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- PDB-1x91: Crystal structure of mutant form A of a pectin methylesterase inh... -

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Basic information

Entry
Database: PDB / ID: 1x91
TitleCrystal structure of mutant form A of a pectin methylesterase inhibitor from Arabidopsis
Componentsinvertase/pectin methylesterase inhibitor family protein
KeywordsPROTEIN BINDING / four-helix bundle / alpha hairpin / disulfide bridge / domain-swapping / linker / proline / mutant
Function / homology
Function and homology information


pectinesterase inhibitor activity / pollen tube tip / pollen tube growth / apoplast
Similarity search - Function
Pectinesterase inhibitor, plant / : / 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
Pectinesterase inhibitor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHothorn, M. / Wolf, S. / Aloy, P. / Greiner, S. / Scheffzek, K.
CitationJournal: Plant Cell / Year: 2004
Title: Structural insights into the target specificity of plant invertase and pectin methylesterase inhibitory proteins
Authors: Hothorn, M. / Wolf, S. / Aloy, P. / Greiner, S. / Scheffzek, K.
History
DepositionAug 19, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 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/pectin methylesterase inhibitor family protein


Theoretical massNumber of molelcules
Total (without water)16,4191
Polymers16,4191
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.399, 62.440, 23.338
Angle α, β, γ (deg.)90.00, 94.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-234-

HOH

21A-237-

HOH

DetailsThe biologically assembly is consistent with the content of the asymmetric unit, monomer

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Components

#1: Protein invertase/pectin methylesterase inhibitor family protein / Pectin Methylesterase Inhibitor


Mass: 16418.689 Da / Num. of mol.: 1 / Fragment: residues 1-149 / Mutation: P28A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: APOPLAST-CELL WALL / Gene: AT1G48020 / Plasmid: pETM 20 / Production host: Escherichia coli (E. coli) / Strain (production host): origami (DE3) / References: UniProt: Q9LNF2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M (NH4)2SO4, 0.3M Na/K tartrate, 0.1M Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 18, 2004 / Details: toroidal mirror
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.5→54.23 Å / Num. all: 24884 / Num. obs: 24884 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.4
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1833 / % possible all: 98.7

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Processing

Software
NameVersionClassification
XDSVersion Dec. 2003data scaling
XDSV. DEC. 2003data reduction
CNSrefinement
REFMACrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X90 CHAIN A

1x90


Resolution: 1.5→54.23 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: TROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1245 -RANDOM
Rwork0.184 ---
all0.185 24884 --
obs0.185 23639 100 %-
Displacement parametersBiso mean: 15.278 Å2
Refinement stepCycle: LAST / Resolution: 1.5→54.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1166 0 0 104 1270
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.017
X-RAY DIFFRACTIONr_bond_other_d0.002
X-RAY DIFFRACTIONr_angle_refined_deg1.51
X-RAY DIFFRACTIONr_angle_other_deg0.885
LS refinement shellResolution: 1.5→1.54 Å
RfactorNum. reflection% reflection
Rfree0.271 92 -
Rwork0.276 --
obs-1835 98.7 %

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