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- PDB-7mwa: Crystal structure of 2-octaprenyl-6-methoxyphenol hydroxylase Ubi... -

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Basic information

Entry
Database: PDB / ID: 7mwa
TitleCrystal structure of 2-octaprenyl-6-methoxyphenol hydroxylase UbiH from Acinetobacter baumannii, apoenzyme
Components2-polyprenyl-6-methoxyphenol 4-hydroxylase
KeywordsLYASE / 2-octaprenyl-6-methoxyphenol hydroxylase / UBIH / UBIQUINONE BIOSYNTHESIS / FAD-BINDING STRUCTURAL GENOMICS / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASEES
Function / homologyUbiquinone biosynthesis hydroxylase UbiH/COQ6 / ubiquinone biosynthetic process / 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 / FAD-binding domain / FAD binding domain / FAD binding / FAD/NAD(P)-binding domain superfamily / CITRIC ACID / Putative 2-polyprenyl-6-methoxyphenol 4-hydroxylase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsStogios, P.J. / Evdokimova, E. / Endres, M. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: UbiH from Acinetobacter baumannii
Authors: Stogios, P.J.
History
DepositionMay 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-polyprenyl-6-methoxyphenol 4-hydroxylase
B: 2-polyprenyl-6-methoxyphenol 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4696
Polymers88,9872
Non-polymers4824
Water6,900383
1
A: 2-polyprenyl-6-methoxyphenol 4-hydroxylase
hetero molecules

B: 2-polyprenyl-6-methoxyphenol 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4696
Polymers88,9872
Non-polymers4824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area5240 Å2
ΔGint-34 kcal/mol
Surface area31680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.378, 71.680, 111.261
Angle α, β, γ (deg.)90.000, 118.940, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-629-

HOH

21A-695-

HOH

31A-811-

HOH

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Components

#1: Protein 2-polyprenyl-6-methoxyphenol 4-hydroxylase / 2-octaprenyl-6-methoxyphenol hydroxylase UbiH


Mass: 44493.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria)
Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81
Gene: HMPREF0010_02947 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold / References: UniProt: D0CDW7
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.91 Å3/Da / Density % sol: 68.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M magnesium chloride, 0.1 M sodium citrate pH 5, 10% (w/v) PEG 20K. Cryoprotectant 25% (w/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.548 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.548 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 42324 / % possible obs: 99 % / Redundancy: 4.1 % / Biso Wilson estimate: 52.05 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.047 / Net I/σ(I): 12.33
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 1.12 / Num. unique obs: 1940 / CC1/2: 0.838 / Rpim(I) all: 0.318 / % possible all: 89.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
MrBUMPphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4k22

