[English] 日本語
Yorodumi
- PDB-4ph6: Structure of 3-Dehydroquinate Dehydratase from Enterococcus faecalis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ph6
TitleStructure of 3-Dehydroquinate Dehydratase from Enterococcus faecalis
Components3-dehydroquinate dehydratase
KeywordsLYASE / (beta/alpha)8 barrel
Function / homology
Function and homology information


3,4-dihydroxybenzoate biosynthetic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
: / 3-dehydroquinate dehydratase, active site / Dehydroquinase class I active site. / 3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsXue, B. / Cheung, V.W. / Yew, W.S. / Robinson, R.C.
CitationJournal: Plos One / Year: 2014
Title: Identification of Polyketide Inhibitors Targeting 3-Dehydroquinate Dehydratase in the Shikimate Pathway of Enterococcus faecalis
Authors: Cheung, V.W. / Xue, B. / Hernandez-Valladares, M. / Go, M.K. / Tung, A. / Aguda, A.H. / Robinson, R.C. / Yew, W.S.
History
DepositionMay 5, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase


Theoretical massNumber of molelcules
Total (without water)56,7892
Polymers56,7892
Non-polymers00
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-18 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.973, 48.288, 67.429
Angle α, β, γ (deg.)108.070, 92.860, 111.830
Int Tables number1
Space group name H-MP1
Detailsbiological unit is the same as asym.

-
Components

#1: Protein 3-dehydroquinate dehydratase / 3-dehydroquinase / Type I DHQase


Mass: 28394.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: ATCC 700802 / V583 / Gene: aroD, ebsD, EF_1731 / Plasmid: pET-15b, modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36923, 3-dehydroquinate dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES sodium salt, pH 7.5, 30% (w/v) PEG 4000, 0.2 M calcium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.541 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jun 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.2→19.789 Å / Num. all: 21267 / Num. obs: 21267 / % possible obs: 89.23 % / Redundancy: 1.73 % / Biso Wilson estimate: 10.966 Å2 / Rmerge(I) obs: 0.0594 / Net I/σ(I): 9.19
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.2072 / Mean I/σ(I) obs: 3.66 / % possible all: 46.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PROTEUM PLUSdata collection
SAINTdata processing
PROTEUM PLUS3.11data scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
PHASERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3J3S
Resolution: 2.2→19.789 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 1063 5 %Randon selection
Rwork0.1854 20204 --
obs0.1889 21267 89.23 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.94 Å2 / Biso mean: 16.0833 Å2 / Biso min: 1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3746 0 0 311 4057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083804
X-RAY DIFFRACTIONf_angle_d1.0425150
X-RAY DIFFRACTIONf_chiral_restr0.04610
X-RAY DIFFRACTIONf_plane_restr0.004660
X-RAY DIFFRACTIONf_dihedral_angle_d13.8621418
