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- PDB-4elx: Structure of apo E.coli. 1,4-dihydroxy-2- naphthoyl CoA synthases... -

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Open data


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Basic information

Entry
Database: PDB / ID: 4elx
TitleStructure of apo E.coli. 1,4-dihydroxy-2- naphthoyl CoA synthases with Cl
Components1,4-Dihydroxy-2-naphthoyl-CoA synthase
KeywordsLYASE / Dihydroxynaphthoic acid synthetase
Function / homology
Function and homology information


1,4-dihydroxy-2-naphthoyl-CoA synthase / 1,4-dihydroxy-2-naphthoyl-CoA synthase activity / bicarbonate binding / menaquinone biosynthetic process / cytosol
Similarity search - Function
1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 ...1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / 1,4-dihydroxy-2-naphthoyl-CoA synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.191 Å
AuthorsSun, Y.R. / Song, H.G. / Li, J. / Jiang, M. / Li, Y. / Zhou, J.H. / Guo, Z.H.
CitationJournal: Biochemistry / Year: 2012
Title: Active site binding and catalytic role of bicarbonate in 1,4-dihydroxy-2-naphthoyl coenzyme A synthases from vitamin K biosynthetic pathways
Authors: Sun, Y.R. / Song, H.G. / Li, J. / Jiang, M. / Li, Y. / Zhou, J.H. / Guo, Z.H.
History
DepositionApr 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
B: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
C: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
D: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
E: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
F: 1,4-Dihydroxy-2-naphthoyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,42125
Polymers190,0276
Non-polymers1,39519
Water11,494638
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36230 Å2
ΔGint-201 kcal/mol
Surface area46990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.470, 133.878, 153.929
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
1,4-Dihydroxy-2-naphthoyl-CoA synthase / DHNA-CoA synthase


Mass: 31671.105 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: menB / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABU0, 1,4-dihydroxy-2-naphthoyl-CoA synthase

