[English] 日本語
Yorodumi
- PDB-3und: Substrate-bound crystal structure of 2-dehydro-3-deoxyphosphoocto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3und
TitleSubstrate-bound crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia pseudomallei
Components2-dehydro-3-deoxyphosphooctonate aldolase 2
KeywordsTRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
ARABINOSE-5-PHOSPHATE / 3-deoxy-8-O-phosphono-D-manno-oct-2-ulosonic acid / PHOSPHOENOLPYRUVATE / 2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionNov 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Sep 13, 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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)125,24923
Polymers121,9414
Non-polymers3,30819
Water12,538696
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20140 Å2
ΔGint-66 kcal/mol
Surface area33560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.840, 146.240, 178.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

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


Mass: 30485.184 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: kdsA, kdsA2, BURPS1710b_3264 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q3JP68, 3-deoxy-8-phosphooctulonate synthase

-
Non-polymers , 5 types, 715 molecules

#2: Chemical
ChemComp-A5P / ARABINOSE-5-PHOSPHATE


Mass: 232.126 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H13O8P
#3: Chemical
ChemComp-PEP / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvic acid


Mass: 168.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5O6P
#4: Chemical
ChemComp-KD0 / 3-deoxy-8-O-phosphono-D-manno-oct-2-ulosonic acid


Mass: 318.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15O11P
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 696 / 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: 2.32 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: EBS internal tracking number 227318B6, from a focus screen based on PACT F12. 0.2 M malonate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG3350. BupsA.00102.a.A1 PS00621 at 30.3 mg/mL, 10 mM D- ...Details: EBS internal tracking number 227318B6, from a focus screen based on PACT F12. 0.2 M malonate, 0.1 M Bis-Tris propane pH 6.5, 20% PEG3350. BupsA.00102.a.A1 PS00621 at 30.3 mg/mL, 10 mM D-arabinose-5-phosphate, 10 mM phosphoenolpyruvate, vapor diffusion, sitting drop, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 71084 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 27.104 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.154.80.3764.423987501494.2
2.15-2.210.3035.826956497196.1
2.21-2.280.276.626821484896.4
2.28-2.350.2586.726381479796.6
2.35-2.420.2327.525723461097.9
2.42-2.510.1968.825291450397.3
2.51-2.60.16710.324605437297.4
2.6-2.710.14511.923841420698.4
2.71-2.830.13212.822769400797.9
2.83-2.970.10316.222122385497.3
2.97-3.130.08718.921133369897.4
3.13-3.320.06724.420153351598.5
3.32-3.550.04833.918998330898.5
3.55-3.830.0394117744308498
3.83-4.20.03446.816202285298.1
4.2-4.70.0352.314778260097.4
4.7-5.420.0324813142232899.1
5.42-6.640.04334.911099200699.3
6.64-9.390.02851.58546158398.9
9.390.01868.2459392896

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.03 Å
Translation2.5 Å47.03 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementMethod to determine structure: molecular replacement
Starting model: PDB ENTRY 3tmq