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.30010.2415680.18151416148449
2.3001-2.42110.28161090.18271967207670
2.4211-2.57250.26761550.18382786294199
2.5725-2.77070.2691570.187727982955100
2.7707-3.04860.26921480.174528633011100
3.0486-3.48760.22781430.179228112954100
3.4876-4.38610.23051450.16842791293698
4.3861-19.78970.27561380.22022772291098
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)
11.86910.68940.98910.48930.79621.29230.01320.13250.2555-0.1860.12550.0469-0.1144-0.0004-0.05270.1528-0.0342-0.02390.13630.06320.1408-24.443235.2904-37.137
20.75920.47910.07072.1694-0.0520.5228-0.0603-0.1450.0238-0.14260.1053-0.11060.02370.0367-0.01190.1079-0.03440.0998-0.01490.13520.1367-28.352626.7427-26.8894
31.0908-0.9001-0.04843.40611.2711.5094-0.0155-0.1803-0.19550.0865-0.1270.3860.1739-0.09330.08970.075-0.02360.02230.18910.01370.1378-38.481818.0253-29.744
41.2347-0.1231-0.31210.26130.21291.9307-0.0732-0.2421-0.11580.11920.13120.10230.26580.0272-0.03550.0938-0.01410.00540.08410.02090.1016-29.418717.8398-28.8517
52.696-1.39760.16841.43430.02390.7298-0.01660.2094-0.2315-0.32820.13550.05040.1162-0.2013-0.04730.1417-0.0533-0.03520.1462-0.07760.2639-30.27110.5863-38.9467
61.0368-0.2054-0.39041.7064-0.60420.8401-0.06380.1486-0.1604-0.24090.0930.04720.1754-0.17910.01380.0723-0.02440.01740.0843-0.00860.0639-30.943521.8755-35.4419
71.13410.6357-1.25431.387-0.49671.4231-0.1152-0.2153-0.45870.1098-0.0077-0.15770.4760.12380.05160.35870.08120.01580.08460.10220.0983-17.314512.2292-23.4574
82.3330.88680.58121.7589-0.53060.742-0.04580.1332-0.1401-0.19890.0993-0.21460.04720.1985-0.01210.40420.08560.0710.1968-0.07510.3567-14.99765.681-32.5282
92.0647-1.12910.92741.2256-1.20421.1948-0.00080.2547-0.4726-0.16570.0360.19570.38490.0123-0.06030.14970.00530.0420.0742-0.02040.1518-20.879114.0591-40.2165
101.44380.54950.18581.5921-0.20240.9219-0.07250.1006-0.37190.08280.0797-0.35320.26380.2651-0.01860.16160.0423-0.01490.1096-0.03130.1247-11.253818.1797-36.1498
111.45740.44191.11121.4182-0.91922.0945-0.12840.3471-0.1351-0.20440.0795-0.0212-0.01620.14160.02640.06770.01030.03650.1404-0.00880.0856-17.096323.4059-41.6425
121.0547-0.1979-0.95172.85391.96072.9944-0.1524-0.1683-0.35070.57090.171-0.15010.4773-0.0475-0.0550.13990.0419-0.04410.10140.02840.3035-11.395520.4281-18.5001
132.6295-2.9422-0.22433.4221-0.2441.8837-0.1135-0.24830.11430.20470.0233-0.3321-0.07410.29240.05540.07570.0077-0.0090.20450.04970.0872-3.576929.1888-19.1881
141.20260.13990.19431.20210.40710.9472-0.07580.38650.0773-0.16430.0586-0.11960.0020.1772-0.013-0.58530.00890.09720.1665-0.03040.1142-5.798227.5208-30.8949
150.949-0.20760.42821.36540.17181.8538-0.15740.01890.11330.13630.0465-0.2785-0.17180.09980.09810.06490.01550.00260.09420.00930.138-10.768232.0397-20.7501
162.3044-2.04720.92362.1715-2.39822.0004-0.0577-0.1334-0.20360.1980.1040.00810.3566-0.3346-0.06390.0020.039-0.14220.01540.0923-0.1774-15.441831.4512-26.7011
