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- PDB-1gq8: Pectin methylesterase from Carrot -

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Basic information

Entry
Database: PDB / ID: 1gq8
TitlePectin methylesterase from Carrot
ComponentsPECTINESTERASE
KeywordsHYDROLASE / CARBOXYLIC ESTER HYDROLASE
Function / homology
Function and homology information


pectinesterase / pectinesterase activity / cell wall modification / pectin catabolic process / extracellular region
Similarity search - Function
Pectinesterase, Tyr active site / Pectinesterase signature 1. / Pectinesterase, Asp active site / Pectinesterase signature 2. / Pectinesterase, catalytic / Pectinesterase / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor ...Pectinesterase, Tyr active site / Pectinesterase signature 1. / Pectinesterase, Asp active site / Pectinesterase signature 2. / Pectinesterase, catalytic / Pectinesterase / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
CACODYLATE ION / Pectinesterase
Similarity search - Component
Biological speciesDAUCUS CAROTA (carrot)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsJohansson, K. / El-Ahmad, M. / Friemann, R. / Jornvall, H. / Markovic, O. / Eklund, H.
CitationJournal: FEBS Lett. / Year: 2002
Title: Crystal Structure of Plant Pectin Methylesterase
Authors: Johansson, K. / El-Ahmad, M. / Friemann, R. / Jornvall, H. / Markovic, O. / Eklund, H.
History
DepositionNov 20, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Mar 11, 2020Group: Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_status ...entity_poly / pdbx_database_status / pdbx_struct_sheet_hbond / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.id / _struct_sheet.number_strands / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PECTINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5003
Polymers34,2261
Non-polymers2742
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.690, 89.410, 49.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PECTINESTERASE / PECTIN METHYLESTERASE / PE


Mass: 34226.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DAUCUS CAROTA (carrot) / Organ: RIPE ROOTS / References: UniProt: P83218, pectinesterase
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE N-TERMINAL GLUTAMINE RESIDUE IS POST-TRANSLATIONALLY MODIFIED INTO A CYCLIC PYRO-GLUTAMATE
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 Å3/Da / Density % sol: 40 %
Crystal growpH: 6.5
Details: 0.2M NA ACETATE, 0.1M NA CACODYLATE PH 6.5, 30% PEG8000
Crystal grow
*PLUS
Temperature: 14 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 Msodium acetate1reservoir
20.1 Msodium cacodylate1reservoirpH6.5
330 %PEG80001reservoir
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.015
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 12, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.015 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. obs: 35580 / % possible obs: 99.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 9.6
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.6 / % possible all: 98.6
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 35380
Reflection shell
*PLUS
% possible obs: 98.6 %

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QJV

1qjv


Resolution: 1.75→24.26 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1750 5 %RANDOM
Rwork0.181 ---
obs0.181 35336 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.7 Å2 / ksol: 0.356336 e/Å3
Displacement parametersBiso mean: 10.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--0.54 Å20 Å2
3----0.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→24.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 10 345 2770
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.257 265 4.6 %
Rwork0.213 5497 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Rfactor obs: 0.182 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Rfactor obs: 0.213

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