[English] 日本語
Yorodumi
- PDB-8a8y: Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a8y
TitleStructure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Klebsiella pneumoniae
Components1-deoxy-D-xylulose-5-phosphate synthase
KeywordsTRANSFERASE / Primary metabolism / synthase
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase activity / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / thiamine biosynthetic process / terpenoid biosynthetic process / thiamine pyrophosphate binding / magnesium ion binding
Similarity search - Function
Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / Transketolase signature 1. / Transketolase binding site / Transketolase signature 2. / Transketolase, N-terminal / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain ...Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / Transketolase signature 1. / Transketolase binding site / Transketolase signature 2. / Transketolase, N-terminal / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
1-deoxy-D-xylulose-5-phosphate synthase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.10000431701 Å
AuthorsAdam, S. / Hirsch, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Klebsiella pneumoniae
Authors: Adam, S. / Hirsch, A.
History
DepositionJun 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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: 1-deoxy-D-xylulose-5-phosphate synthase
B: 1-deoxy-D-xylulose-5-phosphate synthase


Theoretical massNumber of molelcules
Total (without water)126,5082
Polymers126,5082
Non-polymers00
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-55 kcal/mol
Surface area34650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.164, 144.247, 142.911
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein 1-deoxy-D-xylulose-5-phosphate synthase / / 1-deoxyxylulose-5-phosphate synthase / DXP synthase / DXPS


Mass: 63254.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: dxs_3, dxs, dxs_1, dxs_2, BN49_1346, DRB11_07540, FXN67_12755, GPZ86_21160, NCTC11679_04435, NCTC13465_06397, NCTC3279_00555, NCTC5047_01280, NCTC5052_00313, NCTC9140_02292, NCTC9645_03343, ...Gene: dxs_3, dxs, dxs_1, dxs_2, BN49_1346, DRB11_07540, FXN67_12755, GPZ86_21160, NCTC11679_04435, NCTC13465_06397, NCTC3279_00555, NCTC5047_01280, NCTC5052_00313, NCTC9140_02292, NCTC9645_03343, NCTC9661_05006, SAMEA3512100_02923, SAMEA3649733_02709, SAMEA4364603_02966
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0S3F934, 1-deoxy-D-xylulose-5-phosphate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, Magnesium chloride, TRIS

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→91.9 Å / Num. obs: 71565 / % possible obs: 99.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 35.355127569 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.9
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.72 / Num. unique obs: 10344

