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- PDB-1x90: Crystal structure of mutant form B of a pectin methylesterase inh... -

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Basic information

Entry
Database: PDB / ID: 1x90
TitleCrystal structure of mutant form B of a pectin methylesterase inhibitor from Arabidopsis
Componentsinvertase/pectin methylesterase inhibitor family protein
KeywordsPROTEIN BINDING / four-helix bundle / alpha hairpin / disulfide bridge / 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: 2.68 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: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

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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


Theoretical massNumber of molelcules
Total (without water)32,6072
Polymers32,6072
Non-polymers00
Water79344
1
A: invertase/pectin methylesterase inhibitor family protein


Theoretical massNumber of molelcules
Total (without water)16,3041
Polymers16,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: invertase/pectin methylesterase inhibitor family protein


Theoretical massNumber of molelcules
Total (without water)16,3041
Polymers16,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: invertase/pectin methylesterase inhibitor family protein

A: invertase/pectin methylesterase inhibitor family protein

A: invertase/pectin methylesterase inhibitor family protein


Theoretical massNumber of molelcules
Total (without water)48,9113
Polymers48,9113
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_235-y-3,x-y-2,z1
crystal symmetry operation3_425-x+y-1,-x-3,z1
Buried area3190 Å2
ΔGint-39 kcal/mol
Surface area22060 Å2
MethodPISA, PQS
4
B: invertase/pectin methylesterase inhibitor family protein

B: invertase/pectin methylesterase inhibitor family protein

B: invertase/pectin methylesterase inhibitor family protein


Theoretical massNumber of molelcules
Total (without water)48,9113
Polymers48,9113
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_345-y-2,x-y-1,z1
crystal symmetry operation3_435-x+y-1,-x-2,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.410, 82.410, 105.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a monomer. The asymmetric unit consists out of two monomers.

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Components

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


Mass: 16303.602 Da / Num. of mol.: 2 / 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: pETM20 / Production host: Escherichia coli (E. coli) / Strain (production host): origami (DE3) / References: UniProt: Q9LNF2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2.5M (NH4)2SO4, 4%(v/v) isopropanol, pH 0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 23, 2004 / Details: bent mirror
RadiationMonochromator: triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2.68→19.46 Å / Num. all: 7391 / Num. obs: 7391 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.14 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.8
Reflection shellResolution: 2.68→2.85 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 6.56 / Num. unique all: 1184 / % possible all: 93.3

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Processing

Software
NameVersionClassification
XDSVersion Dec. 2003data scaling
XDSV. DEC. 2003data reduction
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X8Z CHAIN A

1x8z


Resolution: 2.68→19.46 Å / Isotropic thermal model: ISOTROPIC RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 370 -RANDOM
Rwork0.215 ---
obs0.215 7021 98.6 %-
all-7391 --
Displacement parametersBiso mean: 48.1 Å2
Baniso -1Baniso -2Baniso -3
1--9.37 Å20.82 Å20 Å2
2---9.37 Å20 Å2
3---18.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.68→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 0 44 2242
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 2.68→2.85 Å / Rfactor Rfree error: 0.041
RfactorNum. reflection% reflection
Rfree0.316 59 -
Rwork0.253 --
obs-1184 93.2 %

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