[English] 日本語
Yorodumi
- PDB-1vl1: Crystal structure of 6-phosphogluconolactonase (TM1154) from Ther... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vl1
TitleCrystal structure of 6-phosphogluconolactonase (TM1154) from Thermotoga maritima at 1.70A resolution
Components6-phosphogluconolactonase
KeywordsHYDROLASE / TM1154 / 6-PHOSPHOGLUCONOLACTONASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


6-phosphogluconolactonase / 6-phosphogluconolactonase activity / pentose-phosphate shunt, oxidative branch / carbohydrate metabolic process / cytosol
Similarity search - Function
6-Phosphogluconolactonase / 6-phosphogluconolactonase, DevB-type / Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / Rossmann fold - #1360 / NagB/RpiA transferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 6-phosphogluconolactonase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of 6-phosphogluconolactonase (TM1154) from Thermotoga maritima at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 6-phosphogluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0142
Polymers26,8221
Non-polymers1921
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.733, 75.146, 148.443
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-465-

HOH

-
Components

#1: Protein 6-phosphogluconolactonase / / 6PGL


Mass: 26821.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: PGL, DEVB, TM1154 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0N8, 6-phosphogluconolactonase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 35.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 0.2M (NH4)2HCitrate, 20% PEG-3350 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.000034
DetectorType: ADSC / Detector: CCD / Date: Apr 2, 2004
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000034 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 24729 / % possible obs: 79.46 % / Redundancy: 3.86 % / Biso Wilson estimate: 23.98 Å2 / Rsym value: 0.075 / Net I/σ(I): 16.59
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 2.57 % / Mean I/σ(I) obs: 2.93 / Num. unique all: 798 / Rsym value: 0.325 / % possible all: 26.04

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0001refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PBT

1pbt


Resolution: 1.55→37.11 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.158 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE NOMINAL RESOLUTION IS 1.70 A WITH 2581 OBSERVED REFLECTIONS BETWEEN 1.70 - 1.55 A (35 % COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.20395 1262 5.1 %RANDOM
Rwork0.16523 ---
obs0.16717 23466 79.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.367 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2--2.44 Å20 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 1.55→37.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 13 167 1946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221822
X-RAY DIFFRACTIONr_bond_other_d0.0010.021684
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9672470
X-RAY DIFFRACTIONr_angle_other_deg0.87633918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2495219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48423.6984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73315323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6941513
X-RAY DIFFRACTIONr_chiral_restr0.1150.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021991
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02376
X-RAY DIFFRACTIONr_nbd_refined0.2180.2335
X-RAY DIFFRACTIONr_nbd_other0.1840.21677
X-RAY DIFFRACTIONr_nbtor_other0.0830.21117
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3640.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.224
X-RAY DIFFRACTIONr_mcbond_it1.1511.51164
X-RAY DIFFRACTIONr_mcbond_other0.3271.5439
X-RAY DIFFRACTIONr_mcangle_it1.53521784
X-RAY DIFFRACTIONr_scbond_it2.7333798
X-RAY DIFFRACTIONr_scangle_it3.9794.5685
LS refinement shellResolution: 1.55→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 29 4.99 %
Rwork0.2 552 -
Refinement TLS params.Method: refined / Origin x: 4.1756 Å / Origin y: 21.4416 Å / Origin z: 17.9626 Å
111213212223313233
T-0.1261 Å2-0.001 Å20.0014 Å2--0.1382 Å20.0104 Å2---0.1137 Å2
L1.3461 °2-0.4957 °2-0.44 °2-1.4108 °20.4254 °2--2.3827 °2
S-0.0115 Å °-0.037 Å °-0.0406 Å °0.0799 Å °-0.0048 Å °-0.0085 Å °0.0308 Å °0.0398 Å °0.0163 Å °
Refinement TLS groupSelection: ALL

+
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