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- PDB-2xqr: Crystal structure of plant cell wall invertase in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 2xqr
TitleCrystal structure of plant cell wall invertase in complex with a specific protein inhibitor
Components
  • BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1
  • INVERTASE INHIBITOR
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / APOPLAST / CELL WALL / HYDROLASE / PROTEIN INHIBITOR / SUGAR METABOLISM / GLYCOSIDASE
Function / homology
Function and homology information


plant-type cell wall modification / beta-fructofuranosidase activity / beta-fructofuranosidase / plant-type cell wall / apoplast / enzyme inhibitor activity / defense response to fungus / response to wounding / carbohydrate metabolic process / hydrolase activity / plasma membrane
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 / : / Glycoside hydrolase, family 32, active site / Glycosyl hydrolases family 32 active site. / Glycosyl hydrolase family 32, C-terminal ...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 / : / Glycoside hydrolase, family 32, active site / Glycosyl hydrolases family 32 active site. / Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Exo-inulinase; domain 1 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
beta-D-fructofuranose / Cell wall / vacuolar inhibitor of fructosidase 1 / Beta-fructofuranosidase, insoluble isoenzyme CWINV1
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
NICOTIANA TABACUM (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsHothorn, M. / Van den Ende, W. / Lammens, W. / Rybin, V. / Scheffzek, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural Insights Into the Ph-Controlled Targeting of Plant Cell-Wall Invertase by a Specific Inhibitor Protein.
Authors: Hothorn, M. / Van Den Ende, W. / Lammens, W. / Rybin, V. / Scheffzek, K.
History
DepositionSep 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 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: BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1
B: INVERTASE INHIBITOR
C: BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1
D: INVERTASE INHIBITOR
E: BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1
F: INVERTASE INHIBITOR
G: BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1
H: INVERTASE INHIBITOR
I: BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1
J: INVERTASE INHIBITOR
K: BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1
L: INVERTASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)475,51449
Polymers462,01912
Non-polymers13,49537
Water14,250791
1
A: BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1
B: INVERTASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3329
Polymers77,0032
Non-polymers2,3297
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1
D: INVERTASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2368
Polymers77,0032
Non-polymers2,2336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1
F: INVERTASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2368
Polymers77,0032
Non-polymers2,2336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1
H: INVERTASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2368
Polymers77,0032
Non-polymers2,2336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
I: BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1
J: INVERTASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2368
Polymers77,0032
Non-polymers2,2336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
K: BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1
L: INVERTASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2368
Polymers77,0032
Non-polymers2,2336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)199.980, 199.980, 111.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

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Protein , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1 / CELL WALL INVERTASE 1 / SUCROSE HYDROLASE 1 / CELL WALL BETA-FRUCTOSIDASE 1


Mass: 61103.039 Da / Num. of mol.: 6 / Fragment: RESIDUES 48-584
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PPICZ / Production host: PICHIA PASTORIS (fungus) / References: UniProt: Q43866, beta-fructofuranosidase
#2: Protein
INVERTASE INHIBITOR


Mass: 15900.205 Da / Num. of mol.: 6 / Fragment: RESIDUES 19-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NICOTIANA TABACUM (common tobacco) / Plasmid: PETM20 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): ORIGAMI / References: UniProt: O49908

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Sugars , 4 types, 24 molecules

#3: Polysaccharide
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-2/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-FRU / beta-D-fructofuranose / beta-D-fructose / D-fructose / fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructofuranoseCOMMON NAMEGMML 1.0
b-D-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 804 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.79 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 6.5 / Details: 15% PEG 5000 MME 0.2 M NH4SO4 0.1 M MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97916
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.818
11-H, H+K, -L20.182
ReflectionResolution: 2.58→48.57 Å / Num. obs: 156347 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.9
Reflection shellResolution: 2.58→2.73 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.95 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0043refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1RJ1 AND 2AC1

1rj1

2ac1


Resolution: 2.58→48.57 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.898 / SU B: 20.113 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21002 7726 5 %RANDOM
Rwork0.18278 ---
obs0.18414 147896 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.262 Å2
Baniso -1Baniso -2Baniso -3
1-5.43 Å20 Å20 Å2
2--5.43 Å20 Å2
3----10.86 Å2
Refinement stepCycle: LAST / Resolution: 2.58→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32460 0 881 791 34132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02234270
X-RAY DIFFRACTIONr_bond_other_d0.0010.0223562
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.97946620
X-RAY DIFFRACTIONr_angle_other_deg0.7833.00157276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82954086
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46724.1871476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.277155634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.07815174
X-RAY DIFFRACTIONr_chiral_restr0.060.25130
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02137122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026720
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1941.520460
X-RAY DIFFRACTIONr_mcbond_other0.0281.58202
X-RAY DIFFRACTIONr_mcangle_it0.379233126
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.618313810
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1014.513494
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: 2.58→2.647 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 505 -
Rwork0.238 11040 -
obs--99.67 %
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)
10.7844-0.1628-0.05261.0285-0.29881.01680.02270.03490.0931-0.106-0.0185-0.1068-0.00160.005-0.00410.02850.00540.01230.00240.0050.019421.105-27.57658.504
20.92910.05030.39260.7217-0.03580.8951-0.0038-0.15370.05940.0738-0.0219-0.0596-0.0656-0.03230.02560.05810.0212-0.00690.0704-0.00730.009483.339-27.31721.179
30.7463-0.01810.09210.91870.37290.8416-0.02540.0929-0.0573-0.13040.00090.0495-0.0354-0.09010.02440.04830.0119-0.00310.0623-0.00670.007373.151-35.5280.332
40.7186-0.0084-0.17890.82650.13140.8287-0.0349-0.10090.01540.0980.03030.10440.0365-0.03180.00460.04860.03860.00780.0907-0.00460.01438.344-34.322-0.83
50.90490.10080.32610.88160.01840.86280.00510.15930.0154-0.1165-0.0030.0858-0.0365-0.0182-0.00220.037-0.0004-0.01130.04040.00140.008521.373-87.83725.417
60.8430.00180.0010.8337-0.32430.8168-0.044-0.1471-0.11960.2020.0005-0.0367-0.00970.0590.04350.1074-0.0146-0.00070.04870.0240.019830.422-98.34877.315
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 541
2X-RAY DIFFRACTION1B2 - 147
3X-RAY DIFFRACTION2C5 - 541
4X-RAY DIFFRACTION2D2 - 147
5X-RAY DIFFRACTION3E5 - 541
6X-RAY DIFFRACTION3F2 - 147
7X-RAY DIFFRACTION4G5 - 541
8X-RAY DIFFRACTION4H2 - 147
9X-RAY DIFFRACTION5I5 - 541
10X-RAY DIFFRACTION5J2 - 147
11X-RAY DIFFRACTION6K5 - 541
12X-RAY DIFFRACTION6L2 - 147

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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