3tmq


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.114 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.192 3581 5 %RANDOM
Rwork0.167 ---
obs0.168 71015 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.112 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2---1.79 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8444 0 204 696 9344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198877
X-RAY DIFFRACTIONr_bond_other_d0.0060.026028
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.99912043
X-RAY DIFFRACTIONr_angle_other_deg1.233314745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07251154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59823.75352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.189151442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4611564
X-RAY DIFFRACTIONr_chiral_restr0.090.21390
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219882
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021719
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 250 -
Rwork0.22 4462 -
all-4712 -
obs--93.68 %
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)
14.64781.2932-2.84924.6681.15793.38630.0765-0.0374-0.41360.6319-0.032-0.20080.3081-0.0778-0.04460.16160.022-0.06450.15670.06830.1959-1.576-22.4061.431
20.555-0.539-0.33861.44110.6461.22330.0189-0.1986-0.12140.1271-0.02170.2260.2215-0.03930.00280.0802-0.05450.01860.1310.04360.2007-16.338-18.123-0.465
30.4548-0.38180.30064.9827-2.27912.3911-0.0017-0.1809-0.08880.27140.00410.41550.0623-0.1716-0.00250.0468-0.0470.06110.19790.00560.1858-18.855-4.5076.326
41.26230.363-0.08831.7144-0.21270.66020.0531-0.1653-0.0610.0821-0.0425-0.05760.09530.0665-0.01070.0397-0.004-0.01040.12970.00510.128-2.817-5.4551.197
50.5908-0.58340.65871.4058-1.03431.3118-0.0332-0.11810.0201-0.1443-0.0161-0.09970.0815-0.07180.04930.06220.0027-0.00840.1176-0.00380.1616-3.241-5.884-10.605
63.8971-1.10450.92910.89-0.56140.5528-0.00450.004-0.0999-0.0464-0.01340.01670.02930.01710.01790.08120.0019-0.01590.0969-0.00650.16-4.173-10.167-12.175
71.10690.1520.03472.18650.0771.02650.0096-0.0176-0.1104-0.1178-0.02120.32180.1336-0.14270.01160.0562-0.0578-0.04050.10220.01690.1718-17.895-13.769-12.569
80.5385-0.10970.3281.22270.07461.25760.00320.062-0.096-0.50040.0140.05660.33210.0212-0.01720.4750.0128-0.04850.0195-0.03980.1197-3.028-23.178-42.662
90.22470.449-0.23552.8946-0.49020.61350.02080.0274-0.0487-0.462-0.0733-0.03130.11530.00780.05250.40820.05420.03360.0273-0.03740.09473.144-14.833-45.043
100.85222.69871.317610.65582.35463.70910.00330.0251-0.0848-0.625-0.0249-0.35530.27460.08920.02160.65030.1076-0.02180.0544-0.07490.16571.769-23.024-53.892
110.716-0.08150.10290.8962-0.01240.7860.0637-0.0002-0.0165-0.4073-0.05380.11240.0629-0.047-0.00990.31350.0209-0.08080.0095-0.01590.0964-10.194-7.166-42.408
123.76620.18920.47210.4737-0.18450.55680.1181-0.1004-0.0786-0.3418-0.02970.07910.10550.0233-0.08840.27490.0118-0.05430.0285-0.03550.1117-7.003-9.129-32
134.76730.101-4.199311.9948-2.86374.37190.1073-0.20220.08290.1732-0.00430.1063-0.05460.2301-0.1030.22360.0624-0.00910.1186-0.04810.12878.897-9.065-29.735
141.5389-0.2329-0.71340.9544-0.19281.680.017-0.0934-0.1178-0.3117-0.0301-0.02250.18360.12850.01310.27060.0359-0.02170.0176-0.0190.13791.551-20.555-31.446
153.6732-1.6328-4.36434.228-1.57068.728-0.1550.03220.12630.40780.1917-0.1133-0.1242-0.3079-0.03660.1015-0.03060.07970.22-0.11930.2168-9.73132.421-2.483
161.5522-0.5840.68511.7701-0.26060.9612-0.0044-0.07010.13780.0559-0.0176-0.127-0.18340.11020.0220.0566-0.03010.01970.1176-0.06940.15885.53529.82-4.607
170.6592-0.0520.11022.68020.55950.69680.0229-0.1691-0.00310.2811-0.0271-0.1761-0.02250.0610.00410.0449-0.034-0.0170.1642-0.04580.14036.54618.0714.377
180.71710.59680.18022.15670.43341.3290.0182-0.09250.08380.0778-0.04710.14-0.0414-0.08120.02890.00550.00270.00630.1355-0.04380.151-9.33415.159-1.293
190.9701-0.4794-1.14921.85161.46123.8822-0.0841-0.10190.0720.00880.05150.20230.10150.00970.03260.01340.00160.01530.1146-0.02190.1762-9.39717.454-7.82
201.20260.29-0.6651.63910.36750.55730.0055-0.07170.0661-0.15960.0361-0.0132-0.04690.0241-0.04160.0594-0.002-0.01330.1187-0.03440.1192-4.60516.268-16.121
211.0829-0.0383-0.00551.4134-0.07410.76140.038-0.01730.09-0.1903-0.0234-0.1811-0.06380.1302-0.01460.0766-0.02980.03240.1089-0.05560.15457.61522.74-15.327
220.5107-0.11410.00811.04190.14040.93630.02710.0820.0677-0.5402-0.01620.077-0.2142-0.0732-0.01090.45370.0576-0.05480.03350.01790.059-10.0922.792-47.925
234.58471.86523.21118.7629-3.48748.92020.00180.56170.448-0.70730.27860.6239-0.04340.038-0.28040.70020.1056-0.0760.13820.05720.1185-11.15628.059-56.863
240.9288-0.0490.10170.6808-0.13590.9540.07740.04210.006-0.3666-0.0413-0.0964-0.06770.0007-0.03610.41240.03960.02540.0082-0.00350.04260.01111.308-47.378
250.8809-0.0291-0.90571.17330.13251.72660.11960.0445-0.0197-0.3341-0.0329-0.0404-0.1125-0.0739-0.08670.24180.02290.00990.0459-0.0120.1080.49511.855-37.028
265.13440.9582-0.7291.3425-0.25980.4382-0.0104-0.08050.0003-0.37050.0426-0.0209-0.0026-0.0603-0.03220.23790.02980.00990.0416-0.01190.0444-3.11514.901-33.851
272.5529-2.43631.95152.6311-1.40832.1693-0.03210.0755-0.21390.1377-0.04090.36650.12450.0820.07290.22690.0183-0.03940.134-0.00160.2031-18.85414.399-32.662
281.5223-0.05740.40341.32360.47321.8928-0.0172-0.07940.1465-0.3597-0.05640.0965-0.1952-0.0990.07360.27450.0604-0.03580.02140.00320.122-11.59726.262-35.1
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 11
2X-RAY DIFFRACTION2A12 - 57
3X-RAY DIFFRACTION3A58 - 85
4X-RAY DIFFRACTION4A86 - 153
5X-RAY DIFFRACTION5A154 - 181
6X-RAY DIFFRACTION6A182 - 205
7X-RAY DIFFRACTION7A206 - 279
8X-RAY DIFFRACTION8B1 - 42
9X-RAY DIFFRACTION9B43 - 73
10X-RAY DIFFRACTION10B74 - 88
11X-RAY DIFFRACTION11B89 - 181
12X-RAY DIFFRACTION12B182 - 209
13X-RAY DIFFRACTION13B210 - 217
14X-RAY DIFFRACTION14B218 - 279
15X-RAY DIFFRACTION15C1 - 7
16X-RAY DIFFRACTION16C8 - 55
17X-RAY DIFFRACTION17C56 - 96
18X-RAY DIFFRACTION18C97 - 154
19X-RAY DIFFRACTION19C155 - 171
20X-RAY DIFFRACTION20C172 - 206
21X-RAY DIFFRACTION21C207 - 279
22X-RAY DIFFRACTION22D1 - 77
23X-RAY DIFFRACTION23D78 - 87
24X-RAY DIFFRACTION24D88 - 150
25X-RAY DIFFRACTION25D151 - 181
26X-RAY DIFFRACTION26D182 - 209
27X-RAY DIFFRACTION27D210 - 217
28X-RAY DIFFRACTION28D218 - 279

+
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