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- PDB-9zw9: Structure of the HMG-CoA reductase from Borrelia burgdorferi boun... -

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Basic information

Entry
Database: PDB / ID: 9zw9
TitleStructure of the HMG-CoA reductase from Borrelia burgdorferi bound to CoA and Mevalonate
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 / (R)-MEVALONATE / Probable 3-hydroxy-3-methylglutaryl-coenzyme A reductase
Similarity search - Component
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)101,1786
Polymers99,3492
Non-polymers1,8294
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13850 Å2
ΔGint-41 kcal/mol
Surface area33030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.435, 109.165, 139.904
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_1chain "A"
d_2ens_1(chain "B" and (resid 10 through 404 or resid 501 through 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_11METMETGLUGLUAA10 - 40415 - 409
d_12COACOACOACOAAC501
d_13MEVMEVMEVMEVAD502
d_21METMETGLUGLUBB10 - 40415 - 409
d_22COACOACOACOABE501
d_23MEVMEVMEVMEVBF502

NCS oper: (Code: givenMatrix: (-0.978086082579, 0.207500488477, 0.0170634799256), (0.20734900543, 0.963400717293, 0.169898345686), (0.0188150209213, 0.16971330296, -0.985313853443)Vector: 17. ...NCS oper: (Code: given
Matrix: (-0.978086082579, 0.207500488477, 0.0170634799256), (0.20734900543, 0.963400717293, 0.169898345686), (0.0188150209213, 0.16971330296, -0.985313853443)
Vector: 17.7220816073, -5.18884542047, 43.0142290572)

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Components

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


Mass: 49674.297 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-MEV / (R)-MEVALONATE


Mass: 147.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris HCl, pH 6.5, and 25% (w/v) PEG 3350, 1 mM Mevalonate, 1 mM CoA
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: 0.979458 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979458 Å / Relative weight: 1
ReflectionResolution: 2.2→24.89 Å / Num. obs: 92897 / % possible obs: 98.99 % / Redundancy: 4 % / Biso Wilson estimate: 39.18 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06165 / Rrim(I) all: 0.07121 / Net I/σ(I): 13.03
Reflection shellResolution: 2.2→2.23 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.815 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 3730 / CC1/2: 0.621 / CC star: 0.875 / Rrim(I) all: 0.9444 / % possible all: 99.36

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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: 2.2→24.89 Å / SU ML: 0.2908 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.6411
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2572 3322 4.1 %
Rwork0.2114 77616 -
obs0.2132 80938 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.29 Å2
Refinement stepCycle: LAST / Resolution: 2.2→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6433 0 116 209 6758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416670
X-RAY DIFFRACTIONf_angle_d0.97298983
X-RAY DIFFRACTIONf_chiral_restr0.05281008
X-RAY DIFFRACTIONf_plane_restr0.01081121
X-RAY DIFFRACTIONf_dihedral_angle_d9.1512940
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 3.93378242677 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.31091390.24973263X-RAY DIFFRACTION99.36
2.23-2.260.27751400.23863322X-RAY DIFFRACTION98.91
2.26-2.30.30561390.24643190X-RAY DIFFRACTION99.64
2.3-2.340.31141390.24473243X-RAY DIFFRACTION98.72
2.34-2.380.331330.24423246X-RAY DIFFRACTION99.68
2.38-2.420.27041390.24183187X-RAY DIFFRACTION98.32
2.42-2.470.31381390.2343239X-RAY DIFFRACTION98.31
2.47-2.520.29441310.22833059X-RAY DIFFRACTION95.31
2.52-2.570.24011410.22563281X-RAY DIFFRACTION98.76
2.57-2.630.2551380.22213199X-RAY DIFFRACTION99.29
2.63-2.70.2541440.23473284X-RAY DIFFRACTION99.94
2.7-2.770.24731390.21383245X-RAY DIFFRACTION99.32
2.77-2.850.29931350.23843280X-RAY DIFFRACTION99.91
2.85-2.940.3261360.23643238X-RAY DIFFRACTION99.53
2.94-3.050.25871420.23523279X-RAY DIFFRACTION99.53
3.05-3.170.24671410.2283206X-RAY DIFFRACTION99.52
3.17-3.320.2991390.24443265X-RAY DIFFRACTION99.71
3.32-3.490.26041380.223264X-RAY DIFFRACTION99.71
3.49-3.710.29251390.21223262X-RAY DIFFRACTION99.79
3.71-3.990.23291390.19943233X-RAY DIFFRACTION99.5
3.99-4.390.22231370.18263247X-RAY DIFFRACTION99.38
4.39-5.020.21921320.17483077X-RAY DIFFRACTION93.94
5.02-6.310.25741440.2073247X-RAY DIFFRACTION99.97
6.31-24.890.21551390.18063260X-RAY DIFFRACTION99.71
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)
10.7413177974350.05342731260390.224236514710.8664751902650.3012174874871.64121389038-0.02589438390650.09481326083950.0121334044719-0.07328287663950.0924172748766-0.1310748871440.09255301070080.231233850566-0.07403040588210.2242023918680.01235672020520.03286980162360.378430044476-0.03146801969690.26525582055517.4869418804-1.0844742515717.9626128908
20.895973693447-0.01774348703250.08268371462991.091952084570.2586431194641.75337157716-0.0172154718349-0.06720750185410.07542190996220.1245138021560.002361666782480.1221412671950.0903258074265-0.2249919191640.001649117345920.236990983230.0005843310146040.03813022104180.411966389627-0.02494455716410.307054431695-0.2257901277120.29532125576124.9237635762
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 7:418)BD7 - 4181 - 412
22(chain A and resseq 10:502)AA - C10 - 5021

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