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- PDB-1x8z: Crystal structure of a pectin methylesterase inhibitor from Arabi... -

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Basic information

Entry
Database: PDB / ID: 1x8z
TitleCrystal structure of a pectin methylesterase inhibitor from Arabidopsis thaliana
Componentsinvertase/pectin methylesterase inhibitor family protein
KeywordsPROTEIN BINDING / four-helix bundle / alpha hairpin / disulfide bridge
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: 2.86 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 1.3Oct 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
Revision 1.4Nov 13, 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
B: invertase/pectin methylesterase inhibitor family protein
C: invertase/pectin methylesterase inhibitor family protein


Theoretical massNumber of molelcules
Total (without water)49,3343
Polymers49,3343
Non-polymers00
Water39622
1
A: invertase/pectin methylesterase inhibitor family protein

A: invertase/pectin methylesterase inhibitor family protein


Theoretical massNumber of molelcules
Total (without water)32,8892
Polymers32,8892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
2
B: invertase/pectin methylesterase inhibitor family protein
C: invertase/pectin methylesterase inhibitor family protein


Theoretical massNumber of molelcules
Total (without water)32,8892
Polymers32,8892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-29 kcal/mol
Surface area15130 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-38 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.770, 106.190, 186.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is a dimer generated from the molecules chain B and C in the asymmetric unit / The biological assembly is a dimer generated from the molecule chain A and its closest symmetry mate

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Components

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


Mass: 16444.725 Da / Num. of mol.: 3 / Fragment: residues 1-149
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.: 22 / 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: 3.05 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 10%(v/v) PEG 8000, 0.3M NaCl, 0.1M Na/K Pi, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2003 / Details: Dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.86→29.06 Å / Num. all: 14136 / Num. obs: 14136 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.91
Reflection shellResolution: 2.86→3.04 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 5.4 / Num. unique all: 2307 / % possible all: 98.1

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Processing

Software
NameVersionClassification
XDSVersion Dec. 2003data scaling
XDSV. DEC. 2003data reduction
EPMRphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: p(ALA) version of PDB entry 1RJ1

1rj1


Resolution: 2.86→29.06 Å / Isotropic thermal model: ISOTROPIC RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 705 -RANDOM
Rwork0.218 ---
all0.22 14129 --
obs0.22 13424 98.5 %-
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.86→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 0 22 3382
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
LS refinement shellResolution: 2.86→3.04 Å / Rfactor Rfree error: 0.032
RfactorNum. reflection% reflection
Rfree0.345 115 -
Rwork0.326 --
obs-2299 98.1 %

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