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- PDB-9zw6: Structure of the HMG-CoA reductase from Borrelia burgdorferi boun... -

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Basic information

Entry
Database: PDB / ID: 9zw6
TitleStructure of the HMG-CoA reductase from Borrelia burgdorferi bound to HMG-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
3-HYDROXY-3-METHYLGLUTARYL-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: 2.55 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)101,4384
Polymers99,6252
Non-polymers1,8132
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13330 Å2
ΔGint-48 kcal/mol
Surface area33250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.539, 108.795, 139.621
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 501))

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_12HMGHMGHMGHMGAC501
d_21METMETMETMETBB10 - 40516 - 411
d_22HMGHMGHMGHMGBD501

NCS oper: (Code: givenMatrix: (-0.973324791325, 0.228588794848, 0.0196472253119), (0.22850429549, 0.958138631456, 0.172499709723), (0.0206067351849, 0.172387719348, -0.984813605046)Vector: 17. ...NCS oper: (Code: given
Matrix: (-0.973324791325, 0.228588794848, 0.0196472253119), (0.22850429549, 0.958138631456, 0.172499709723), (0.0206067351849, 0.172387719348, -0.984813605046)
Vector: 17.6516224247, -5.33204314148, 43.0366233582)

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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-HMG / 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A / (S)-HMG-COA


Mass: 906.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H39N7O20P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: with 0.1 M Bis-Tris HCl and varied pH from 5.5 to 7, and 19 to 29% (w/v) PEG 3350, 1 mM HMG-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 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979458 Å / Relative weight: 1
ReflectionResolution: 2.546→24.86 Å / Num. obs: 50333 / % possible obs: 98.66 % / Redundancy: 3 % / Biso Wilson estimate: 40.85 Å2 / CC1/2: 0.825 / CC star: 0.951 / Rmerge(I) obs: 0.166 / Rrim(I) all: 0.2003 / Net I/σ(I): 7.51
Reflection shellResolution: 2.55→2.61 Å / Redundancy: 2.6 % / Rmerge(I) obs: 1.037 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 3147 / CC1/2: 0.337 / CC star: 0.71 / Rrim(I) all: 1.282 / % possible all: 97.68

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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: 2.55→24.86 Å / SU ML: 0.3198 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.8196
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2664 2000 7.25 %
Rwork0.2174 25600 -
obs0.2209 27600 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.33 Å2
Refinement stepCycle: LAST / Resolution: 2.55→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6419 0 116 54 6589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00356657
X-RAY DIFFRACTIONf_angle_d0.80648969
X-RAY DIFFRACTIONf_chiral_restr0.04771006
X-RAY DIFFRACTIONf_plane_restr0.00991121
X-RAY DIFFRACTIONf_dihedral_angle_d9.643943
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 4.25761242747 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.610.31921400.24931796X-RAY DIFFRACTION97.68
2.61-2.680.28731400.24441789X-RAY DIFFRACTION99.79
2.68-2.760.2811430.22871834X-RAY DIFFRACTION99.8
2.76-2.850.29661430.2381830X-RAY DIFFRACTION99.85
2.85-2.950.34071410.25021802X-RAY DIFFRACTION99.79
2.95-3.070.34851430.2491838X-RAY DIFFRACTION99.45
3.07-3.210.30451440.2451821X-RAY DIFFRACTION98.74
3.21-3.370.26251370.23611771X-RAY DIFFRACTION98
3.37-3.590.30591430.22221819X-RAY DIFFRACTION97.71
3.59-3.860.25551400.20261804X-RAY DIFFRACTION97.3
3.86-4.250.23591440.19711842X-RAY DIFFRACTION99.75
4.25-4.860.20771460.18321862X-RAY DIFFRACTION99.26
4.86-6.110.25891480.21961888X-RAY DIFFRACTION98.6
6.11-24.860.24441480.20851904X-RAY DIFFRACTION95.89
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)
10.7480119794420.237700801310.1245776025361.003346470970.5850280155561.89296828913-0.05136543108890.08209052311960.0006567439666430.03277125074510.109491235091-0.1694940900380.09533547375170.240308332521-0.07166246001840.2261468929620.04247451465520.01526300010380.387594550159-0.02006682874710.24651679679517.3495125613-1.0759318724418.0411778293
20.76036725430.07621794645750.1271932707951.19276666997-0.1019245473091.92240893737-0.0498950208627-0.0109223885192-0.001431741283770.06926892837250.03435834731140.1123292527840.102830480146-0.2478734468070.0001008609618640.197647688137-8.2107179198E-50.03776214139480.380931219939-0.03313977176820.246485189481-0.2399480899780.38234737204224.6468582494
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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