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- PDB-9zw7: Structure of the HMG-CoA reductase from Borrelia burgdorferi boun... -

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Basic information

Entry
Database: PDB / ID: 9zw7
TitleStructure of the HMG-CoA reductase from Borrelia burgdorferi bound to CoA and Lovastatin
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
LOVASTATIN / 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: 2.3 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)101,5645
Polymers99,6252
Non-polymers1,9403
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13370 Å2
ΔGint-52 kcal/mol
Surface area33320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.463, 139.917, 54.581
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 or resid 502))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETMETMETAA10 - 40516 - 411
d_12COACOACOACOAAC501
d_21METMETMETMETBB10 - 40516 - 411
d_22COACOACOACOABE501

NCS oper: (Code: givenMatrix: (0.958340765324, 0.173580320779, -0.226832206171), (0.172967471758, -0.984665139712, -0.0227335951877), (-0.227299870726, -0.017448062204, -0.973668492811)Vector: 5. ...NCS oper: (Code: given
Matrix: (0.958340765324, 0.173580320779, -0.226832206171), (0.172967471758, -0.984665139712, -0.0227335951877), (-0.227299870726, -0.017448062204, -0.973668492811)
Vector: 5.37540655929, -43.0402251414, 17.6292004812)

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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.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-803 / LOVASTATIN / MK-803 / LOVALIP / MEVACOR


Mass: 404.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H36O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris HCl and varied pH from 5.5 to 7, and 19 to 29% (w/v) PEG 3350
PH range: 5.5 - 7

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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 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→28.74 Å / Num. obs: 81141 / % possible obs: 98.46 % / Redundancy: 3.5 % / Biso Wilson estimate: 43.65 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.0813 / Rrim(I) all: 0.09621 / Net I/σ(I): 9.3
Reflection shellResolution: 2.3→2.33 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.038 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3227 / CC1/2: 0.612 / CC star: 0.872 / Rrim(I) all: 1.228 / % possible all: 99.73

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→28.74 Å / SU ML: 0.2721 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2615 3300 4.66 %
Rwork0.2087 67514 -
obs0.2111 70814 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.83 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6419 0 108 88 6615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00626651
X-RAY DIFFRACTIONf_angle_d0.99388960
X-RAY DIFFRACTIONf_chiral_restr0.05661010
X-RAY DIFFRACTIONf_plane_restr0.00771118
X-RAY DIFFRACTIONf_dihedral_angle_d7.6343943
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 4.20629420764 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.31621390.252832X-RAY DIFFRACTION99.73
2.33-2.370.30621430.24422898X-RAY DIFFRACTION99.48
2.37-2.40.29261370.25462796X-RAY DIFFRACTION99.69
2.4-2.440.2981390.23652850X-RAY DIFFRACTION99.27
2.44-2.490.28611360.23932748X-RAY DIFFRACTION95.97
2.49-2.530.26161320.23342739X-RAY DIFFRACTION96.8
2.53-2.580.29921400.22252864X-RAY DIFFRACTION99.17
2.58-2.630.28121390.2222836X-RAY DIFFRACTION99.5
2.63-2.690.30531360.2192837X-RAY DIFFRACTION99.53
2.69-2.750.29491420.22192831X-RAY DIFFRACTION99.66
2.75-2.820.25251380.21342874X-RAY DIFFRACTION99.6
2.82-2.90.2811360.23962832X-RAY DIFFRACTION99.4
2.9-2.980.28211410.23012859X-RAY DIFFRACTION99.54
2.98-3.080.27951390.22652816X-RAY DIFFRACTION99.43
3.08-3.190.27671380.22472842X-RAY DIFFRACTION99.37
3.19-3.320.33421380.23392845X-RAY DIFFRACTION99.17
3.32-3.470.2811380.22072815X-RAY DIFFRACTION99.33
3.47-3.650.2711380.21322862X-RAY DIFFRACTION98.68
3.65-3.880.26761370.20832790X-RAY DIFFRACTION98.22
3.88-4.180.21441370.19922799X-RAY DIFFRACTION97.74
4.18-4.590.24161330.17972720X-RAY DIFFRACTION95.93
4.59-5.260.22731240.18112572X-RAY DIFFRACTION90.29
5.26-6.610.27951410.2132820X-RAY DIFFRACTION98.8
6.61-28.740.21311390.17942837X-RAY DIFFRACTION98.8
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)
11.148657758150.639439714689-0.2374739324482.22963874034-0.4611212205920.9069726069870.109685619181-0.1438044744330.07551405253320.248386350711-0.0688495619157-0.165027382944-0.1003788699760.0222341517113-0.03959548971810.301389768463-0.033375630678-0.02509387127460.291355026181-0.05118918472890.316772875321.03796610191-18.123792941217.349523885
21.502320175450.23439258547-0.008076257478842.0335741661-0.0001994188696131.0804894128-0.02778055202530.0893834513704-0.0875398224646-0.2537071405290.0724960435789-0.1746805884990.037911021944-0.0326542261145-0.0386446709750.290779432632-0.04615769026710.004464183641870.268893310223-0.03199883607160.277599327106-0.463044006607-24.5858566316-0.280363879115
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain B and resseq 10:418)BC10 - 4181 - 409
22(chain A and resseq 10:405)AA10 - 4051 - 396

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