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- PDB-7xp7: Crystal Structure of the Flavoprotein ColB1 Catalyzing Assembly L... -

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Basic information

Entry
Database: PDB / ID: 7xp7
TitleCrystal Structure of the Flavoprotein ColB1 Catalyzing Assembly Line-Tethered Cysteine Dehydrogenation
ComponentsCyclohexanecarboxyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Acyl-CoA dehydrogenase / flavin
Function / homology
Function and homology information


acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily ...Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Cyclohexanecarboxyl-CoA dehydrogenase
Similarity search - Component
Biological speciesStreptomyces filamentosus NRRL 11379 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMa, X.Y. / Tang, Z.J. / Liu, W. / Ma, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Structure-Based Mechanistic Insights into ColB1, a Flavoprotein Functioning in-trans in the 2,2'-Bipyridine Assembly Line for Cysteine Dehydrogenation.
Authors: Ma, X. / Tang, Z. / Ding, W. / Liu, T. / Yang, D. / Liu, W. / Ma, M.
History
DepositionMay 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclohexanecarboxyl-CoA dehydrogenase
B: Cyclohexanecarboxyl-CoA dehydrogenase
C: Cyclohexanecarboxyl-CoA dehydrogenase
D: Cyclohexanecarboxyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,6078
Polymers175,4654
Non-polymers3,1424
Water15,997888
1
A: Cyclohexanecarboxyl-CoA dehydrogenase
B: Cyclohexanecarboxyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3044
Polymers87,7322
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-34 kcal/mol
Surface area26950 Å2
MethodPISA
2
C: Cyclohexanecarboxyl-CoA dehydrogenase
D: Cyclohexanecarboxyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3044
Polymers87,7322
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-33 kcal/mol
Surface area26630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.328, 131.235, 191.859
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
Cyclohexanecarboxyl-CoA dehydrogenase


Mass: 43866.207 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces filamentosus NRRL 11379 (bacteria)
Gene: SSIG_05949
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: W9FXI8
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 888 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.75 Å3/Da / Density % sol: 67.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 800mM K2HPO4, 100mM HEPES/NaOH pH 7.5, 800mM NaH2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.95→49.37 Å / Num. obs: 177111 / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 19.8
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.475 / Num. unique obs: 8708

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2jif

2jif


Resolution: 1.95→23.37 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.955 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1796 1996 1.1 %RANDOM
Rwork0.1578 ---
obs0.158 174681 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.75 Å2 / Biso mean: 18.442 Å2 / Biso min: 7.5 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.95→23.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11010 0 212 888 12110
Biso mean--12.29 26.24 -
Num. residues----1482
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 146 -
Rwork0.175 12791 -
all-12937 -
obs--99.75 %

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