[English] 日本語
Yorodumi
- PDB-6mdy: Crystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mdy
TitleCrystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase from Legionella pneumophila Philadelphia 1
Components2-dehydro-3-deoxyphosphooctonate aldolase
KeywordsHYDROLASE / NIAID / structural genomics / aldolase / phosphoenolpyruvate / D-arabinose 5-phosphate / 3-deoxy-D-manno-octulosonate 8-phosphate / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / cytoplasm
Similarity search - Function
3-deoxy-8-phosphooctulonate synthase / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase from Legionella pneumophila Philadelphia 1
Authors: Edwards, T.E. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionSep 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-dehydro-3-deoxyphosphooctonate aldolase
B: 2-dehydro-3-deoxyphosphooctonate aldolase
C: 2-dehydro-3-deoxyphosphooctonate aldolase
D: 2-dehydro-3-deoxyphosphooctonate aldolase


Theoretical massNumber of molelcules
Total (without water)124,1914
Polymers124,1914
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint-55 kcal/mol
Surface area33720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.520, 87.320, 160.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 36 or (resid 37...
21(chain B and ((resid 0 and (name N or name...
31(chain C and (resid 0 through 22 or (resid 23...
41(chain D and (resid 0 through 1 or (resid 2...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISLEULEU(chain A and (resid 0 through 36 or (resid 37...AA0 - 368 - 44
12LYSLYSGLUGLU(chain A and (resid 0 through 36 or (resid 37...AA37 - 3845 - 46
13HISHISPHEPHE(chain A and (resid 0 through 36 or (resid 37...AA0 - 2748 - 282
14HISHISPHEPHE(chain A and (resid 0 through 36 or (resid 37...AA0 - 2748 - 282
15HISHISPHEPHE(chain A and (resid 0 through 36 or (resid 37...AA0 - 2748 - 282
16HISHISPHEPHE(chain A and (resid 0 through 36 or (resid 37...AA0 - 2748 - 282
21HISHISHISHIS(chain B and ((resid 0 and (name N or name...BB08
22HISHISPHEPHE(chain B and ((resid 0 and (name N or name...BB0 - 2748 - 282
23HISHISPHEPHE(chain B and ((resid 0 and (name N or name...BB0 - 2748 - 282
24HISHISPHEPHE(chain B and ((resid 0 and (name N or name...BB0 - 2748 - 282
25HISHISPHEPHE(chain B and ((resid 0 and (name N or name...BB0 - 2748 - 282
31HISHISVALVAL(chain C and (resid 0 through 22 or (resid 23...CC0 - 228 - 30
32ILEILEGLUGLU(chain C and (resid 0 through 22 or (resid 23...CC23 - 2431 - 32
33HISHISPHEPHE(chain C and (resid 0 through 22 or (resid 23...CC0 - 2748 - 282
34HISHISPHEPHE(chain C and (resid 0 through 22 or (resid 23...CC0 - 2748 - 282
35HISHISPHEPHE(chain C and (resid 0 through 22 or (resid 23...CC0 - 2748 - 282
36HISHISPHEPHE(chain C and (resid 0 through 22 or (resid 23...CC0 - 2748 - 282
41HISHISMETMET(chain D and (resid 0 through 1 or (resid 2...DD0 - 18 - 9
42ARGARGARGARG(chain D and (resid 0 through 1 or (resid 2...DD210
43HISHISPHEPHE(chain D and (resid 0 through 1 or (resid 2...DD-1 - 2747 - 282

-
Components

#1: Protein
2-dehydro-3-deoxyphosphooctonate aldolase / 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase / KDO-8-phosphate synthase / KDOPS / Phospho- ...3-deoxy-D-manno-octulosonic acid 8-phosphate synthase / KDO-8-phosphate synthase / KDOPS / Phospho-2-dehydro-3-deoxyoctonate aldolase