171.21170.53680.37663.0764-1.28682.072-0.0783-0.043-0.03540.22940.05350.4804-0.2003-0.2530.00560.14060.01450.01810.12710.00120.2115-20.148728.2415-12.088
181.55940.2132-0.17080.0275-0.02081.48010.0831-0.25940.1781-0.0288-0.0508-0.0085-0.12430.0081-0.02180.12880.04360.0144-0.04040.00290.0956-20.457434.89-21.4651
190.0542-0.20520.18150.7113-0.650.5850.0223-0.1082-0.04160.1537-0.06980.2640.0359-0.44460.0370.25840.0109-0.00680.37650.01190.1243-31.877232.766-18.6556
202.68790.11140.56321.88840.11212.5971-0.08770.21590.3158-0.0904-0.04080.0818-0.25840.0410.10510.3108-0.0051-0.0630.12050.00380.3368-26.706243.1172-19.0889
211.8068-1.27-0.211.28810.52110.9399-0.0189-0.1834-0.08730.07180.1795-0.0020.29990.0128-0.08690.17270.0320.02960.10910.00370.0893-24.271240.444512.3515
220.8042-0.2966-0.10221.9240.04090.6898-0.1238-0.03910.03960.10270.03620.0296-0.1228-0.15980.050.09130.0327-0.04330.1060.02460.1197-29.650150.97762.4606
231.35450.53160.29032.15381.1070.56010.04940.14990.0213-0.0569-0.12050.1283-0.0551-0.09180.02290.09910.0432-0.04690.15640.01070.1328-38.242256.12544.9239
240.3633-0.1276-0.11390.1085-0.05650.1632-0.1320.08020.0145-0.14690.2165-0.0244-0.12-0.0102-0.05390.0749-0.0248-0.01670.096-0.01470.0751-30.491951.6883.9682
252.06790.39340.40190.4579-0.53751.0549-0.10420.07730.2967-0.1012-0.03430.1573-0.287-0.11820.06970.15-0.02340.00030.160.01440.2525-27.600167.40244.146
260.39010.227-0.350.1294-0.19810.30770.0910.0010.16630.01220.02140.0641-0.1961-0.1359-0.04730.21220.069-0.03180.2545-0.14320.2816-27.338468.853313.3231
271.30180.98160.76722.926-0.01851.11140.0728-0.2465-0.00690.4023-0.20990.2002-0.1087-0.37970.08520.12130.0020.03950.1950.01440.1088-34.168459.278214.187
280.1356-0.21080.14810.3883-0.09750.5371-0.0692-0.0023-0.0063-0.1345-0.00040.044-0.10280.03740.04440.10160.01630.00720.0396-0.00070.0635-26.201954.38397.8857
29-0.00110.0254-0.00561.09620.57410.51740.01760.08270.47040.1260.0323-0.1624-0.26640.18240.01380.233-0.05040.03170.18310.00060.2149-16.418666.15330.7222
302.5625-0.2363-0.08630.9253-0.36481.4429-0.0292-0.24020.46920.19120.0249-0.0413-0.33780.0780.04310.1991-0.0246-0.00530.1065-0.02380.1189-19.799261.268413.9378
310.6841-0.0078-0.07430.6846-0.18521.338-0.1819-0.09350.0694-0.0584-0.1372-0.323-0.17320.20840.14930.0837-0.05560.02050.1510.00730.1312-8.950658.456711.8836
321.3776-0.2161-1.01610.9332-0.30421.5362-0.1276-0.19780.20520.04410.0007-0.0731-0.04030.04920.0850.0742-0.0255-0.00770.1146-0.01040.0955-16.097152.844712.774
332.1941-1.7209-0.88091.71591.39631.7212-0.07840.08360.4088-0.1547-0.0558-0.1737-0.38810.09780.11530.2926-0.0928-0.01350.2267-0.0010.2037-11.008856.3545-9.6858
342.38271.51240.46681.537-0.69841.7915-0.05270.0561-0.0159-0.1664-0.1083-0.29540.19530.1560.06450.11220.0261-0.00420.1414-0.10570.1101-3.362847.0786-6.3813
350.6864-0.0432-0.31930.5110.02930.8196-0.1553-0.2040.20570.0013-0.0735-0.1002-0.19540.24240.14810.02830.0155-0.02260.1189-0.01240.1068-9.02248.55813.8211
361.4074-0.30860.77951.23720.04371.6149-0.04620.1757-0.0302-0.175-0.0983-0.19880.20420.35820.14350.05820.00420.03150.1169-0.00720.1232-10.17241.7668-4.5103
