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- PDB-6na3: Crystal Structure of Apo-form of ECR -

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Basic information

Entry
Database: PDB / ID: 6na3
TitleCrystal Structure of Apo-form of ECR
ComponentsPutative crotonyl-CoA reductase
KeywordsOXIDOREDUCTASE / C-cycling ECR
Function / homology
Function and homology information


crotonyl-CoA reductase activity / NADPH:quinone reductase activity / NADPH binding / mRNA 3'-UTR binding / cytosol
Similarity search - Function
Crotonyl-CoA reductase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily ...Crotonyl-CoA reductase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pyrrolidine / Putative crotonyl-CoA reductase
Similarity search - Component
Biological speciesKitasatospora setae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsDeMirci, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-1231306 United States
CitationJournal: Acs Cent.Sci. / Year: 2022
Title: Intersubunit Coupling Enables Fast CO2-Fixation by Reductive Carboxylases
Authors: DeMirci, H. / Rao, Y. / Stoffel, G.M. / Vogeli, B. / Schell, K. / Gomez, A. / Batyuk, A. / Gati, C. / Sierra, R.G. / Hunter, M.S. / Dao, E.H. / Ciftci, H.I. / Hayes, B. / Poitevin, F. / Li, ...Authors: DeMirci, H. / Rao, Y. / Stoffel, G.M. / Vogeli, B. / Schell, K. / Gomez, A. / Batyuk, A. / Gati, C. / Sierra, R.G. / Hunter, M.S. / Dao, E.H. / Ciftci, H.I. / Hayes, B. / Poitevin, F. / Li, P.N. / Kaur, M. / Tono, K. / Saez, D.A. / Deutsch, S. / Yoshikuni, Y. / Grubmuller, H. / Erb, T.J. / Vohringer-Martinez, E. / Wakatsuki, S.
History
DepositionDec 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative crotonyl-CoA reductase
B: Putative crotonyl-CoA reductase
C: Putative crotonyl-CoA reductase
D: Putative crotonyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,03817
Polymers195,2924
Non-polymers74613
Water24,5001360
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15590 Å2
ΔGint-88 kcal/mol
Surface area62390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.100, 153.000, 202.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative crotonyl-CoA reductase


Mass: 48823.055 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora setae (strain ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054) (bacteria)
Strain: ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054
Gene: ccr1, KSE_56510 / Production host: Escherichia coli (E. coli) / References: UniProt: E4N096
#2: Chemical
ChemComp-VES / Pyrrolidine


Mass: 71.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H9N
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1360 / 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: 3.1 Å3/Da / Density % sol: 60.33 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.1M TRIS ph 8.0 20% w/v Poly(acrylic acid sodium salt) 5100 30% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→16.966 Å / Num. obs: 223907 / % possible obs: 91.5 % / Redundancy: 6.14 % / Biso Wilson estimate: 26.44 Å2 / Net I/σ(I): 12.32
Reflection shellResolution: 1.8→1.86 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementResolution: 1.8→16.966 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Phase error: 37.25
RfactorNum. reflection% reflection
Rfree0.242 1011 5 %
Rwork0.1991 --
obs0.1994 204747 91.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.08 Å2 / Biso mean: 48.5681 Å2 / Biso min: 19.21 Å2
Refinement stepCycle: final / Resolution: 1.8→16.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13737 0 5 1369 15111
Biso mean--54.81 48.9 -
Num. residues----1786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114165
