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- PDB-4elw: Structure of E. coli. 1,4-dihydroxy-2- naphthoyl coenzyme A synth... -

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Basic information

Entry
Database: PDB / ID: 4elw
TitleStructure of E. coli. 1,4-dihydroxy-2- naphthoyl coenzyme A synthases (MENB) in complex with nitrate
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
NITRATE ION / SUCCINIC ACID / 1,4-dihydroxy-2-naphthoyl-CoA synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.551 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)191,16321
Polymers190,0276
Non-polymers1,13615
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35900 Å2
ΔGint-137 kcal/mol
Surface area48620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.503, 133.874, 153.407
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 , 5 types, 225 molecules

#2: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 40.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2% Tacsimate, 100mM Tris buffer, 20% PEG 3350, pH 8.0, 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: 2.55→42.85 Å / Num. obs: 51971 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 44.16 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.551→42.849 Å / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.8167 / SU ML: 0.35 / σ(F): 1.33 / Phase error: 24.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 2637 5.11 %Random
Rwork0.1725 ---
obs0.1755 51645 99.26 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.702 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 112.44 Å2 / Biso mean: 50.6134 Å2 / Biso min: 26.47 Å2
Baniso -1Baniso -2Baniso -3
1-17.4515 Å2-0 Å2-0 Å2
2---5.5144 Å20 Å2
3----11.9371 Å2
Refinement stepCycle: LAST / Resolution: 2.551→42.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12033 0 73 210 12316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812331
X-RAY DIFFRACTIONf_angle_d1.08816618
X-RAY DIFFRACTIONf_chiral_restr0.0721780
X-RAY DIFFRACTIONf_plane_restr0.0052205
X-RAY DIFFRACTIONf_dihedral_angle_d14.5974574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5513-2.59770.36471380.262477261598
2.5977-2.64770.3191180.24942575269399
2.6477-2.70170.32991270.22762522264999
2.7017-2.76040.33851240.22332567269199
2.7604-2.82470.28831320.22442559269199
2.8247-2.89530.27021300.20922538266899
2.8953-2.97350.31781500.201325482698100
2.9735-3.0610.28231420.19322574271699
3.061-3.15980.26641500.18932528267899
3.1598-3.27270.22731250.193925892714100
3.2727-3.40370.25121360.18382567270399
3.4037-3.55850.26131400.181325872727100
3.5585-3.7460.22041440.157825792723100
3.746-3.98050.17541640.14262553271799
3.9805-4.28760.18341370.127626142751100
4.2876-4.71860.1971440.12922593273799
4.7186-5.40030.22651400.14522616275699
5.4003-6.79940.20251390.183326712810100
6.7994-42.85460.20031570.17162751290899
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)
11.604-0.52090.05992.29550.56020.80380.1230.09170.3563-0.15570.0499-0.096-0.5196-0.0543-0.00010.3917-0.00290.0310.31850.04190.37250.391131.252414.9527
20.66760.0040.18320.4854-0.35110.68070.0209-0.044-0.00770.0383-0.03510.0123-0.0717-0.024800.27540.00930.01690.3048-0.01650.336949.537416.055718.5899
30.77690.45420.11070.3125-0.12140.5160.46820.1328-0.1032-0.1202-0.3064-0.2096-0.22470.4979-00.85130.0467-0.13050.54230.01970.469923.885910.6153-13.0528
40.2967-0.08770.09540.8716-0.55571.5791-0.0261-0.1512-0.13120.21220.0065-0.02180.0072-0.011400.3425-0.00490.00540.36510.0110.400818.5495-16.450144.4358
5-0.12380.1396-0.010.7707-0.4020.53420.03620.00220.0264-0.0627-0.0237-0.05620.0452-0.0021-00.33470.0180.00520.3429-0.0210.339625.3225-11.590330.0976
60.2180.1431-0.20740.1531-0.1290.17590.22490.4146-0.40850.13150.2963-0.0985-0.25430.19380.00060.67320.14380.04850.6886-0.00470.746567.4435-24.74826.042