371.1638-1.41551.03222.0894-1.43711.003-0.0935-0.03260.1011-0.0741-0.03750.2846-0.1746-0.49120.06750.28610.0275-0.05010.0964-0.10220.1319-18.635548.4098-10.3148
382.14931.3318-1.44787.66180.6132.9956-0.0370.53570.0647-0.3585-0.05290.2569-0.0412-0.14260.04470.1038-0.0163-0.01950.1923-0.00460.078-21.762742.714-9.0068
390.9436-0.2327-0.43250.96960.5732.01950.21940.2502-0.1568-0.31380.06130.225-0.0907-0.5635-0.05290.21530.00470.04720.1165-0.00010.0439-25.141142.4619-3.6165
400.8336-0.3284-0.44940.85930.70390.615-0.0695-0.0394-0.31850.0208-0.07680.05190.32240.03980.0910.189-0.00840.02560.21680.09720.1794-28.46134.897-5.6284
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:12)A3 - 12
2X-RAY DIFFRACTION2(chain A and resid 13:26)A13 - 26
3X-RAY DIFFRACTION3(chain A and resid 27:38)A27 - 38
4X-RAY DIFFRACTION4(chain A and resid 39:56)A39 - 56
5X-RAY DIFFRACTION5(chain A and resid 57:67)A57 - 67
6X-RAY DIFFRACTION6(chain A and resid 68:81)A68 - 81
7X-RAY DIFFRACTION7(chain A and resid 82:90)A82 - 90
8X-RAY DIFFRACTION8(chain A and resid 91:96)A91 - 96
9X-RAY DIFFRACTION9(chain A and resid 97:111)A97 - 111
10X-RAY DIFFRACTION10(chain A and resid 112:129)A112 - 129
11X-RAY DIFFRACTION11(chain A and resid 130:140)A130 - 140
12X-RAY DIFFRACTION12(chain A and resid 141:149)A141 - 149
13X-RAY DIFFRACTION13(chain A and resid 150:154)A150 - 154
14X-RAY DIFFRACTION14(chain A and resid 155:165)A155 - 165
15X-RAY DIFFRACTION15(chain A and resid 166:197)A166 - 197
16X-RAY DIFFRACTION16(chain A and resid 198:203)A198 - 203
17X-RAY DIFFRACTION17(chain A and resid 204:211)A204 - 211
18X-RAY DIFFRACTION18(chain A and resid 212:225)A212 - 225
19X-RAY DIFFRACTION19(chain A and resid 226:245)A226 - 245
20X-RAY DIFFRACTION20(chain A and resid 246:251)A246 - 251
21X-RAY DIFFRACTION21(chain B and resid 3:12)B3 - 12
22X-RAY DIFFRACTION22(chain B and resid 13:28)B13 - 28
23X-RAY DIFFRACTION23(chain B and resid 29:38)B29 - 38
24X-RAY DIFFRACTION24(chain B and resid 39:49)B39 - 49
25X-RAY DIFFRACTION25(chain B and resid 50:56)B50 - 56
26X-RAY DIFFRACTION26(chain B and resid 57:61)B57 - 61
27X-RAY DIFFRACTION27(chain B and resid 62:71)B62 - 71
28X-RAY DIFFRACTION28(chain B and resid 72:83)B72 - 83
29X-RAY DIFFRACTION29(chain B and resid 84:94)B84 - 94
30X-RAY DIFFRACTION30(chain B and resid 95:115)B95 - 115
31X-RAY DIFFRACTION31(chain B and resid 116:129)B116 - 129
32X-RAY DIFFRACTION32(chain B and resid 130:143)B130 - 143
33X-RAY DIFFRACTION33(chain B and resid 144:148)B144 - 148
34X-RAY DIFFRACTION34(chain B and resid 149:153)B149 - 153
35X-RAY DIFFRACTION35(chain B and resid 154:174)B154 - 174
36X-RAY DIFFRACTION36(chain B and resid 175:201)B175 - 201
37X-RAY DIFFRACTION37(chain B and resid 202:209)B202 - 209
38X-RAY DIFFRACTION38(chain B and resid 210:215)B210 - 215
39X-RAY DIFFRACTION39(chain B and resid 216:242)B216 - 242
40X-RAY DIFFRACTION40(chain B and resid 243:251)B243 - 251

+
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