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- PDB-6na5: Crystal Structure of ECR in complex with NADP+ -

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Basic information

Entry
Database: PDB / ID: 6na5
TitleCrystal Structure of ECR in complex with NADP+
ComponentsPutative crotonyl-CoA reductase
KeywordsOXIDOREDUCTASE / ECR C-cycling NADP+
Function / homology
Function and homology information


crotonyl-CoA reductase activity
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
Chem-NDP / Putative crotonyl-CoA reductase
Similarity search - Component
Biological speciesKitasatospora setae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 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)198,2748
Polymers195,2924
Non-polymers2,9824
Water31,5081749
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19970 Å2
ΔGint-49 kcal/mol
Surface area59590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.000, 146.700, 200.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1749 / 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: 2.89 Å3/Da / Density % sol: 57.51 %
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: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→49.361 Å / Num. obs: 223595 / % possible obs: 93.8 % / Redundancy: 6.213 % / CC1/2: 0.997 / Rmerge(I) obs: 0.218 / Rrim(I) all: 0.237 / Χ2: 1.365 / Net I/σ(I): 4.37
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible allCC1/2
1.36-1.443.19713.1940.049930215.74565.7
1.44-1.545.03214.6510.0513607116.36195.9
1.54-1.677.0618.6450.171320769.324100
1.67-1.836.9233.8010.511214694.10899.90.126
1.83-2.046.8641.431.641100691.5471000.622
2.04-2.367.10.65.02968770.64899.90.926
2.36-2.886.80.2510.27818930.2711000.979
2.88-4.076.9310.09620.28633420.1041000.995
4.07-49.3616.5230.06427.03348760.0799.80.997

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementResolution: 1.75→49.361 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 25.17
RfactorNum. reflection% reflection
Rfree0.2171 1121 0.51 %
Rwork0.195 --
obs0.1951 220094 96.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.47 Å2 / Biso mean: 33.5883 Å2 / Biso min: 15.14 Å2
Refinement stepCycle: final / Resolution: 1.75→49.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13748 0 192 1749 15689
Biso mean--39.36 37.33 -
Num. residues----1777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714340
X-RAY DIFFRACTIONf_angle_d1.15519492
X-RAY DIFFRACTIONf_chiral_restr0.0842096
X-RAY DIFFRACTIONf_plane_restr0.0052528
X-RAY DIFFRACTIONf_dihedral_angle_d25.8365160
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.82960.38291280.3542249072503589
1.8296-1.92610.30221330.295260362616992
1.9261-2.04680.241370.2481268522698996
2.0468-2.20480.22371410.2094275582769998
2.2048-2.42670.23511430.199278612800499
2.4267-2.77780.23711440.1998281422828699
2.7778-3.49960.21371460.1862846628612100
3.4996-49.3810.17981490.16152915129300100
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)
11.56490.1425-0.32651.0785-0.22981.6935-0.0361-0.3279-0.16650.0757-0.0838-0.13440.13690.0288-0.03450.2611-0.05630.01460.33880.06490.1986-33.232119.4202-35.1742
20.18430.3401-0.1430.4477-0.04690.50670.0147-0.0345-0.09480.0147-0.0015-0.10310.0291-0.076800.2355-0.04170.00970.29520.01330.2008-30.007727.6367-44.0463
31.37-0.4018-0.03390.71420.11360.95170.0689-0.0449-0.3076-0.0248-0.03590.1190.1444-0.11850.00360.22-0.0475-0.02010.1570.01650.2707-31.489717.1385-69.929
41.00540.1533-0.11830.47310.10521.0267-0.01650.0395-0.06250.01740.01690.05220.1249-0.3371-00.2168-0.06770.01350.33330.00930.201-45.205723.6105-50.0419
51.35630.9726-0.53581.5741-0.11250.8980.1204-0.3650.34570.1654-0.03090.3245-0.04870.07940.00020.2582-0.0520.04810.3373-0.08770.2809-7.005854.1586-34.2464
60.73910.3287-0.22440.20380.08310.4782-0.0078-0.04630.01550.0351-0.01030.09350.03350.048400.2337-0.02780.0220.2882-0.02920.2195-9.307342.8064-42.0847
71.7811-0.4311-0.15840.774-0.18960.9130.1599-0.11390.3974-0.019-0.0476-0.0962-0.14140.17120.03840.2134-0.05880.06740.1354-0.04680.2746-6.022855.1888-68.2912
81.17190.2326-0.33340.3442-0.23740.7886-0.03870.01560.01370.0080.0368-0.054-0.02720.2534-00.1804-0.05490.01230.3189-0.04110.20086.117848.3013-47.9846
91.989-0.6869-0.80391.4270.39920.78330.09340.31550.407-0.0250.0238-0.2690.0332-0.13640.02370.2320.02720.01740.19410.06820.2593-32.026254.1379-101.1372
100.31220.17450.00870.2352-0.03930.76130.031800.14210.00040.00260.0345-0.062-0.115600.19250.0420.03780.17310.00450.2296-34.901949.5623-78.478
111.77370.05090.59810.6603-0.0670.62810.05170.2705-0.2949-0.12280.00230.01630.07940.15140.00380.25990.03430.00050.2117-0.06420.208-0.382618.4558-100.265
120.1656-0.3008-0.02320.62510.04960.46430.02840.116-0.07720.1313-0.02950.30610.050.0207-0.00050.2466-0.00190.00230.2038-0.01860.2667-11.175720.9496-100.6791
130.31840.2199-0.02040.22410.10030.6127-0.00640.01830.0049-0.026-0.00240.03070.00960.020400.20420.0243-0.00140.1813-0.01310.1939-5.379829.3597-85.7433
141.197-0.04730.02840.7018-0.21190.98730.0332-0.1148-0.22960.0121-0.0012-0.04420.15310.12530.00080.2370.0314-0.01760.17580.02840.2483-5.211715.3862-64.9631
151.16890.23650.52970.3632-0.03680.49790.0224-0.0543-0.062-0.03660.0168-0.06820.01960.157300.18740.02520.00560.21910.00170.1678.333526.1492-85.9892
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 139 )A-1 - 139
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 203 )A140 - 203
3X-RAY DIFFRACTION3chain 'A' and (resid 204 through 368 )A204 - 368
4X-RAY DIFFRACTION4chain 'A' and (resid 369 through 443 )A369 - 443
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 128 )B-1 - 128
6X-RAY DIFFRACTION6chain 'B' and (resid 129 through 203 )B129 - 203
7X-RAY DIFFRACTION7chain 'B' and (resid 204 through 368 )B204 - 368
8X-RAY DIFFRACTION8chain 'B' and (resid 369 through 443 )B369 - 443
9X-RAY DIFFRACTION9chain 'C' and (resid -1 through 128 )C-1 - 128
10X-RAY DIFFRACTION10chain 'C' and (resid 129 through 443 )C129 - 443
11X-RAY DIFFRACTION11chain 'D' and (resid -1 through 92 )D-1 - 92
12X-RAY DIFFRACTION12chain 'D' and (resid 93 through 128 )D93 - 128
13X-RAY DIFFRACTION13chain 'D' and (resid 129 through 247 )D129 - 247
14X-RAY DIFFRACTION14chain 'D' and (resid 248 through 368 )D248 - 368
15X-RAY DIFFRACTION15chain 'D' and (resid 369 through 443 )D369 - 443

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