[English] 日本語
Yorodumi
- PDB-1q6o: Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bou... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1q6o
TitleStructure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L-gulonaet 6-phosphate
Components3-keto-L-gulonate 6-phosphate decarboxylase
KeywordsLYASE / BETA BARREL
Function / homology
Function and homology information


3-dehydro-L-gulonate-6-phosphate decarboxylase / 3-dehydro-L-gulonate-6-phosphate decarboxylase activity / L-ascorbic acid catabolic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' pyrimidine nucleobase biosynthetic process / magnesium ion binding
Similarity search - Function
3-keto-L-gulonate-6-phosphate decarboxylase, UlaD / HPS/KGPDC domain / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
L-GULURONIC ACID 6-PHOSPHATE / 3-keto-L-gulonate-6-phosphate decarboxylase UlaD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.202 Å
AuthorsWise, E.L. / Yew, W.S. / Gerlt, J.A. / Rayment, I.
CitationJournal: Biochemistry / Year: 2003
Title: Structural Evidence for a 1,2-Enediolate Intermediate in the Reaction Catalyzed by 3-Keto-l-Gulonate 6-Phosphate Decarboxylase, a Member of the Orotidine 5'-Monophosphate Decarboxylase Suprafamily
Authors: Wise, E.L. / Yew, W.S. / Gerlt, J.A. / Rayment, I.
History
DepositionAug 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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: 3-keto-L-gulonate 6-phosphate decarboxylase
B: 3-keto-L-gulonate 6-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8076
Polymers47,2062
Non-polymers6014
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-63 kcal/mol
Surface area16030 Å2
MethodPISA
2
A: 3-keto-L-gulonate 6-phosphate decarboxylase
B: 3-keto-L-gulonate 6-phosphate decarboxylase
hetero molecules

A: 3-keto-L-gulonate 6-phosphate decarboxylase
B: 3-keto-L-gulonate 6-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,61412
Polymers94,4124
Non-polymers1,2028
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area11200 Å2
ΔGint-133 kcal/mol
Surface area29720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.240, 41.775, 90.958
Angle α, β, γ (deg.)90.00, 97.15, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

-
Components

#1: Protein 3-keto-L-gulonate 6-phosphate decarboxylase / E.C.4.1.2.- / Probable hexulose-6-phosphate synthase / HUMPS / D-arabino 3-hexulose 6-phosphate formaldehyde lyase


Mass: 23603.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P39304, Lyases; Carbon-carbon lyases; Aldehyde-lyases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-LG6 / L-GULURONIC ACID 6-PHOSPHATE


Mass: 276.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O10P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.13 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7
Details: 16% MePEG 2000, 50 mM BTP pH 7.0, 5 mM MgCl2, microbatch, temperature 298K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMHEPES11pH7.5
25 mM11MgCl2
3100 mM11NaCl
415 mg/mlprotein11
5100 mMBTP11pH7.0
65 mM11MgCl2
716 %PEG5000 ME11

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.0247 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0247 Å / Relative weight: 1
ReflectionResolution: 1.202→100 Å / Num. obs: 131568 / % possible obs: 92.4 % / Observed criterion σ(I): 2 / Net I/σ(I): 29.6
Reflection shellResolution: 1.202→1.24 Å / Mean I/σ(I) obs: 4.5 / % possible all: 69.7
Reflection
*PLUS
Highest resolution: 1.2 Å / Num. obs: 142337 / Num. measured all: 931685 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
Highest resolution: 1.2 Å / % possible obs: 69.7 % / Rmerge(I) obs: 0.302

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.202→91.29 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.493 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.036 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1605 6607 5 %RANDOM
Rwork0.1408 ---
obs0.1418 124961 92.02 %-
all-131568 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.279 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20.22 Å2
2--1.01 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.202→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 36 561 3894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213386
X-RAY DIFFRACTIONr_bond_other_d0.0020.023176
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9484599
X-RAY DIFFRACTIONr_angle_other_deg2.0737343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9065426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023754
X-RAY DIFFRACTIONr_gen_planes_other0.010.02680
X-RAY DIFFRACTIONr_nbd_refined0.2330.2720
X-RAY DIFFRACTIONr_nbd_other0.250.23778
X-RAY DIFFRACTIONr_nbtor_other0.0890.21987
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2364
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2930.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.6462.52117
X-RAY DIFFRACTIONr_mcangle_it2.45243397
X-RAY DIFFRACTIONr_scbond_it2.93151269
X-RAY DIFFRACTIONr_scangle_it4.2796.51202
X-RAY DIFFRACTIONr_rigid_bond_restr1.40123386
X-RAY DIFFRACTIONr_sphericity_free3.7912563
X-RAY DIFFRACTIONr_sphericity_bonded3.61723331
LS refinement shellResolution: 1.202→1.234 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.251 347
Rwork0.215 6265
Refinement
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 500 Å / Rfactor Rfree: 0.16 / Rfactor Rwork: 0.141
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5

+
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