X-RAY DIFFRACTIONf_angle_d1.16719198
X-RAY DIFFRACTIONf_chiral_restr0.1012061
X-RAY DIFFRACTIONf_plane_restr0.0092514
X-RAY DIFFRACTIONf_dihedral_angle_d11.4938321
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.89480.43591310.4173265042663584
1.8948-2.01330.37411360.3273274282756487
2.0133-2.16850.29431400.2531282882842889
2.1685-2.38620.25111430.2146288772902091
2.3862-2.73020.23871490.1977297822993194
2.7302-3.43510.2241530.1857308613101496
3.4351-16.96670.19891590.1541319963215598
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)
14.52782.26981.2766.70090.54164.87340.0749-0.4868-0.28540.39790.0723-0.54950.07210.9657-0.18530.37410.0355-0.01560.72260.0170.35623.09621.83833.2433
22.03530.9021-0.77333.2032-3.05842.9621-0.0330.04260.87320.14250.1269-0.3279-1.70240.20840.07161.4285-0.27190.10430.4841-0.0850.61514.32130.776121.4064
31.26360.3046-0.55844.0673-0.17441.82610.07740.05530.4036-0.26340.03220.0792-1.00920.3087-0.0910.6277-0.11440.02340.324-0.02030.321212.86617.833121.5815
43.4843-0.5758-0.53722.45670.19813.82450.1353-0.08140.2437-0.0591-0.06630.2364-0.780.1155-0.0640.3792-0.01110.01120.2257-0.03670.23286.42311.398824.3892
51.30050.95161.09511.20180.65933.9105-0.0806-0.04040.2679-0.0516-0.03960.1991-0.6945-0.00270.16270.39510.03410.03870.22570.00390.33114.40869.377714.8456
63.17631.51820.45982.36940.95997.41750.11160.28250.0674-0.08820.06-0.0686-0.29311.1846-0.16680.26710.0077-0.00890.3182-0.01890.266519.02974.882516.3939
71.7377-1.3279-0.84581.3599-0.6385.56570.01930.0270.24090.00460.0012-0.2302-0.78940.91730.00870.3644-0.07590.00840.30130.00120.316615.62869.5913-3.945
86.44492.55170.64016.1449-1.37852.66040.0862-0.4180.48790.2616-0.1718-0.8931-1.11131.08170.08290.6389-0.28860.05650.7142-0.01510.467926.182618.7749-8.9689
93.3502-2.54980.54146.54190.37880.41150.08070.32930.8524-0.31480.0822-0.593-1.3840.30350.00461.153-0.21850.07020.47150.13210.572813.646128.6415-17.2686
101.3464-0.79430.34951.3164-0.11640.12340.080.21920.3723-0.0163-0.0437-0.0917-1.13870.3348-0.00720.6568-0.02460.03830.21810.04880.35626.559518.7309-10.9985
116.26053.12541.6335.24612.64954.6033-0.09620.24810.2032-0.09930.2861-0.1699-0.44021.241-0.1820.3401-0.06780.02880.43910.02660.262821.11527.2259.1774
123.3314-0.7480.43179.66220.16394.21880.15010.42940.0287-0.4507-0.0957-0.4329-0.03290.9181-0.07090.35610.05820.04920.69230.03820.308826.0437-1.8052-50.4984
133.30280.18411.05236.3669-3.00484.46450.0821-0.1302-0.9924-0.11040.0106-0.41341.66680.1851-0.02711.13880.2554-0.06380.4924-0.06810.590716.3892-30.7361-39.2264
142.08371.089-0.78524.53970.17663.51640.0578-0.0951-0.4240.173-0.07730.00920.74270.1910.03760.47380.1573-0.00580.4104-0.00680.349915.0033-17.8041-39.5725
155.0653.48211.11634.78940.36944.77450.0972-0.0088-0.2074-0.009-0.10660.15890.5613-0.08420.00310.30490.12460.0430.2563-0.02060.24828.7634-11.3535-42.817
160.84640.1222-1.20290.6080.54462.6904-0.12780.0189-0.09930.0625-0.0060.04830.3531-0.03420.13110.36360.1114-0.00120.37280.0060.33386.0966-9.3341-33.4531
172.9598-0.28790.94991.95320.74573.80630.06-0.3903-0.22180.12760.0932-0.01620.16620.6017-0.16130.27870.11280.01410.4795-0.01560.289320.7946-4.8588-33.946
181.82680.30731.08081.2089-0.43160.98630.01430.3289-0.208-0.040.0088-0.06350.3380.72210.01150.33610.19370.01680.387-0.03470.347615.8441-9.4887-13.8498
193.0102-2.0561-0.18485.2947-1.34130.56720.06280.6063-0.61590.0518-0.1585-0.56950.71380.92340.11410.58280.3631-0.04590.6984-0.0990.532726.0965-18.8852-8.1283
202.53981.06890.63925.13010.91161.2831-0.0735-0.0231-0.61060.22060.0575-0.22811.03980.3248-0.20010.99930.4729-0.00270.29130.02230.514913.0447-28.6074-0.7445
