[English] 日本語
Yorodumi
- PDB-3b90: Crystal Structure of the Catalytic Domain of Pectate Lyase PelI f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b90
TitleCrystal Structure of the Catalytic Domain of Pectate Lyase PelI from Erwinia chrysanthemi
ComponentsEndo-pectate lyase
KeywordsLYASE / Pectate Lyase / Pectin / Galacturonic Acid / Erwinia chrysanthemi / right-handed parallel beta helix fold / catalytic domain
Function / homology
Function and homology information


pectate lyase / pectate lyase activity / pectin catabolic process / extracellular region / metal ion binding
Similarity search - Function
Pectate lyase PlyH/PlyE-like / Pectate lyase / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Biological speciesErwinia chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsCreze, C. / Castang, S. / Derivery, E. / Haser, R. / Shevchik, V. / Gouet, P.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The Crystal Structure of Pectate Lyase PelI from Soft Rot Pathogen Erwinia chrysanthemi in Complex with Its Substrate
Authors: Creze, C. / Castang, S. / Derivery, E. / Haser, R. / Hugouvieux-Cotte-Pattat, N. / Shevchik, V.E. / Gouet, P.
History
DepositionNov 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endo-pectate lyase
B: Endo-pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,23710
Polymers47,7032
Non-polymers5348
Water5,855325
1
A: Endo-pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1195
Polymers23,8521
Non-polymers2674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Endo-pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1195
Polymers23,8521
Non-polymers2674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: Endo-pectate lyase
hetero molecules

A: Endo-pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,23710
Polymers47,7032
Non-polymers5348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area2500 Å2
ΔGint-192 kcal/mol
Surface area17890 Å2
MethodPISA
4
A: Endo-pectate lyase
hetero molecules

B: Endo-pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,23710
Polymers47,7032
Non-polymers5348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area2260 Å2
ΔGint-183 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.400, 62.600, 128.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Endo-pectate lyase


Mass: 23851.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Gene: pelI / Plasmid: pT7-6 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O50325, pectate lyase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE AUTHORS STATE THAT AT THIS POSITION IT IS INDEED ARG171 AND THE DATABASE IS INCORRECT.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.01 M zinc sulfate heptahydrate, 0.1 M MES, 25% PEG 550, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 21791 / Num. obs: 20021 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 6.3 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 8.2
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 5.3 / Num. unique all: 2172 / Rsym value: 0.186 / % possible all: 77.8

-
Processing

Software
NameVersionClassification
CNS1.2refinement
DNAdata collection
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→19.83 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1891203.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.273 974 4.9 %RANDOM
Rwork0.21 ---
obs0.21 20020 91.9 %-
all-21785 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.7373 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.03 Å20 Å20 Å2
2--9.68 Å20 Å2
3----5.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.11→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 16 325 3671
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.42.5
LS refinement shellResolution: 2.11→2.23 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 130 4.8 %
Rwork0.217 2575 -
obs-2600 75 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2SO4.parSO4.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more