70.2858-0.1961-0.17170.18670.14060.10570.03240.532-0.6529-0.63870.033-0.22460.32150.0986-0.00060.7722-0.03040.14470.5822-0.05580.458156.0741-19.8651-8.4884
80.81160.26440.39770.78511.1231.5721-0.11340.2174-0.1184-0.51240.07040.06290.0042-0.05710.00010.53590.05370.04770.4662-0.04670.501954.2426-13.0859-4.1114
9-0.44230.1123-0.32660.93270.34360.125-0.0051-0.02020.059-0.2684-0.05480.0486-0.06960.0153-00.38090.05140.03660.43390.00080.465752.7334-1.32625.1688
100.4115-0.3666-0.47240.74830.42911.0813-0.1391-0.14470.0492-0.09310.0929-0.2250.17450.098100.28250.06070.01410.3363-0.00720.405960.0943-10.406411.3077
110.6967-0.45770.17190.2683-0.06940.26640.26430.1974-0.08260.7764-0.3905-0.32840.4416-0.0662-0.00040.62930.0199-0.01990.5364-0.02260.461537.3293-19.11716.3851
120.9271-0.38350.31580.17940.00220.5280.1798-0.2949-0.19830.9157-0.1659-0.27770.01220.30810.00010.73090.025-0.13310.50070.0020.408656.8246-2.887552.2137
130.7270.735-0.26821.2483-1.0771.44650.1026-0.216-0.09360.2679-0.1101-0.0720.3502-0.100300.57150.0281-0.03440.51080.02680.402450.6183-10.520943.1299
14-0.15040.16740.16860.66160.44411.23950.0443-0.1149-0.16130.21790.0321-0.09810.06560.0433-0.00010.35320.0527-0.01510.4309-0.00230.357857.7084-6.828330.2134
150.40960.0813-0.02560.5571-0.08610.3395-0.0049-0.15190.01840.0857-0.03610.10220.08020.0058-0.00010.47780.0131-0.02490.3698-0.03290.402138.02636.09236.2808
160.55820.22870.36420.22940.32130.40790.4032-0.28450.34670.3985-0.3358-0.2313-0.16290.00790.00010.91260.21460.00470.862-0.07770.516219.923718.554444.5401
171.1637-0.4467-0.48311.23360.08271.33110.1120.2646-0.1818-0.573-0.09120.00130.25280.029-0.00010.4524-0.0533-0.04950.3564-0.060.370922.3069-18.6726-8.2232
181.554-0.5295-0.00120.44560.4581.4394-0.016-0.0349-0.1005-0.1530.0356-0.01880.3251-0.0462-0.00010.3817-0.0285-0.00740.3557-0.03140.385622.6754-17.30193.6034
19-0.45620.1792-0.53140.6480.15691.745-0.0373-0.04880.04530.0152-0.0254-0.02520.0144-0.1850.00010.31660.017-0.04370.38140.00970.384418.7604-9.44648.1708
200.4729-0.369-0.51950.4577-0.09250.49410.30580.1389-0.0329-0.4788-0.16960.0655-0.81610.1248-0.00010.845-0.03010.02270.43490.00470.429542.344211.369-4.4727
212.06560.3040.06831.6079-0.64821.2285-0.11920.08270.3860.03130.11710.0625-0.4592-0.185600.57260.1366-0.03990.3881-0.00440.510614.696326.632116.4438
220.11580.1537-0.17210.5650.13490.87480.00460.0113-0.03880.070.01360.0691-0.1570.017800.38380.0493-0.01240.382-0.00010.354821.812.1621.0661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:86 )A4 - 86
2X-RAY DIFFRACTION2( CHAIN A AND RESID 87:259 )A87 - 259
3X-RAY DIFFRACTION3( CHAIN A AND RESID 260:285 )A260 - 285
4X-RAY DIFFRACTION4( CHAIN B AND RESID 5:86 )B5 - 86
5X-RAY DIFFRACTION5( CHAIN B AND RESID 87:285 )B87 - 285
6X-RAY DIFFRACTION6( CHAIN C AND RESID 5:17 )C5 - 17
7X-RAY DIFFRACTION7( CHAIN C AND RESID 18:30 )C18 - 30
8X-RAY DIFFRACTION8( CHAIN C AND RESID 31:107 )C31 - 107
9X-RAY DIFFRACTION9( CHAIN C AND RESID 108:186 )C108 - 186
10X-RAY DIFFRACTION10( CHAIN C AND RESID 187:238 )C187 - 238
11X-RAY DIFFRACTION11( CHAIN C AND RESID 239:261 )C239 - 261
12X-RAY DIFFRACTION12( CHAIN D AND RESID 4:30 )D4 - 30
13X-RAY DIFFRACTION13( CHAIN D AND RESID 31:128 )D31 - 128
14X-RAY DIFFRACTION14( CHAIN D AND RESID 129:222 )D129 - 222
15X-RAY DIFFRACTION15( CHAIN D AND RESID 223:258 )D223 - 258
16X-RAY DIFFRACTION16( CHAIN D AND RESID 259:285 )D259 - 285
17X-RAY DIFFRACTION17( CHAIN E AND RESID 5:65 )E5 - 65
18X-RAY DIFFRACTION18( CHAIN E AND RESID 66:159 )E66 - 159
19X-RAY DIFFRACTION19( CHAIN E AND RESID 160:241 )E160 - 241
20X-RAY DIFFRACTION20( CHAIN E AND RESID 242:285 )E242 - 285
21X-RAY DIFFRACTION21( CHAIN F AND RESID 4:107 )F4 - 107
22X-RAY DIFFRACTION22( CHAIN F AND RESID 108:285 )F108 - 285

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