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- PDB-9zw8: Structure of the HMG-CoA reductase from Borrelia burgdorferi boun... -

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Basic information

Entry
Database: PDB / ID: 9zw8
TitleStructure of the HMG-CoA reductase from Borrelia burgdorferi bound to CoA
ComponentsProbable 3-hydroxy-3-methylglutaryl-coenzyme A reductase
KeywordsOXIDOREDUCTASE / class II HMGR / Bacterial / isoprenoid biosynthesis
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA reductase (NADH) activity / hydroxymethylglutaryl-CoA reductase / hydroxymethylglutaryl-CoA reductase (NADPH) activity / coenzyme A metabolic process
Similarity search - Function
Hydroxymethylglutaryl-CoA reductase, bacterial-type / Hydroxymethylglutaryl-CoA reductase, class I/II / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, catalytic domain superfamily / Hydroxymethylglutaryl-coenzyme A reductase / Hydroxymethylglutaryl-coenzyme A reductases family profile.
Similarity search - Domain/homology
COENZYME A / COENZYME A / Probable 3-hydroxy-3-methylglutaryl-coenzyme A reductase
Similarity search - Component
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsPaddy, I. / Dassma, L.M.K.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM150910 United States
CitationJournal: Protein Sci. / Year: 2026
Title: A cofactor-promiscuous HMGR from the Lyme disease pathogen illuminates diversity in bacterial isoprenoid biosynthesis.
Authors: Paddy, I.A. / McCausland, J. / Frazier, M. / Chatterjee, P. / Setegne, M. / Eidam, O. / Jacobs-Wagner, C. / Dassama, L.M.K.
History
DepositionJan 1, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable 3-hydroxy-3-methylglutaryl-coenzyme A reductase
B: Probable 3-hydroxy-3-methylglutaryl-coenzyme A reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1604
Polymers99,6252
Non-polymers1,5352
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12900 Å2
ΔGint-53 kcal/mol
Surface area33860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.856, 108.869, 139.687
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 10 through 404 or (resid 405...
d_2ens_1(chain "B" and resid 10 through 405)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 10 - 405 / Label seq-ID: 16 - 411

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.976108824387, 0.216560709864, -0.017692424852), (0.216369528879, 0.961325624174, -0.170403260765), (-0.0198944697504, -0.170160228167, -0.985215563632)Vector: 36. ...NCS oper: (Code: given
Matrix: (-0.976108824387, 0.216560709864, -0.017692424852), (0.216369528879, 0.961325624174, -0.170403260765), (-0.0198944697504, -0.170160228167, -0.985215563632)
Vector: 36.278696295, -0.676779091936, 43.5911779157)

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Components

#1: Protein Probable 3-hydroxy-3-methylglutaryl-coenzyme A reductase / HMG-CoA reductase


Mass: 49812.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_0685 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O51628, hydroxymethylglutaryl-CoA reductase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COZ / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.09 Å3/Da / Density % sol: 41.24 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris HCl and pH from 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.71→29.73 Å / Num. obs: 49262 / % possible obs: 99.59 % / Redundancy: 3.6 % / Biso Wilson estimate: 55.22 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.1274 / Rrim(I) all: 0.1497 / Net I/σ(I): 7.5
Reflection shellResolution: 2.71→2.75 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.9731 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 1851 / CC1/2: 0.577 / CC star: 0.855 / Rrim(I) all: 1.147 / % possible all: 99.89

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→29.73 Å / SU ML: 0.3645 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.8342
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2594 3329 7.62 %
Rwork0.214 40344 -
obs0.2175 43673 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.78 Å2
Refinement stepCycle: LAST / Resolution: 2.71→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6442 0 96 36 6574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00376661
X-RAY DIFFRACTIONf_angle_d0.82328971
X-RAY DIFFRACTIONf_chiral_restr0.04931007
X-RAY DIFFRACTIONf_plane_restr0.00951121
X-RAY DIFFRACTIONf_dihedral_angle_d7.6245934
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 4.14990955351 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.750.33781360.25861677X-RAY DIFFRACTION99.89
2.75-2.790.33521370.27261681X-RAY DIFFRACTION100
2.79-2.830.34331410.27571680X-RAY DIFFRACTION99.84
2.83-2.880.27021460.26971717X-RAY DIFFRACTION99.95
2.88-2.930.35431330.27051651X-RAY DIFFRACTION99.89
2.93-2.980.2941400.24571696X-RAY DIFFRACTION99.89
2.98-3.040.3231470.2651702X-RAY DIFFRACTION99.89
3.04-3.10.30761340.26131676X-RAY DIFFRACTION99.94
3.1-3.170.29011370.24561678X-RAY DIFFRACTION99.89
3.17-3.240.28061440.25091679X-RAY DIFFRACTION99.95
3.24-3.320.26571360.23921676X-RAY DIFFRACTION99.83
3.32-3.410.31881470.2291729X-RAY DIFFRACTION100
3.41-3.510.30761400.22181662X-RAY DIFFRACTION99.78
3.51-3.630.24381370.22211684X-RAY DIFFRACTION99.78
3.63-3.760.20731380.21311667X-RAY DIFFRACTION99.72
3.76-3.910.22371370.20031711X-RAY DIFFRACTION99.68
3.91-4.080.22761430.20441675X-RAY DIFFRACTION99.62
4.08-4.30.26261340.18971663X-RAY DIFFRACTION99.17
4.3-4.570.24821420.18661681X-RAY DIFFRACTION98.7
4.57-4.920.24771320.18161633X-RAY DIFFRACTION96.45
4.92-5.410.2481350.20171666X-RAY DIFFRACTION99.61
5.41-6.190.281460.22641698X-RAY DIFFRACTION99.73
6.19-7.770.25451320.20361691X-RAY DIFFRACTION99.73
7.77-29.730.1971350.17561671X-RAY DIFFRACTION99.29
Refinement TLS params.Method: refined / Origin x: 18.5160963458 Å / Origin y: 0.408080934618 Å / Origin z: 21.2481367542 Å
111213212223313233
T0.331141604695 Å20.00341700422986 Å2-0.0209127997711 Å2-0.384698572474 Å20.0298357310792 Å2--0.332965600522 Å2
L0.666995889187 °20.0929952276132 °2-0.14821685345 °2-0.976381486916 °2-0.206337737588 °2--1.22801438817 °2
S-0.0192273379915 Å °0.0372730405326 Å °-0.0251778253172 Å °-0.00492093453401 Å °0.0642678551378 Å °0.0108907078134 Å °-0.0695867713516 Å °-0.0264198618293 Å °-0.0445387712046 Å °
Refinement TLS groupSelection details: all

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