Mass: 31047.689 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: kdsA, lpg1182 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5ZWA3, 3-deoxy-8-phosphooctulonate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.02 Å3/Da / Density % sol: 39.05 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: LepnA.00102.a.B1.PS38404 at 22.83 mg/mL against JCSG+ screen condition H3 25% PEG 3350, 0.1 M BisTris pH 5.5, supplemented with 15% ethylene glycol as cryo-protectant, crystal tracking ID ...Details: LepnA.00102.a.B1.PS38404 at 22.83 mg/mL against JCSG+ screen condition H3 25% PEG 3350, 0.1 M BisTris pH 5.5, supplemented with 15% ethylene glycol as cryo-protectant, crystal tracking ID 298231h3, unique puck ID uya9-5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98782 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98782 Å / Relative weight: 1
ReflectionResolution: 2.55→45.554 Å / Num. obs: 33563 / % possible obs: 99.9 % / Redundancy: 6.166 % / Biso Wilson estimate: 44.776 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.098 / Χ2: 1.003 / Net I/σ(I): 17.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.55-2.626.2850.5773.2724150.8750.631100
2.62-2.696.2640.5213.6123880.8950.569100
2.69-2.776.2450.4184.3923210.9160.456100
2.77-2.856.2650.355.3722390.9430.382100
2.85-2.946.2780.2936.3221810.960.3299.9
2.94-3.056.2480.2527.2421470.9690.275100
3.05-3.166.2340.1989.2920290.9790.216100
3.16-3.296.2360.15811.5219650.9860.173100
3.29-3.446.2040.12114.7419100.9910.13299.9
3.44-3.616.2110.08520.0318020.9960.093100
3.61-3.86.1940.07222.7917460.9970.07999.9
3.8-4.036.1710.05927.1616360.9980.065100
4.03-4.316.1620.0473315510.9980.052100
4.31-4.666.1180.04236.5814550.9990.046100
4.66-5.16.0760.03938.7313430.9990.043100
5.1-5.76.0490.0436.2612090.9990.044100
5.7-6.585.9560.04732.511020.9990.052100
6.58-8.065.8420.03239.3194110.035100
8.06-11.45.6490.02153.474110.023100
11.4-45.5544.8940.02348.814420.9990.02696.9

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.14_3219)refinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TML

