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- PDB-6na6: Serial Femtosecond X-ray Crystallography Structure of ECR in comp... -

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Basic information

Entry
Database: PDB / ID: 6na6
TitleSerial Femtosecond X-ray Crystallography Structure of ECR in complex with NADPH
ComponentsPutative crotonyl-CoA reductase
KeywordsOXIDOREDUCTASE / C-cycling / ECR / NADPH / SFX Ambient temperature
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 / FREE ELECTRON LASER / Resolution: 2.1 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 1.1Apr 29, 2020Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2May 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 1.3May 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
D: Putative crotonyl-CoA reductase
C: Putative crotonyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,2748
Polymers195,2924
Non-polymers2,9824
Water10,575587
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19600 Å2
ΔGint-56 kcal/mol
Surface area59740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.760, 78.050, 138.000
Angle α, β, γ (deg.)90.000, 107.760, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 587 / 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: 2.88 Å3/Da / Density % sol: 57.33 %
Crystal growTemperature: 277 K / Method: batch mode / Details: MIDAS screen

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1 Å
DetectorType: MPCCD / Detector: CCD / Date: May 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→131 Å / Num. obs: 131589 / % possible obs: 100 % / Redundancy: 43.93 % / Net I/σ(I): 6.65
Reflection shellResolution: 2.1→2.2 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.24data extraction
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementResolution: 2.1→31.817 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 39.7
RfactorNum. reflection% reflection
Rfree0.3334 3074 1.22 %
Rwork0.2742 --
obs0.275 251104 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.93 Å2 / Biso mean: 36.0315 Å2 / Biso min: 3.51 Å2
Refinement stepCycle: final / Resolution: 2.1→31.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13748 0 192 587 14527
Biso mean--41.62 37.11 -
Num. residues----1777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114340
X-RAY DIFFRACTIONf_angle_d1.219492
X-RAY DIFFRACTIONf_chiral_restr0.0682096
X-RAY DIFFRACTIONf_plane_restr0.0072528
X-RAY DIFFRACTIONf_dihedral_angle_d27.1815160
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.13280.48441170.427799271004487
2.1328-2.16780.39781340.4085106721080692
2.1678-2.20520.41451380.3908109281106696
2.2052-2.24520.38871370.3713112501138798
2.2452-2.28840.40351440.3602113891153399
2.2884-2.33510.38461410.35461133611477100
2.3351-2.38590.40541430.34431139211535100
2.3859-2.44140.35591430.33941146411607100
2.4414-2.50240.39141410.3221139011531100
2.5024-2.570.37111420.30981138511527100
2.57-2.64560.35421410.30151142411565100
2.6456-2.7310.32421410.2891146411605100
2.731-2.82850.35651400.28081141711557100
2.8285-2.94170.36681450.26971142011565100
2.9417-3.07550.31021410.26421139811539100
3.0755-3.23740.3161390.24411141711556100
3.2374-3.44010.31671420.23911143511577100
3.4401-3.70530.31271410.23281141411555100
3.7053-4.07750.32271460.22831145511601100
4.0775-4.66590.28211420.22461139311535100
4.6659-5.87250.30841420.23571138911531100
5.8725-31.82020.2721340.2375112711140599
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)
10.0070.0009-0.01340.0183-0.01450.01850.0019-0.0541-0.01670.02210.0425-0.037-0.0146-0.013800.27330.04750.05830.35410.01670.3123-19.146613.578342.4305
20.0864-0.0070.03580.05810.02860.0951-0.085-0.09730.02630.0517-0.00850.0305-0.0373-0.0437-0.16440.08440.0091-0.04080.09360.03110.1012-0.973312.384135.261
30.00680.01020.00170.05670.0180.02030.01540.00470.0098-0.07520.0235-0.0018-0.03040.02340.06590.01150.0165-0.1192-0.01240.1047-0.07436.276810.606412.7773
40.02820.0212-0.00590.0203-0.0090.08390.0502-0.10050.0611-0.00110.0793-0.00150.029-0.00590.04930.19130.04830.01820.109-0.00460.1967-5.193424.038135.4591
50.0050.01450.00120.02850.01010.0084-0.01590.0811-0.02580.00440.0492-0.07880.0565-0.0072-00.20350.00630.00760.29470.00410.309952.493914.486722.7316
60.07030.0508-0.05490.0373-0.0230.03760.0420.0349-0.01050.00580.0104-0.0048-0.0115-0.0050.00920.1150.0023-0.03220.12750.00680.117232.784515.863537.9475
70.00710.0079-0.01440.0085-0.00390.01730.0095-0.0020.15690.09510.098-0.0208-0.0097-0.179600.44430.00580.06550.35070.04340.44242.0418-11.332363.8508
80.0577-0.0414-0.05830.13-0.00410.1247-0.04920.0147-0.03230.08460.0192-0.0230.0609-0.0588-0.04450.0976-0.0070.00990.07870.01430.071420.4105-17.997250.2345
90.00510.0066-0.01010.0142-0.03240.0274-0.03250.00490.054-0.09930.0883-0.04550.00410.023400.2609-0.00150.03770.2795-0.00960.176632.0536-14.4023-0.8183
100.07770.03290.03840.0292-0.0240.10210.03270.04540.0154-0.0501-0.00090.0011-0.02750.1070.040.10470.0002-0.01040.0848-0.02960.094527.1175-13.462416.2358
110.00430.00560.00190.00990.0110.0102-0.0548-0.0281-0.0097-0.0277-0.02630.05920.07570.0831-00.2258-0.01810.02820.2170.01130.2821-0.03-21.441816.865
120.00370.006-0.00230.0316-0.01630.0293-0.01250.0267-0.0539-0.15070.0410.0650.01220.07320.00220.1175-0.0097-0.0180.110.00520.11512.2019-13.615316.9142
130.0130.00070.00590.0263-0.04180.06780.0251-0.0195-0.0128-0.00420.05990.0207-0.00040.03560.02590.21110.05270.10280.206-0.02610.212626.4566-31.537713.1689
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 258 )A140 - 258
3X-RAY DIFFRACTION3chain 'A' and (resid 259 through 363 )A259 - 363
4X-RAY DIFFRACTION4chain 'A' and (resid 364 through 443 )A364 - 443
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 139 )B-1 - 139
6X-RAY DIFFRACTION6chain 'B' and (resid 140 through 443 )B140 - 443
7X-RAY DIFFRACTION7chain 'D' and (resid -1 through 171 )D-1 - 171
8X-RAY DIFFRACTION8chain 'D' and (resid 172 through 443 )D172 - 443
9X-RAY DIFFRACTION9chain 'C' and (resid -1 through 128 )C-1 - 128
10X-RAY DIFFRACTION10chain 'C' and (resid 129 through 247 )C129 - 247
11X-RAY DIFFRACTION11chain 'C' and (resid 248 through 306 )C248 - 306
12X-RAY DIFFRACTION12chain 'C' and (resid 307 through 405 )C307 - 405
13X-RAY DIFFRACTION13chain 'C' and (resid 406 through 443 )C406 - 443

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