210.55450.0233-0.08870.9098-0.5520.5973-0.0210.2053-0.178-0.07030.0677-0.01070.90180.19870.05410.65950.3028-0.0117-0.0212-0.06720.40216.4029-18.9694-7.6059
224.9965-2.1293-0.5252.71061.11612.50420.0123-0.4403-0.18550.02470.1359-0.20450.42040.7392-0.18710.34780.1449-0.00080.54980.03320.28622.3893-7.2027-26.6184
233.57290.33490.78831.63730.77883.07620.2048-0.4746-0.37040.1822-0.0186-0.00870.72791.0146-0.17480.46620.267-0.01490.83510.05930.391530.1503-12.8264-28.8148
242.1329-1.4247-0.33746.9787-1.30193.63010.04480.5616-0.08-0.39370.14460.3927-0.0521-0.971-0.2130.39940.064-0.05210.90080.04980.3552-23.13291.7229-52.2359
252.4265-0.42830.7183.22333.00373.823-0.42360.02490.875-0.26050.21120.2591-2.0209-0.19970.2911.52620.3145-0.03930.66160.18870.7255-14.311430.6557-40.3298
261.1560.40810.69483.6684-0.3764.3272-0.09270.08480.40120.1175-0.078-0.0601-1.2188-0.16210.17930.65990.2025-0.00570.50230.09790.4088-12.851917.7493-40.6173
273.88911.45320.23392.85930.29024.96530.01210.32350.2119-0.0528-0.0423-0.2738-0.79010.11930.02660.42280.1095-0.00430.42780.10780.3175-6.425511.3076-43.4161
283.0005-0.53343.10520.5136-0.47584.7132-0.16620.35450.36360.0173-0.0615-0.0678-0.7086-0.01020.22560.38310.12340.02590.3720.04580.3176-4.41889.3046-33.8569
293.8652-1.86251.19032.667-0.51812.34090.0755-0.0963-0.08060.11740.02150.1941-0.2865-0.946-0.09240.31720.1301-0.00980.62190.05490.2727-19.05884.8192-35.3931
301.7984-0.6036-0.91551.05490.62120.6034-0.02970.25630.2437-0.05970.08850.0955-0.4951-0.8491-0.0160.42330.2570.00260.43950.06810.3849-15.5199.4977-15.0245
314.1933-2.99880.82165.5105-0.36730.18230.01380.43510.3527-0.112-0.07480.6694-0.8419-0.8140.03910.71850.46270.0140.86450.07260.544-26.198118.8254-10.1269
322.35220.4565-0.38543.5143-0.60481.2678-0.0701-0.09850.76290.13680.00670.309-1.092-0.3213-0.29461.16770.48850.04140.4023-0.02950.5948-13.618428.7486-1.8524
330.90480.14690.5330.52570.06130.8642-0.03680.01090.2918-0.05410.03870.0745-1.06-0.15820.02180.69790.24110.02730.28390.05380.3996-6.565218.7434-8.0734
343.5424-1.03261.32170.8144-0.29740.55830.1183-0.0720.19490.0897-0.03720.2873-0.5205-1.025-0.20040.4220.31980.0330.77170.05640.3597-21.11237.1769-28.1786
353.0133-0.2229-0.1080.18690.07712.48180.0313-0.23930.320.05660.03020.1268-0.8634-1.4197-0.01810.58240.39230.01911.07390.03650.4437-28.958112.7373-31.277
364.0752.27490.56418.9915-0.11575.60870.1235-0.46270.20840.3777-0.01170.457-0.0549-1.1993-0.14030.3160.0420.05210.6974-0.05330.2887-26.0594-1.685631.5343
372.3734-0.57160.75784.56881.81843.2913-0.13010.117-0.7274-0.07520.0820.38541.2124-0.12980.06650.9308-0.23350.0590.44930.0740.493-16.5467-30.57520.1733
381.48180.297-0.3033.64110.54913.74510.06420.0016-0.31980.0709-0.0992-0.09340.8789-0.41090.04380.4553-0.08570.00240.37240.03920.2994-15.0725-17.696320.6175
394.627-1.38370.53394.0626-0.17454.97130.0471-0.191-0.24490.0646-0.0652-0.28650.54220.03720.01890.2765-0.03160.0220.23370.04720.2068-8.8009-11.273823.8508
401.87220.5125-0.50080.5027-0.38682.7588-0.045-0.069-0.2083-0.0955-0.0836-0.27190.4466-0.28490.12170.38750.03060.01080.13560.02840.355-6.1298-9.263714.4905
413.65531.40480.52982.59730.11115.91280.05160.22250.0273-0.03820.03890.0874-0.0232-1.0001-0.0870.2440.03260.02590.36950.03650.2344-20.8464-4.751914.9749
422.7016-1.60081.31261.11530.25927.82670.02590.0927-0.14120.006-0.030.10710.478-0.81160.00720.2654-0.0160.01730.254-0.00640.2916-15.8999-9.4639-5.0924
436.15182.7254-0.7286.980.94752.18850.0805-0.103-0.68790.0514-0.1350.65320.779-1.13170.03690.5486-0.268-0.04780.79050.02290.4742-25.9289-19.1627-10.7515
