X-RAY DIFFRACTIONc_scbond_it4.582
X-RAY DIFFRACTIONc_scangle_it6.322.5
LS refinement shellResolution: 1.87→1.99 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.238 100 4.7 %
Rwork0.215 2034 -
obs-2210 93.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17

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