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- PDB-5u95: Structure of the open conformation of 4-coumarate-CoA ligase from... -

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Basic information

Entry
Database: PDB / ID: 5u95
TitleStructure of the open conformation of 4-coumarate-CoA ligase from Nicotiana tabacum
Components4-coumarate--CoA ligase 2
KeywordsLIGASE / Lignin biosynthesis
Function / homology
Function and homology information


trans-feruloyl-CoA synthase / trans-feruloyl-CoA synthase activity / (E)-caffeate-CoA ligase activity / trans-cinnamate-CoA ligase activity / 4-coumarate-CoA ligase activity / 4-coumarate-CoA ligase / phenylpropanoid metabolic process / CoA-ligase activity / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / response to jasmonic acid ...trans-feruloyl-CoA synthase / trans-feruloyl-CoA synthase activity / (E)-caffeate-CoA ligase activity / trans-cinnamate-CoA ligase activity / 4-coumarate-CoA ligase activity / 4-coumarate-CoA ligase / phenylpropanoid metabolic process / CoA-ligase activity / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / response to jasmonic acid / response to wounding / ATP binding
Similarity search - Function
Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. ...Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
4-coumarate--CoA ligase 2
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMorioka, W.P. / Bianchetti, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
University of Wisconsin Oshkosh The Oshkosh Student Scholarship and Creative Activity Program United States
CitationJournal: To Be Published
Title: Structure of the open conformation of 4-coumarate-CoA ligase from Nicotiana tabacum
Authors: Morioka, W.P. / Bianchetti, C.M.
History
DepositionDec 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-coumarate--CoA ligase 2
B: 4-coumarate--CoA ligase 2
C: 4-coumarate--CoA ligase 2
D: 4-coumarate--CoA ligase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,1039
Polymers237,9024
Non-polymers2005
Water7,296405
1
A: 4-coumarate--CoA ligase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5563
Polymers59,4761
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 4-coumarate--CoA ligase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5162
Polymers59,4761
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 4-coumarate--CoA ligase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5162
Polymers59,4761
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 4-coumarate--CoA ligase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5162
Polymers59,4761
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.259, 108.259, 183.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
4-coumarate--CoA ligase 2 / 4CL 2 / 4-coumaroyl-CoA synthase 2


Mass: 59475.535 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: 4CL2 / Plasmid: pVP-67K / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O24146, 4-coumarate-CoA ligase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM HEPES pH 7.0, 25% PEG 6000, 200 mM CaCl2 and 15% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2016
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 99637 / % possible obs: 100 % / Redundancy: 7.6 % / Rsym value: 0.141 / Net I/σ(I): 13.64
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.14 / CC1/2: 0.58 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BSR