3tml


Resolution: 2.55→45.554 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.96
RfactorNum. reflection% reflection
Rfree0.2269 1903 5.68 %
Rwork0.176 --
obs0.1788 33490 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.31 Å2 / Biso mean: 48.3604 Å2 / Biso min: 17.47 Å2
Refinement stepCycle: final / Resolution: 2.55→45.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7272 0 0 140 7412
Biso mean---35.62 -
Num. residues----978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067445
X-RAY DIFFRACTIONf_angle_d0.88110106
X-RAY DIFFRACTIONf_dihedral_angle_d6.635725
X-RAY DIFFRACTIONf_chiral_restr0.0531183
X-RAY DIFFRACTIONf_plane_restr0.0061291
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2724X-RAY DIFFRACTION6.133TORSIONAL
12B2724X-RAY DIFFRACTION6.133TORSIONAL
13C2724X-RAY DIFFRACTION6.133TORSIONAL
14D2724X-RAY DIFFRACTION6.133TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5499-2.61360.33231290.234921932322100
2.6136-2.68430.33411330.221622182351100
2.6843-2.76330.29731310.208522482379100
2.7633-2.85250.26671420.203722092351100
2.8525-2.95440.30181380.203122062344100
2.9544-3.07270.2371330.209322352368100
3.0727-3.21250.27541590.196722362395100
3.2125-3.38180.26091500.187722192369100
3.3818-3.59360.21041250.176722542379100
3.5936-3.87090.21141280.16622612389100
3.8709-4.26020.21271200.152522922412100
4.2602-4.87610.17181350.133522812416100
4.8761-6.14090.19441460.155923082454100
6.1409-45.56120.19221340.18192427256199
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)
13.24070.15660.34272.15250.03061.0386-0.05320.73110.0173-0.62910.0652-0.2285-0.05940.268-0.01540.4655-0.01060.04450.4631-0.09640.30590.0035-10.1893-8.025
21.88310.2395-0.10742.1666-0.05393.61330.02650.2268-0.1827-0.3641-0.06230.43340.34820.08970.03610.24430.0196-0.02930.2388-0.03640.311-12.5535-12.63934.1055
34.1816-0.31610.63850.99590.03184.6981-0.10210.23130.1346-0.25090.1568-0.2745-0.15480.1714-0.08440.28710.0130.05080.2745-0.04870.31813.7007-13.35758.7375
44.50092.7322-1.28817.6748-0.52946.60440.014-0.3391-0.35830.5769-0.11970.31360.54280.01970.15060.38540.0988-0.02140.28330.07820.3207-3.3066-23.701937.8069
51.9506-0.538-0.22442.96480.31444.2388-0.1136-0.496-0.21380.79760.06220.00080.5657-0.3144-0.0710.4731-0.08270.01550.46150.07180.2766-10.6391-18.219248.4547
63.1777-0.17130.08763.0655-0.92615.6806-0.0515-0.2270.12960.3059-0.00560.0541-0.3026-0.0193-0.03970.28920.0105-0.03350.3046-0.01720.2121-8.1817-5.998440.5026
71.61760.15150.38121.2767-0.94344.84570.0871-0.240.17650.2256-0.04810.0284-0.0855-0.04230.03180.24310.0167-0.01790.19690.01750.2591-4.7135-4.06229.3509
81.9674-1.2950.04032.0061-1.16034.86760.0274-0.3817-0.4643-0.40780.01470.62520.2665-0.9278-0.01810.3084-0.0249-0.02930.36450.08920.3986-8.4943-15.366126.0498
91.88791.55360.90913.88771.64013.4740.0298-0.3457-0.5870.28330.05050.45970.388-0.3435-0.06770.28040.01520.0010.32930.08740.4431-6.9041-20.753225.3116
103.88223.6681-4.89893.9451-4.6037.61740.1184-0.21870.22340.58630.0356-0.22860.01590.5386-0.16270.33360.0487-0.01520.3286-0.0350.49413.8494-22.425423.5074
113.62061.36012.61612.8308-0.0626.439-0.0602-0.66760.39320.5251-0.05340.1457-0.723-0.44620.04230.53240.18920.11870.5624-0.03180.3348-32.242817.72941.2656
122.45980.2106-0.61151.0214-0.15374.0608-0.0978-0.6321-0.31690.33090.13920.05830.2296-0.1255-0.10450.3410.07220.02160.42450.10420.3109-28.98671.505635.4901
133.26330.3138-0.4017.0605-0.74735.69160.0124-0.38440.1060.38360.2323-0.1455-0.4328-0.1693-0.26680.32510.10520.05140.33660.0050.2533-31.598816.468225.4873
142.9087-1.22410.38762.4880.69573.86180.10390.4194-0.17440.007-0.06790.1440.2160.11840.02510.23540.0402-0.0170.33440.03160.3002-34.9812.7325-5.799
151.3215-0.2370.14691.8334-0.12452.37420.05340.26380.0039-0.2288-0.027-0.1910.05880.2072-0.03730.22250.01190.03730.25610.01010.2793-21.61219.8972-4.6515
166.10190.5862-0.16953.25630.18265.8868-0.0026-0.0294-0.364-0.01110.1520.164-0.022-0.2906-0.11080.2260.0318-0.00380.24250.05940.2493-35.076612.86747.7831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 139 )A0 - 139
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 185 )A140 - 185
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 274 )A186 - 274
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 68 )B0 - 68
5X-RAY DIFFRACTION5chain 'B' and (resid 69 through 101 )B69 - 101
6X-RAY DIFFRACTION6chain 'B' and (resid 102 through 139 )B102 - 139
7X-RAY DIFFRACTION7chain 'B' and (resid 140 through 185 )B140 - 185
8X-RAY DIFFRACTION8chain 'B' and (resid 186 through 212 )B186 - 212
9X-RAY DIFFRACTION9chain 'B' and (resid 213 through 249 )B213 - 249
10X-RAY DIFFRACTION10chain 'B' and (resid 250 through 274 )B250 - 274
11X-RAY DIFFRACTION11chain 'C' and (resid 0 through 82 )C0 - 82
12X-RAY DIFFRACTION12chain 'C' and (resid 83 through 185 )C83 - 185
13X-RAY DIFFRACTION13chain 'C' and (resid 186 through 274 )C186 - 274
14X-RAY DIFFRACTION14chain 'D' and (resid -1 through 60 )D-1 - 60
15X-RAY DIFFRACTION15chain 'D' and (resid 61 through 185 )D61 - 185
16X-RAY DIFFRACTION16chain 'D' and (resid 186 through 274 )D186 - 274

+
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