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Non-polymers , 6 types, 657 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 300mM NaCl, 20% PEG 3350, 100mM Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.19→37.4 Å / Num. obs: 81295 / Biso Wilson estimate: 30.97 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.191→37.389 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8304 / SU ML: 0.25 / σ(F): 1.35 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 4051 5.01 %
Rwork0.1673 76807 -
obs0.1703 80858 98.81 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.254 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso max: 119.12 Å2 / Biso mean: 36.8158 Å2 / Biso min: 8.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.8776 Å2-0 Å20 Å2
2---4.2721 Å2-0 Å2
3---2.3945 Å2
Refinement stepCycle: LAST / Resolution: 2.191→37.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11869 0 82 638 12589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712202
X-RAY DIFFRACTIONf_angle_d1.03216483
X-RAY DIFFRACTIONf_chiral_restr0.071785
X-RAY DIFFRACTIONf_plane_restr0.0042186
X-RAY DIFFRACTIONf_dihedral_angle_d13.9274452
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1913-2.21710.30231050.22412114221981
2.2171-2.24410.27061370.182926522789100
2.2441-2.27250.26881340.183626552789100
2.2725-2.30240.31151510.192614276599
2.3024-2.33390.25741360.17892633276999
2.3339-2.36730.27051360.18022637277399
2.3673-2.40260.28541440.17732629277399
2.4026-2.44010.27111350.17882632276799
2.4401-2.48010.25761550.177226512806100
2.4801-2.52290.2391500.18382611276199
2.5229-2.56880.29851280.1832655278399
2.5688-2.61820.24781410.175626282769100
2.6182-2.67160.27451200.17432661278199
2.6716-2.72970.26091570.17542635279299
2.7297-2.79310.23161240.17912655277999
2.7931-2.8630.2771420.19612648279099
2.863-2.94030.30681310.185826592790100
2.9403-3.02680.26841660.19232624279099
3.0268-3.12450.21981330.17392659279299
3.1245-3.23610.27851510.18712645279699
3.2361-3.36560.251400.171426752815100
3.3656-3.51870.2181470.17292670281799
3.5187-3.7040.1791540.161526642818100
3.704-3.93580.22561260.145727022828100
3.9358-4.23930.16191210.13242713283499
4.2393-4.66520.17161530.12327012854100
4.6652-5.33860.16691460.136127292875100
5.3386-6.71980.22711300.184927862916100
6.7198-37.39410.19641580.18062870302899
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)
10.1761-0.00660.07750.1282-0.00450.3788-0.04460.07350.286-0.12020.0356-0.0627-0.3643-0.0489-0.03210.23970.00550.02970.15690.01850.242849.7596165.955914.5073
20.1999-0.00360.08070.18-0.02190.03030.0745-0.10550.0890.0874-0.02690.04-0.1008-0.09710.00010.2253-0.00020.00930.1934-0.00710.224948.322154.6812.865
30.1094-0.00340.05060.28950.07850.03030.0121-0.0217-0.0542-0.0787-0.0213-0.0678-0.0330.0307-00.10790.01710.01770.1654-0.00820.128550.7216147.303715.2544
40.05150.00450.01810.01160.0120.01890.15260.1329-0.13480.0002-0.07780.0644-0.03930.0145-0.00710.57590.041-0.15140.25110.0040.231824.4062144.2694-12.8335
50.0661-0.0203-0.00070.11-0.16090.2171-0.0698-0.0529-0.10160.10320.07060.0622-0.0372-0.010100.24280.01910.02160.20340.02530.213918.7094117.489444.3845
60.0671-0.0355-0.06130.1522-0.06950.07160.0007-0.1117-0.00840.0914-0.00930.0983-0.0879-0.0274-00.15360.02010.01980.1753-0.00140.13911.872132.724.309
70.0249-0.018-0.01370.0271-0.03990.1895-0.0802-0.0362-0.1429-0.1431-0.01080.03610.1019-0.0518-0.00020.16760.00510.0160.182-0.00950.224926.1782115.026528.1615
80.17490.15430.00760.1555-0.0280.13550.05140.0097-0.140.1964-0.0398-0.10250.05280.03540.05820.7230.28770.00660.21780.01190.536552.5729101.889221.1016
90.0291-0.02790.020.0286-0.00980.0179-0.0266-0.0478-0.05310.02540.056-0.0203-0.00880.02310.01340.21240.20610.04720.3299-0.14990.596667.589109.31026.4959
100.0650.02590.01010.02970.03590.0521-0.04430.1755-0.1213-0.18430.0008-0.18850.01640.1388-0.03320.37060.05780.1070.2586-0.04480.267357.5178119.1564-7.0084
110.0162-0.00570.00330.00680.00690.0116-0.02770.0024-0.269-0.03240.04990.0788-0.02850.069700.25530.0439-0.00420.3165-0.11750.308847.8597117.537-4.7771
120.2407-0.07430.00780.0874-0.07770.1640.06190.1596-0.1972-0.1260.02560.0332-0.0521-0.0310.07970.25140.10190.09430.1417-0.05160.194857.8992120.1377-0.1765
130.08240.00820.02430.04570.02390.0184-0.08380.17180.2398-0.3088-0.11030.0613-0.1426-0.0047-0.0010.30690.0703-0.01970.2603-0.03780.2844.1464126.6905-1.8384
140.03410.0067-0.03280.0260.02660.09060.03020.05020.0353-0.09350.0459-0.0533-0.04120.14230.00640.18560.07050.04980.2073-0.01740.245157.3381129.79093.5921
150.0225-0.0255-0.03750.04980.00960.0475-0.0727-0.0398-0.1841-0.07140.0741-0.06-0.048-0.0328-0.00150.14340.04270.01880.1844-0.02110.214355.6498137.86079.0488
