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- PDB-4k22: Structure of the C-terminal truncated form of E.Coli C5-hydroxyla... -

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Basic information

Entry
Database: PDB / ID: 4k22
TitleStructure of the C-terminal truncated form of E.Coli C5-hydroxylase UBII involved in ubiquinone (Q8) biosynthesis
ComponentsProtein VisC
KeywordsOXIDOREDUCTASE / Rossmann Fold / hydroxylase
Function / homology
Function and homology information


2-polyprenylphenol 6-hydroxylase / 2-octaprenylphenol hydroxylase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / ubiquinone biosynthetic process / FAD binding / oxidoreductase activity / cytoplasm
Similarity search - Function
Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6, conserved site / ubiH/COQ6 monooxygenase family signature. / Ubiquinone biosynthesis hydroxylase UbiH/COQ6 / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6, conserved site / ubiH/COQ6 monooxygenase family signature. / Ubiquinone biosynthesis hydroxylase UbiH/COQ6 / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 2-octaprenylphenol hydroxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD then molecular replacement / Resolution: 2 Å
AuthorsPecqueur, L. / Lombard, M. / Golinelli-pimpaneau, B. / Fontecave, M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: ubiI, a New Gene in Escherichia coli Coenzyme Q Biosynthesis, Is Involved in Aerobic C5-hydroxylation.
Authors: Chehade, M.H. / Loiseau, L. / Lombard, M. / Pecqueur, L. / Ismail, A. / Smadja, M. / Golinelli-Pimpaneau, B. / Mellot-Draznieks, C. / Hamelin, O. / Aussel, L. / Kieffer-Jaquinod, S. / ...Authors: Chehade, M.H. / Loiseau, L. / Lombard, M. / Pecqueur, L. / Ismail, A. / Smadja, M. / Golinelli-Pimpaneau, B. / Mellot-Draznieks, C. / Hamelin, O. / Aussel, L. / Kieffer-Jaquinod, S. / Labessan, N. / Barras, F. / Fontecave, M. / Pierrel, F.
History
DepositionApr 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Refinement description
Revision 1.2Aug 21, 2013Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein VisC
B: Protein VisC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,61014
Polymers80,7182
Non-polymers89312
Water8,881493
1
A: Protein VisC
B: Protein VisC
hetero molecules

A: Protein VisC
B: Protein VisC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,22128
Polymers161,4354
Non-polymers1,78524
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area17680 Å2
ΔGint-139 kcal/mol
Surface area50080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.730, 124.140, 71.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Protein VisC


Mass: 40358.855 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: visC, b2906, JW2874 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P25535, Oxidoreductases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN EXPRESSED WITH A C-TERMINAL HIS-TAG. PRIOR TO CRYSTALLISATION, UBII WAS SUBJECTED TO ...PROTEIN EXPRESSED WITH A C-TERMINAL HIS-TAG. PRIOR TO CRYSTALLISATION, UBII WAS SUBJECTED TO LIMITED PROTEOLYSIS WITH TRYPSIN. TWO CLEAVAGE SITES WERE IDENTIFIED BY MASS SPECTROMETRY TO BE LOCATED AT THE C-TERMINAL OF RESIDUE LYS 364 and LYS 365. THE C-TERMINAL FRAGMENT (34 RESIDUES) CONTAINING THE HIS-TAG WAS REMOVED BY NI-NTA PURIFICATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3948.44
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2921vapor diffusion, hanging drop8.50.1M Tris pH 8.5, 12% PEG 4000, 0.1M NaCl, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 292K
2922vapor diffusion, hanging drop90.1M BisTris-propane pH 9.0, 14% PEG 4000, 0.1M NaCl, 0.15M MgCl2', VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 110.98011
SYNCHROTRONSOLEIL PROXIMA 120.97918
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELSep 12, 2012
PSI PILATUS 6M2PIXELOct 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.980111
20.979181
ReflectionResolution: 2→46.98 Å / Num. obs: 58014 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Biso Wilson estimate: 35.15 Å2 / Rmerge(I) obs: 0.0666 / Net I/σ(I): 14.5

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Processing

Software
NameVersionClassification
PHASER2.5.2phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD then molecular replacement
Resolution: 2→46.98 Å / SU ML: 0.2 / σ(F): 2 / Phase error: 19.78 / Stereochemistry target values: ML
Details: Model calculated from experimental phases derived by SAD with selenomethionylated protein. Data used for SAD phasing stored in crystal2 dataset. Data for MR and refinement to 2.0 A ...Details: Model calculated from experimental phases derived by SAD with selenomethionylated protein. Data used for SAD phasing stored in crystal2 dataset. Data for MR and refinement to 2.0 A resolution stored in crystal1 dataset'
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 2894 5 %RANDOM
Rwork0.1625 ---
obs0.1643 57894 99.85 %-
all-58014 --
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5495 0 53 493 6041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125787
X-RAY DIFFRACTIONf_angle_d1.2537840
X-RAY DIFFRACTIONf_dihedral_angle_d14.1022109
X-RAY DIFFRACTIONf_chiral_restr0.055848
X-RAY DIFFRACTIONf_plane_restr0.0081028
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.03280.29971330.2493254099
2.0328-2.06780.27051360.22752589100
2.0678-2.10540.25221360.2112583100
2.1054-2.14590.26771370.20142595100
2.1459-2.18970.24371350.18882567100
2.1897-2.23740.21111380.18652623100
2.2374-2.28940.23821360.18482590100
2.2894-2.34670.25281360.17382570100
2.3467-2.41010.19921370.17482607100
2.4101-2.4810.19911380.16742622100
2.481-2.56110.23671370.17362599100
2.5611-2.65260.22491370.17382607100
2.6526-2.75880.21771370.17142600100
2.7588-2.88440.20991380.17062616100
2.8844-3.03640.20641370.16652610100
3.0364-3.22660.17881380.15522625100
3.2266-3.47560.17871390.14982637100
3.4756-3.82530.18631390.14642651100
3.8253-4.37850.14591400.14172653100
4.3785-5.5150.18671430.14112708100
5.515-46.99440.19831470.1679280899
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)
11.63360.4764-0.1313.67890.84241.6718-0.0277-0.2107-0.03270.5928-0.04790.36710.1739-0.0280.07730.2220.05170.02750.2624-0.01760.2322-18.549517.7978-24.0577
20.95130.55990.24733.34661.11761.1813-0.0409-0.12990.01810.22740.09-0.00160.11890.0505-0.0370.15410.04980.00420.20020.0210.1659-9.55516.019-30.5627
32.7833-0.9941-0.53661.53060.31471.49780.11620.67360.1588-0.4243-0.1272-0.1247-0.2085-0.0962-0.01240.3786-0.1137-0.01850.38480.05910.21887.808324.744-61.6267
42.6226-0.8110.34361.24550.07570.69260.06540.3448-0.0337-0.2374-0.02270.0086-0.0694-0.0861-0.05060.2853-0.05170.0050.26220.01960.16440.893118.636-54.9824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:140 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 141:363 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 2:140 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 141:362 )

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