5bsr


Resolution: 2.25→48.415 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2598 1936 1.98 %
Rwork0.1929 --
obs0.1943 97856 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→48.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15208 0 5 405 15618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01215549
X-RAY DIFFRACTIONf_angle_d1.18821080
X-RAY DIFFRACTIONf_dihedral_angle_d15.6389481
X-RAY DIFFRACTIONf_chiral_restr0.0642451
X-RAY DIFFRACTIONf_plane_restr0.0082713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2503-2.30660.36741260.29266392X-RAY DIFFRACTION92
2.3066-2.3690.33561360.26376572X-RAY DIFFRACTION95
2.369-2.43870.32111290.24826695X-RAY DIFFRACTION96
2.4387-2.51740.29091350.23536767X-RAY DIFFRACTION97
2.5174-2.60730.3331370.22546813X-RAY DIFFRACTION98
2.6073-2.71170.28811390.22276915X-RAY DIFFRACTION99
2.7117-2.83510.29431420.22356940X-RAY DIFFRACTION99
2.8351-2.98460.29021420.21516900X-RAY DIFFRACTION100
2.9846-3.17150.26551390.21046947X-RAY DIFFRACTION100
3.1715-3.41640.26151460.19956965X-RAY DIFFRACTION100
3.4164-3.76010.25391430.17666967X-RAY DIFFRACTION100
3.7601-4.30380.21221380.16056988X-RAY DIFFRACTION100
4.3038-5.42120.23351430.15357010X-RAY DIFFRACTION100
5.4212-48.42610.22461410.17627049X-RAY DIFFRACTION100
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)
12.27571.4782-0.82415.4902-0.01670.53830.05460.2032-0.1020.20010.1003-0.3362-0.0446-0.0071-0.18850.22660.00690.05250.2075-0.04530.233942.688340.7532-17.9073
21.87230.28450.07492.76220.19281.3127-0.0992-0.0646-0.20110.5001-0.00850.55710.2214-0.27630.08580.4663-0.05970.15460.2138-0.00180.371923.943325.6468-3.9902
30.70750.873-0.50532.9097-0.30391.283-0.0950.0035-0.18530.3720.00420.13330.1226-0.09190.06660.32380.00770.08970.1742-0.00890.299431.270830.1128-7.4065
40.70550.54280.07742.19111.0813.564-0.0923-0.10440.06290.79240.06530.0620.5578-0.42470.00290.584-0.03560.03510.24170.00570.257133.561237.32965.6844
54.7126-0.90710.13233.98560.16134.12520.0676-0.120.20030.9753-0.16250.3806-0.2378-0.02440.05870.5233-0.01550.04850.2249-0.02080.366534.337647.886110.3958
60.52760.711-0.12611.6057-0.43222.1655-0.0065-0.16510.19190.3193-0.0724-0.0699-0.3448-0.07370.06030.470.0511-0.00270.2417-0.01650.332738.862652.2994-1.7774
72.0010.6574-0.92833.6110.7311.58530.06040.37830.3802-0.250.15440.2247-0.2005-0.117-0.19220.33090.07860.02480.22760.07850.24130.99352.931-19.9549
83.4337-1.03830.23071.5819-0.17391.3685-0.04520.385-0.0498-0.3080.01990.2494-0.0424-0.20210.02750.3442-0.125-0.07460.3644-0.01120.299326.070427.2245-52.649
92.3028-0.81620.77611.46010.36073.0937-0.16960.1974-0.0008-0.1440.09680.0356-0.10890.29590.09380.2809-0.10520.05410.3206-0.01350.298740.935621.5487-43.4773
102.5193-0.12910.02981.0562-0.71391.2141-0.06470.84360.1006-0.3193-0.0424-0.2564-0.03010.19010.10730.4247-0.05410.08270.6199-0.03610.342552.939421.9626-57.946
112.7082-1.288-1.7585.13080.91753.5046-0.42010.7526-0.4708-0.8705-0.5322-0.45511.0612-0.82870.73310.6431-0.09550.24570.6225-0.12960.715154.84946.6805-74.3836
122.9920.9866-0.08691.70560.10050.81430.0476-0.2426-0.12510.2557-0.09480.23750.1382-0.05430.04840.34750.09630.04860.39950.01140.2727-26.972926.776-53.8843
132.76691.94450.2882.39830.15862.99140.226-0.746-0.06290.4567-0.2833-0.06490.118-0.27330.07670.41650.07760.04120.4311-0.03130.3041-25.149630.2497-46.8458
141.84740.5406-1.59481.79860.79422.2132-0.1634-0.1116-0.02850.14470.0603-0.09470.09980.27830.09880.28640.0587-0.05190.3650.02350.2374-12.595233.7812-66.4674
152.71840.68970.63521.6281-0.12160.45320.1298-0.7411-0.14350.492-0.1276-0.2257-0.09630.1041-0.00020.42490.0493-0.06410.5857-0.03090.345-2.973934.9525-47.7651
160.9792.3778-1.04856.2749-1.56350.8964-0.03940.1752-0.33880.1099-0.1529-0.74070.0562-0.05370.2350.42910.042-0.18390.5122-0.09830.58491.281918.1227-41.2318
175.25640.41792.58168.96241.1487.5001-0.004-0.64250.11131.1234-0.6913-0.72630.1473-0.78040.58190.42260.0292-0.11920.4936-0.08140.5690.64072.0925-30.7151
181.06471.20440.70071.59370.31011.5466-0.3447-0.11340.261.0207-0.5496-0.8617-0.8871-0.03840.6330.8451-0.1108-0.42820.4761-0.01490.88884.375510.0626-32.2037
191.1841-0.8414-0.1433.0320.21310.82010.07540.0169-0.0703-0.3372-0.0128-0.30750.07030.1894-0.0540.33640.02630.09150.20110.01040.28225.8147-25.6609-7.8741
202.3739-1.4544-1.06733.47221.03162.6358-0.0275-0.08370.0104-0.09440.1262-0.48240.04110.309-0.09010.30230.01040.06060.18930.02960.319628.1952-27.0319-4.2216
211.2091-0.0094-0.55092.1512-0.49770.62360.1490.05220.2618-0.1427-0.0355-0.0702-0.13040.1145-0.08850.40830.02420.08130.2155-0.00740.326420.9069-5.6471-8.622
222.19-1.5968-1.76292.05641.04912.049-0.2419-0.57780.85780.13580.5148-0.45750.36820.0835-0.25990.85120.26770.13650.76530.01080.753448.12961.351311.9728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 151 )
3X-RAY DIFFRACTION3chain 'A' and (resid 152 through 237 )
4X-RAY DIFFRACTION4chain 'A' and (resid 238 through 273 )
5X-RAY DIFFRACTION5chain 'A' and (resid 274 through 313 )
6X-RAY DIFFRACTION6chain 'A' and (resid 314 through 363 )
7X-RAY DIFFRACTION7chain 'A' and (resid 364 through 437 )
8X-RAY DIFFRACTION8chain 'B' and (resid 9 through 187 )
9X-RAY DIFFRACTION9chain 'B' and (resid 188 through 313 )
10X-RAY DIFFRACTION10chain 'B' and (resid 314 through 448 )
11X-RAY DIFFRACTION11chain 'B' and (resid 449 through 538 )
12X-RAY DIFFRACTION12chain 'C' and (resid 9 through 161 )
13X-RAY DIFFRACTION13chain 'C' and (resid 162 through 214 )
14X-RAY DIFFRACTION14chain 'C' and (resid 215 through 313 )
15X-RAY DIFFRACTION15chain 'C' and (resid 314 through 420 )
16X-RAY DIFFRACTION16chain 'C' and (resid 421 through 470 )
17X-RAY DIFFRACTION17chain 'C' and (resid 471 through 503 )
18X-RAY DIFFRACTION18chain 'C' and (resid 504 through 538 )
19X-RAY DIFFRACTION19chain 'D' and (resid 9 through 145 )
20X-RAY DIFFRACTION20chain 'D' and (resid 146 through 214 )
21X-RAY DIFFRACTION21chain 'D' and (resid 215 through 457 )
22X-RAY DIFFRACTION22chain 'D' and (resid 458 through 523 )

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