160.00660.0073-0.02550.0104-0.02660.0901-0.0361-0.046-0.09180.00850.0136-0.06320.02580.1119-0.0610.11110.14850.13090.24570.0520.314265.915117.12199.0473
170.0179-0.01160.02620.06070.01090.0841-0.0499-0.0853-0.0373-0.1107-0.0065-0.0094-0.02350.0247-0.01710.09110.08650.03340.13230.02110.18647.4985117.682516.1548
180.01330.0080.00430.01240.01740.02910.1116-0.0295-0.0841-0.06980.10010.05530.25070.013500.26510.0339-0.05790.1425-0.01220.277637.0081113.384515.9527
190.17-0.0344-0.04960.18420.0990.1301-0.0158-0.3423-0.13260.4439-0.0462-0.11520.1610.0769-0.01590.29840.0279-0.08160.30510.06810.197153.4505125.352648.9225
200.21930.09390.0760.37250.04530.5193-0.01-0.1396-0.0620.13290.0021-0.0680.01480.05540.02720.14970.0335-0.02920.18230.01930.145347.6604132.326635.3867
210.08010.0520.00110.05090.02890.03430.01550.2398-0.1272-0.3734-0.04530.16750.1188-0.1541-00.353-0.0145-0.05750.3052-0.0770.285519.6474114.8695-9.0087
220.009-0.00280.01020.0053-0.00390.00880.07790.2488-0.0235-0.0192-0.0633-0.06180.05420.0499-00.2797-0.01070.0120.2834-0.10080.248831.6171115.1637-5.7409
230.1245-0.0150.02360.1236-0.020.07080.08160.2037-0.0695-0.1175-0.0897-0.04380.1290.04160.00050.3179-0.0097-0.05130.2345-0.08750.249420.5119116.7671-3.5727
240.0410.0261-0.00820.03780.02130.0578-0.0343-0.0618-0.0575-0.02960.08830.03570.2212-0.05810.00120.24920.0066-0.02850.1872-0.06620.200526.1884117.27744.2583
250.0743-0.0219-0.08550.00660.02790.09750.00940.1329-0.07070.0398-0.0853-0.05530.075-0.1878-0.00880.1717-0.0703-0.03870.2069-0.01030.221416.2843116.30778.8849
260.02340.03680.03250.0410.02230.0794-0.00270.1261-0.13590.027-0.0928-0.03370.07480.0633-0.00040.18520.0205-0.02790.2604-0.03370.198718.4964119.455116.1104
270.1021-0.0068-0.11590.07070.0150.0967-0.0038-0.0774-0.0421-0.1606-0.03140.0138-0.1198-0.11790.00020.22420.0097-0.0550.1817-0.02960.178119.6728130.0654-2.1286
280.0005-0.00880.00110.0074-0.00410.0080.08190.141-0.0792-0.1505-0.06880.01740.0076-0.010400.29260.0561-0.01760.2064-0.02430.180438.281140.542-1.624
290.07610.1197-0.01830.2499-0.14910.23170.03010.09580.1039-0.12710.1131-0.0516-0.04710.07020.18190.7549-0.06210.28020.3860.07070.445448.064150.5727-9.2943
300.36690.0581-0.03590.05010.00470.28730.02010.00530.42930.04360.04170.2914-0.3625-0.09510.05790.23510.3302-0.0896-0.17350.070.275914.4694160.497717.0184
310.05680.04210.05050.0984-0.00430.0665-0.06450.13180.0597-0.11060.0279-0.0152-0.1524-0.0239-0.00130.20980.0604-0.04250.2432-00.243819.7011148.733410.2757
320.2379-0.1239-0.2320.5675-0.06310.23560.0166-0.0538-0.01530.14750.00750.067-0.0401-0.04350.04290.17370.0639-0.00940.1835-0.02820.151522.9015144.986725.2941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:65 )A4 - 65
2X-RAY DIFFRACTION2( CHAIN A AND RESID 122:122 )A122
3X-RAY DIFFRACTION3( CHAIN A AND RESID 169:258 )A169 - 258
4X-RAY DIFFRACTION4( CHAIN A AND RESID 259:285 )A259 - 285
5X-RAY DIFFRACTION5( CHAIN B AND RESID 5:86 )B5 - 86
6X-RAY DIFFRACTION6( CHAIN B AND RESID 198:198 )B198
7X-RAY DIFFRACTION7( CHAIN B AND RESID 207:259 )B207 - 259
8X-RAY DIFFRACTION8( CHAIN B AND RESID 260:285 )B260 - 285
9X-RAY DIFFRACTION9( CHAIN C AND RESID 4:17 )C4 - 17
10X-RAY DIFFRACTION10( CHAIN C AND RESID 18:49 )C18 - 49
11X-RAY DIFFRACTION11( CHAIN C AND RESID 50:65 )C50 - 65
12X-RAY DIFFRACTION12( CHAIN C AND RESID 66:86 )C66 - 86
13X-RAY DIFFRACTION13( CHAIN C AND RESID 87:117 )C87 - 117
14X-RAY DIFFRACTION14( CHAIN C AND RESID 118:159 )C118 - 159
15X-RAY DIFFRACTION15( CHAIN C AND RESID 160:206 )C160 - 206
16X-RAY DIFFRACTION16( CHAIN C AND RESID 207:222 )C207 - 222
17X-RAY DIFFRACTION17( CHAIN C AND RESID 223:241 )C223 - 241
18X-RAY DIFFRACTION18( CHAIN C AND RESID 242:260 )C242 - 260
19X-RAY DIFFRACTION19( CHAIN D AND RESID 4:65 )D4 - 65
20X-RAY DIFFRACTION20( CHAIN D AND RESID 66:285 )D66 - 285
21X-RAY DIFFRACTION21( CHAIN E AND RESID 5:49 )E5 - 49
22X-RAY DIFFRACTION22( CHAIN E AND RESID 50:65 )E50 - 65
23X-RAY DIFFRACTION23( CHAIN E AND RESID 66:86 )E66 - 86
24X-RAY DIFFRACTION24( CHAIN E AND RESID 87:140 )E87 - 140
25X-RAY DIFFRACTION25( CHAIN E AND RESID 141:158 )E141 - 158
26X-RAY DIFFRACTION26( CHAIN E AND RESID 159:206 )E159 - 206
27X-RAY DIFFRACTION27( CHAIN E AND RESID 207:241 )E207 - 241
28X-RAY DIFFRACTION28( CHAIN E AND RESID 253:253 )E253
29X-RAY DIFFRACTION29( CHAIN E AND RESID 260:285 )E260 - 285
30X-RAY DIFFRACTION30( CHAIN F AND RESID 4:86 )F4 - 86
31X-RAY DIFFRACTION31( CHAIN F AND RESID 87:168 )F87 - 168
32X-RAY DIFFRACTION32( CHAIN F AND RESID 169:285 )F169 - 285

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