444.5126-2.2812-0.32696.93070.11851.59190.00110.2146-0.8971-0.32230.12790.39041.3289-0.4873-0.06680.9329-0.1995-0.0370.4342-0.11440.5087-13.1152-28.6409-18.111
451.9823-0.7069-0.80171.13140.09211.83290.02020.2487-0.3928-0.0644-0.05280.05760.9025-0.31790.02580.5019-0.0212-0.01310.2241-0.03950.3345-6.5876-18.9029-11.3191
465.72382.6823-0.36272.6638-0.79794.1187-0.03280.3635-0.2686-0.04720.12370.03030.2779-0.9067-0.1080.25880.01660.01660.4518-0.01730.2601-22.3703-7.18567.6828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 25 )A0 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 54 )A26 - 54
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 92 )A55 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 139 )A93 - 139
5X-RAY DIFFRACTION5chain 'A' and (resid 140 through 179 )A140 - 179
6X-RAY DIFFRACTION6chain 'A' and (resid 180 through 203 )A180 - 203
7X-RAY DIFFRACTION7chain 'A' and (resid 204 through 247 )A204 - 247
8X-RAY DIFFRACTION8chain 'A' and (resid 248 through 279 )A248 - 279
9X-RAY DIFFRACTION9chain 'A' and (resid 280 through 306 )A280 - 306
10X-RAY DIFFRACTION10chain 'A' and (resid 307 through 368 )A307 - 368
11X-RAY DIFFRACTION11chain 'A' and (resid 369 through 396 )A369 - 396
12X-RAY DIFFRACTION12chain 'B' and (resid 0 through 25 )B0 - 25
13X-RAY DIFFRACTION13chain 'B' and (resid 26 through 54 )B26 - 54
14X-RAY DIFFRACTION14chain 'B' and (resid 55 through 92 )B55 - 92
15X-RAY DIFFRACTION15chain 'B' and (resid 93 through 139 )B93 - 139
16X-RAY DIFFRACTION16chain 'B' and (resid 140 through 179 )B140 - 179
17X-RAY DIFFRACTION17chain 'B' and (resid 180 through 203 )B180 - 203
18X-RAY DIFFRACTION18chain 'B' and (resid 204 through 247 )B204 - 247
19X-RAY DIFFRACTION19chain 'B' and (resid 248 through 279 )B248 - 279
20X-RAY DIFFRACTION20chain 'B' and (resid 280 through 306 )B280 - 306
21X-RAY DIFFRACTION21chain 'B' and (resid 307 through 368 )B307 - 368
22X-RAY DIFFRACTION22chain 'B' and (resid 369 through 396 )B369 - 396
23X-RAY DIFFRACTION23chain 'B' and (resid 397 through 442 )B397 - 442
24X-RAY DIFFRACTION24chain 'C' and (resid 0 through 25 )C0 - 25
25X-RAY DIFFRACTION25chain 'C' and (resid 26 through 54 )C26 - 54
26X-RAY DIFFRACTION26chain 'C' and (resid 55 through 92 )C55 - 92
27X-RAY DIFFRACTION27chain 'C' and (resid 93 through 139 )C93 - 139
28X-RAY DIFFRACTION28chain 'C' and (resid 140 through 179 )C140 - 179
29X-RAY DIFFRACTION29chain 'C' and (resid 180 through 203 )C180 - 203
30X-RAY DIFFRACTION30chain 'C' and (resid 204 through 247 )C204 - 247
31X-RAY DIFFRACTION31chain 'C' and (resid 248 through 279 )C248 - 279
32X-RAY DIFFRACTION32chain 'C' and (resid 280 through 306 )C280 - 306
33X-RAY DIFFRACTION33chain 'C' and (resid 307 through 368 )C307 - 368
34X-RAY DIFFRACTION34chain 'C' and (resid 369 through 396 )C369 - 396
35X-RAY DIFFRACTION35chain 'C' and (resid 397 through 442 )C397 - 442
36X-RAY DIFFRACTION36chain 'D' and (resid 0 through 25 )D0 - 25
37X-RAY DIFFRACTION37chain 'D' and (resid 26 through 54 )D26 - 54
38X-RAY DIFFRACTION38chain 'D' and (resid 55 through 92 )D55 - 92
39X-RAY DIFFRACTION39chain 'D' and (resid 93 through 139 )D93 - 139
40X-RAY DIFFRACTION40chain 'D' and (resid 140 through 179 )D140 - 179
41X-RAY DIFFRACTION41chain 'D' and (resid 180 through 203 )D180 - 203
42X-RAY DIFFRACTION42chain 'D' and (resid 204 through 247 )D204 - 247
43X-RAY DIFFRACTION43chain 'D' and (resid 248 through 279 )D248 - 279
44X-RAY DIFFRACTION44chain 'D' and (resid 280 through 306 )D280 - 306
45X-RAY DIFFRACTION45chain 'D' and (resid 307 through 368 )D307 - 368
46X-RAY DIFFRACTION46chain 'D' and (resid 369 through 396 )D369 - 396

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