[English] 日本語
Yorodumi
- PDB-5tpr: Desmethyl-4-deoxygadusol synthase from Anabaena variabilis (Ava_3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tpr
TitleDesmethyl-4-deoxygadusol synthase from Anabaena variabilis (Ava_3858) with NAD+ and Zn2+ bound
Components3-dehydroquinate synthase
KeywordsLYASE / sugar phosphate cyclase / sedoheptulose 7-phosphate cyclase / natural products / Rossmann fold / secondary metabolism
Function / homology
Function and homology information


demethyl-4-deoxygadusol synthase / antibiotic biosynthetic process / lyase activity / nucleotide binding / metal ion binding
Similarity search - Function
2-epi-5-epi-valiolone synthase-like / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Demethyl-4-deoxygadusol synthase
Similarity search - Component
Biological speciesAnabaena variabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKean, K.M. / Karplus, P.A.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Evolution and Distribution of C7-Cyclitol Synthases in Prokaryotes and Eukaryotes.
Authors: Osborn, A.R. / Kean, K.M. / Alseud, K.M. / Almabruk, K.H. / Asamizu, S. / Lee, J.A. / Karplus, P.A. / Mahmud, T.
History
DepositionOct 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Data collection / Database references
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-dehydroquinate synthase
B: 3-dehydroquinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,69916
Polymers100,2692
Non-polymers2,43014
Water23,3111294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12160 Å2
ΔGint-229 kcal/mol
Surface area27990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.500, 120.261, 133.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein 3-dehydroquinate synthase /


Mass: 50134.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis (strain ATCC 29413 / PCC 7937) (bacteria)
Strain: ATCC 29413 / PCC 7937 / Gene: Ava_3858 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3M6C3, 3-dehydroquinate synthase

-
Non-polymers , 6 types, 1308 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1294 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 5% PEG 8000, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate pH 7.0

-
Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→66.63 Å / Num. obs: 118029 / % possible obs: 99.9 % / Redundancy: 27.5 % / CC1/2: 0.995 / Net I/σ(I): 9.5

-
Processing

Software
NameVersionClassification
PHENIX(dev_2386: ???)refinement
Aimlessdata scaling
MR-Rosettaphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P53

4p53


Resolution: 1.7→66.63 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.87
RfactorNum. reflection% reflection
Rfree0.1833 5828 4.94 %
Rwork0.1561 --
obs0.1574 117877 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→66.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6363 0 146 1294 7803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086827
X-RAY DIFFRACTIONf_angle_d0.959303
X-RAY DIFFRACTIONf_dihedral_angle_d14.3094153
X-RAY DIFFRACTIONf_chiral_restr0.0541060
X-RAY DIFFRACTIONf_plane_restr0.0071225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71940.38021600.3573623X-RAY DIFFRACTION98
1.7194-1.73960.34121830.33263729X-RAY DIFFRACTION100
1.7396-1.76080.30322090.31733654X-RAY DIFFRACTION100
1.7608-1.78310.28952050.30063652X-RAY DIFFRACTION100
1.7831-1.80660.29732000.27453745X-RAY DIFFRACTION100
1.8066-1.83130.2611950.25733662X-RAY DIFFRACTION100
1.8313-1.85750.27651990.24433692X-RAY DIFFRACTION100
1.8575-1.88520.27281710.23223734X-RAY DIFFRACTION100
1.8852-1.91470.26341780.21083688X-RAY DIFFRACTION100
1.9147-1.9460.21322020.20273714X-RAY DIFFRACTION100
1.946-1.97960.23051970.19633702X-RAY DIFFRACTION100
1.9796-2.01560.23232060.18593740X-RAY DIFFRACTION100
2.0156-2.05440.19232000.18793667X-RAY DIFFRACTION100
2.0544-2.09630.22992090.17783699X-RAY DIFFRACTION100
2.0963-2.14190.19222320.17273686X-RAY DIFFRACTION100
2.1419-2.19170.18261670.14973728X-RAY DIFFRACTION100
2.1917-2.24650.17931780.14553734X-RAY DIFFRACTION100
2.2465-2.30730.17891850.14193756X-RAY DIFFRACTION100
2.3073-2.37520.16821880.13473742X-RAY DIFFRACTION100
2.3752-2.45180.18491740.12863747X-RAY DIFFRACTION100
2.4518-2.53950.15972120.12683675X-RAY DIFFRACTION100
2.5395-2.64120.14421720.12483782X-RAY DIFFRACTION100
2.6412-2.76140.16081870.12353761X-RAY DIFFRACTION100
2.7614-2.9070.17831960.12643743X-RAY DIFFRACTION100
2.907-3.08910.14961910.12663780X-RAY DIFFRACTION100
3.0891-3.32760.14672020.12073777X-RAY DIFFRACTION100
3.3276-3.66240.14192160.11963761X-RAY DIFFRACTION100
3.6624-4.19230.13481970.10983813X-RAY DIFFRACTION100
4.1923-5.28160.13052060.11093847X-RAY DIFFRACTION100
5.2816-66.68110.20912110.19034016X-RAY DIFFRACTION100
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)
10.17640.0157-0.08460.14390.11290.52250.01330.02050.02230.00790.0073-0.00110.00110.03830.00050.09610.00280.00260.0883-0.00640.115516.846340.988817.9637
20.32740.0124-0.17760.1436-0.08280.480.0054-0.01310.02210.01850.01250.00530.0066-0.02160.0010.11450.00180.00770.0835-0.01680.11542.63141.12252.9824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

+
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