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2o1s
Resolution: 2.10000431701→45.934906016 Å / SU ML: 0.219294682671 / Cross valid method: FREE R-VALUE / σ(F): 1.35282638344 / Phase error: 20.7565773698
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.201051462019 3562 4.98042505593 %
Rwork0.17914882105 67958 -
obs0.18023954443 71520 99.4922445573 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.2053769734 Å2
Refinement stepCycle: LAST / Resolution: 2.10000431701→45.934906016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7384 0 0 392 7776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002378048485857526
X-RAY DIFFRACTIONf_angle_d0.52725060939410204
X-RAY DIFFRACTIONf_chiral_restr0.04271220659551171
X-RAY DIFFRACTIONf_plane_restr0.002567554042671321
X-RAY DIFFRACTIONf_dihedral_angle_d15.09811315474507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1000044-2.12880.3018844479851420.2645333940562731X-RAY DIFFRACTION99.6877168633
2.1288-2.15920.3021410253341470.2599286071372670X-RAY DIFFRACTION99.6815286624
2.1592-2.19140.2927899482791540.2394113176012687X-RAY DIFFRACTION99.7191997192
2.1914-2.22570.2771902743871580.2340971613922638X-RAY DIFFRACTION98.5200845666
2.2257-2.26210.2666245915211350.2247238293592683X-RAY DIFFRACTION99.4354269584
2.2621-2.30110.2622997058361370.2159753339932707X-RAY DIFFRACTION99.649614576
2.3011-2.3430.2466718460941620.2101407583682685X-RAY DIFFRACTION99.7197898424
2.343-2.38810.2367637953381510.2129340467362683X-RAY DIFFRACTION99.5783555868
2.3881-2.43680.240871765711550.1974566824482684X-RAY DIFFRACTION99.5790950544
2.4368-2.48980.1993820442741310.1965559883192698X-RAY DIFFRACTION99.6828752643
2.4898-2.54770.2449546342541440.1947042369822716X-RAY DIFFRACTION99.6515679443
2.5477-2.61140.2503103146211290.1974748704252715X-RAY DIFFRACTION99.5101469559
2.6114-2.6820.2183651335061570.1915406205582683X-RAY DIFFRACTION99.5094604064
2.682-2.76090.2332654702161380.190725298952735X-RAY DIFFRACTION99.4806094183
2.7609-2.850.2105465888621420.1839111138762691X-RAY DIFFRACTION99.9294532628
2.85-2.95190.209449501571440.1804622257022723X-RAY DIFFRACTION99.8954703833
2.9519-3.070.2273625791621470.1772469552192706X-RAY DIFFRACTION99.5116846878
3.07-3.20970.1938258117041270.1739493049812753X-RAY DIFFRACTION99.6884735202
3.2097-3.37890.1749712706691250.1627632602632711X-RAY DIFFRACTION98.780912574
3.3789-3.59050.1564590263931340.1580327924782757X-RAY DIFFRACTION99.8963372495
3.5905-3.86760.1983325609761440.152965157752748X-RAY DIFFRACTION99.8274076631
3.8676-4.25660.1664307522841370.147821832152759X-RAY DIFFRACTION99.6558843772
4.2566-4.87190.1515275394651370.1381374279252753X-RAY DIFFRACTION99.4152046784
4.8719-6.13580.1551997192831370.1718319111542786X-RAY DIFFRACTION99.2866847826
6.1358-45.9330.2081200280511480.2055392766472856X-RAY DIFFRACTION98.1699346405
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.37059340361-0.4600154609440.4066091255163.317527067750.4342291366442.64576063668-0.1954990935220.1845720494580.765455017265-0.109735172839-0.026068905961-0.291453248917-1.019729855520.3447721244330.2250308002950.72107132867-0.174176613167-0.08724776824180.5155276290020.04645377602840.588879201994-4.50997369119-11.899969549317.2252325317
22.12790162690.9191589154820.511739042373.44803773220.6875849436272.33751292097-0.128123896714-0.3360749927270.2995780745170.333196516504-0.1271041716020.0817537008859-0.382950811035-0.02189903413170.2604936512840.475767341692-0.00632631857031-0.03683191393130.401173831942-0.03825751438310.373106791354-14.5089711296-22.275511861225.5411203662
31.64153727709-0.5908826660362.112788273610.587628409266-0.524811617993.74342187214-0.07428208850020.02797621239670.2807801165270.0197306841769-0.0964143839474-0.00666417409024-0.3420945877670.005231826635740.2076515031510.3260731956020.0002399392893730.01630560691270.3572234620490.006547353985560.391757633078-30.7391327265-21.33727845222.20302380366
41.69589287297-0.324897787069-0.7343077386360.5073083127630.1028911234522.122938747620.05507574471560.1645656626180.0266290858479-0.0931300617241-0.01695794007960.02811506894770.0422243066738-0.0599003303627-0.03069127983850.267323978299-0.0141519507619-0.03314075864470.2899560973610.008798454244320.280660373507-25.0295577481-33.9049469117-12.3437066025
52.210438544520.9073145965680.2789480239472.8579497036-0.6664482400541.257515967990.05372172506520.2295140562080.261468507081-0.122863809242-0.06994182205180.036213470389-0.06137148797530.1829520100770.003820287223110.294702115278-0.00916491620080.007192446904420.4184200962830.05037049235130.302127753717-8.71416833845-34.4603505235-19.2924130925
63.818274658620.1689290164350.7068839943943.154986118750.7670302296133.07342696336-0.0333371762871-0.182642394761-0.9955110566520.264980238010.04186422314230.3066556744860.989147254005-0.540303108084-0.05233640109890.734318193847-0.1997791119830.06053499734830.5601700867820.09667469935460.793135703601-45.6533841382-61.399587874323.4688828027
73.1516254997-0.4829982058080.03267251745694.16235393216-1.154745183612.48304906081-0.03102107976670.220394535506-0.462282700417-0.2144565816270.150674846814-0.05660142365070.588808506425-0.106835226787-0.1221781209340.46942565411-0.0612944980584-0.008163018173270.485551995898-0.05176893127890.395016645795-40.4864391913-46.909281935612.9855576472
81.838693048380.676572778844-1.21958113954.20977609216-1.394108797233.54857679299-0.00684705263355-0.0982185005278-0.01394580671380.1990905025410.142283163330.3810647604050.0408377303793-0.239815004345-0.1116314712930.3093429608860.0120806307420.02830961037860.3720632376990.01311577678080.302630263835-37.7600105741-39.275929484522.8195954331
92.9621872851-1.15819530102-0.9629230507781.002590381650.3257788493110.678680872008-0.112178170133-0.132209055258-0.2951639014710.1043103089410.02326489759240.04408836053950.03566419305210.06341274214720.1138691443670.363688345365-0.00875806144358-0.02008210417630.3478972803250.04914237797740.295102494472-11.7563475243-49.769094700620.6457732704
102.40320008735-0.2326855233150.7961331737642.367442462681.040414143554.88219901199-0.0368160255277-0.149192338904-0.004942606912310.130754803636-0.04900037251820.1171879378270.148958833411-0.251623868250.0897298239250.205492280581-0.008352926811330.003806191975270.2710614208470.0301853715890.23024627818-10.4200955935-42.76795913211.6870822149
111.48669213271-0.3075824015270.4380774336030.605789234273-0.1965041662941.438723549690.09611588593010.05683150936-0.215136046814-0.0894349330411-0.0429822517258-0.04270764552670.2439097929660.0451196501142-0.05236384878840.3146569166960.0042848992937-0.001222919928490.289916556862-0.005470263765940.320786680679-5.21937311842-55.58855042-6.34374367831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 140 )
2X-RAY DIFFRACTION2chain 'A' and (resid 141 through 237 )
3X-RAY DIFFRACTION3chain 'A' and (resid 238 through 324 )
4X-RAY DIFFRACTION4chain 'A' and (resid 325 through 530 )
5X-RAY DIFFRACTION5chain 'A' and (resid 531 through 586 )
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 66 )
7X-RAY DIFFRACTION7chain 'B' and (resid 67 through 140 )
8X-RAY DIFFRACTION8chain 'B' and (resid 141 through 237 )
9X-RAY DIFFRACTION9chain 'B' and (resid 238 through 324 )
10X-RAY DIFFRACTION10chain 'B' and (resid 325 through 400 )
11X-RAY DIFFRACTION11chain 'B' and (resid 401 through 586 )

+
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