4k22


Resolution: 2.6→30 Å / SU ML: 0.3132 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.0206
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1999 4.74 %RANDOM
Rwork0.1999 40156 --
obs0.2021 42155 98.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.47 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5975 0 31 383 6389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00186109
X-RAY DIFFRACTIONf_angle_d0.49228280
X-RAY DIFFRACTIONf_chiral_restr0.0413938
X-RAY DIFFRACTIONf_plane_restr0.00361085
X-RAY DIFFRACTIONf_dihedral_angle_d21.03412255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.33171270.29572435X-RAY DIFFRACTION84.3
2.66-2.730.3541280.29572806X-RAY DIFFRACTION97.96
2.73-2.810.33061490.28042889X-RAY DIFFRACTION99.31
2.81-2.90.28931400.25412869X-RAY DIFFRACTION99.87
2.9-3.010.31631420.23332917X-RAY DIFFRACTION100
3.01-3.130.26521580.22712872X-RAY DIFFRACTION99.97
3.13-3.270.27121440.24052908X-RAY DIFFRACTION99.84
3.27-3.440.23381330.20052904X-RAY DIFFRACTION99.87
3.44-3.660.25091500.18892896X-RAY DIFFRACTION99.93
3.66-3.940.23051390.18962901X-RAY DIFFRACTION99.77
3.94-4.330.21441480.17212904X-RAY DIFFRACTION99.84
4.33-4.960.17791470.14962906X-RAY DIFFRACTION99.74
4.96-6.240.23811460.19242955X-RAY DIFFRACTION99.81
6.24-30.010.25421480.19152994X-RAY DIFFRACTION99.27
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)
12.552508637481.374696393412.696291617212.062148363361.802221199344.77784172980.231423391412-0.719482406738-0.3220565307410.213410970685-0.1289563556150.2219909192770.357045841604-0.630623045899-0.07279889052840.359869317959-0.02915499345750.03114102109210.522701375620.1340979887270.48119000792547.70576888430.984196515743.5422734474
25.156375079190.226632311699-4.163956762441.598701499741.122814548254.36795126277-0.261150000134-0.291344403975-0.4490099587590.188424278753-0.102353579325-0.0137142161270.6996090462090.4288898801930.397083347580.32890436422-0.02973773111680.01316921217140.3310264361760.005669870499650.43449149439150.897262466724.904494855126.1191809388
33.300511319420.947120557434-0.898322848062.163700221630.7632512449033.004166312050.0810279042943-0.3338312511860.348298266224-0.03623667783380.2088436807520.305721691113-0.511150772299-0.783108733432-0.2716326718610.3407184569670.1359855932370.005716101506420.6110721753350.07778027488650.50315852849750.74708051847.621958467349.3967161813
42.398277520612.430170616621.312533126823.93378842620.8974617305552.10690708731-0.1718799503210.02481448760810.251353306904-0.2906765318180.07901766318630.112491526608-0.2154588653290.09549912607760.1019162369780.330899579654-0.03021309786390.06770135591690.3597671276010.018347073270.43146290390941.378338988234.455205680416.9719427196
50.741294009644-0.35355538438-0.05138476889530.6908427808390.8187066307421.67322031157-0.04006063034910.0123068661176-0.0510511484937-0.2343936903690.0713698498542-0.0826052679548-0.0715903673136-0.279789520423-0.02417532652580.365736356276-0.07280303065090.03976730427810.3895247460470.02969040328920.40900417958462.663639416140.420705281631.2372265976
63.36889013954-0.217912739324-0.559091435343.35175775328-1.239992704081.67657252670.05560326687030.588033851543-0.493913092423-0.760811465178-0.263132651421-0.4505170746380.5260640997030.1918654354060.2167744716440.5622295426970.09107863013840.04545983979180.56532799177-0.1492101594360.50911476500826.816819278933.893342884672.2426987784
74.801836784692.11204152494-5.163940057424.28457477228-4.874520608618.54836661768-0.1677593043820.337009738043-0.0536967627032-0.3563918274080.2890080401070.2863025197590.407232642331-0.554742454576-0.1012682062150.338578612332-0.0594845708468-0.01718287000390.335451552209-0.1280186432330.43495531193613.425951348927.745253355684.937299971
85.961212138530.452763077419-2.244793847153.680463816731.332230772216.805838067110.107067968029-0.0201481744130.170831159016-0.4202778794910.0197805879246-0.8746031056750.2313144136760.602584214615-0.1316311272190.3692649432760.1129907460460.101323077860.5918466634150.07936911336030.54084460907335.889764839147.325919969869.6433393987
91.732188945952.41977503959-0.1973373386047.73530456574-2.639708507291.516505076190.102541834301-0.216943298425-0.3786950720780.296324948869-0.259532730767-0.710145740070.06286626400140.2430218616070.1716272698210.3805399885150.03203095735730.03151039360120.456529516033-0.09743388612030.4478667093726.159273945223.605894301195.7077860297
101.946010093060.619255003699-1.355126869631.23411934579-1.024688563022.817871318960.0543832983039-0.249031719533-0.09760136482950.0626396172726-0.179461839346-0.0921385282260.209335478410.006121646379150.1346003532830.340052668431-0.0139926396053-0.0006362111058860.342079578781-0.07151899188630.33280434858519.25353449144.77527904390.4490082833
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 71 )AA3 - 711 - 69
22chain 'A' and (resid 72 through 127 )AA72 - 12770 - 125
33chain 'A' and (resid 128 through 191 )AA128 - 191126 - 189
44chain 'A' and (resid 192 through 284 )AA192 - 284190 - 282
55chain 'A' and (resid 285 through 385 )AA285 - 385283 - 383
66chain 'B' and (resid 3 through 59 )BB3 - 591 - 55
77chain 'B' and (resid 60 through 126 )BB60 - 12656 - 122
88chain 'B' and (resid 127 through 175 )BB127 - 175123 - 171
99chain 'B' and (resid 176 through 284 )BB176 - 284172 - 280
1010chain 'B' and (resid 285 through 385 )BB285 - 385281 - 381

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