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- PDB-9goj: Crystal structure of HpeI from Rhodococcus rhodochrous GD02 -

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Basic information

Entry
Database: PDB / ID: 9goj
TitleCrystal structure of HpeI from Rhodococcus rhodochrous GD02
ComponentsPhosphoenolpyruvate synthase
KeywordsTRANSFERASE / kinase / lignin
Function / homology
Function and homology information


pyruvate, water dikinase / pyruvate, water dikinase activity / pyruvate metabolic process / ATP binding / metal ion binding
Similarity search - Function
Phosphoenolpyruvate synthase / Pyruvate phosphate dikinase, AMP/ATP-binding / Pyruvate phosphate dikinase, AMP/ATP-binding domain / ATP-grasp fold, subdomain 1
Similarity search - Domain/homology
Phosphoenolpyruvate synthase
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsZahn, M. / Wheatley, E.J. / Grigg, J.C. / Eltis, L.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Research England United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Characterization of a two-component kinase that initiates the bacterial catabolism of hydroxyphenylethanones.
Authors: Dexter, G.N. / Grigg, J.C. / Zahn, M. / Wheatley, E.J. / Lian, J. / Mohn, W.W. / Eltis, L.D.
History
DepositionSep 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoenolpyruvate synthase


Theoretical massNumber of molelcules
Total (without water)42,2521
Polymers42,2521
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.902, 57.27, 67.118
Angle α, β, γ (deg.)90, 99.591, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphoenolpyruvate synthase / Pyruvate / water dikinase


Mass: 42251.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Gene: KUM34_002985 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AA46WYF7, pyruvate, water dikinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
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: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% PEG 1500, 0.1 M PCTP (Sodium propionate, Sodium cacodylate trihydrate, Bis-Tris propane) pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.803→66.18 Å / Num. obs: 14742 / % possible obs: 90.7 % / Redundancy: 7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.067 / Net I/σ(I): 6.9
Reflection shellResolution: 1.803→1.972 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.312 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 737 / CC1/2: 0.642 / Rpim(I) all: 0.528 / % possible all: 66

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.82)refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.803→66.18 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.892 / SU B: 8.83 / SU ML: 0.135 / Cross valid method: FREE R-VALUE / ESU R: 0.432 / ESU R Free: 0.263 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2552 715 4.85 %
Rwork0.2072 14027 -
all0.21 --
obs-14742 46.353 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.712 Å2
Baniso -1Baniso -2Baniso -3
1--0.256 Å20 Å20.07 Å2
2---0.057 Å20 Å2
3---0.274 Å2
Refinement stepCycle: LAST / Resolution: 1.803→66.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 0 88 2629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122612
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.823549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5015338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.976526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84110445
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.65510121
X-RAY DIFFRACTIONr_chiral_restr0.1250.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022006
X-RAY DIFFRACTIONr_nbd_refined0.2330.21168
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21790
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2152
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2540.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.120.210
X-RAY DIFFRACTIONr_mcbond_it1.6861.8981328
X-RAY DIFFRACTIONr_mcangle_it2.7513.3981659
X-RAY DIFFRACTIONr_scbond_it2.3172.0781284
X-RAY DIFFRACTIONr_scangle_it3.6563.7031885
X-RAY DIFFRACTIONr_lrange_it6.02219.9933962
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.803-1.850.35820.206420.21723350.9950.9721.88440.202
1.85-1.9010.50370.2641950.27122760.8040.968.87520.255
1.901-1.9560.246170.2673370.26621980.9650.95316.10560.258
1.956-2.0160.325250.2384380.24221650.9160.96321.38570.227
2.016-2.0820.277220.2535190.25420990.9640.95825.77420.233
2.082-2.1550.409310.2385910.24620020.8960.96431.06890.218
2.155-2.2360.326220.2296750.23219500.9250.96735.74360.206
2.236-2.3270.276440.2117300.21518860.9590.9741.03920.187
2.327-2.4310.28490.2147820.21818100.9530.97245.91160.193
2.431-2.5490.25360.2168470.21717250.9570.97151.18840.184
2.549-2.6870.352590.2268910.23316390.9020.96857.96220.206
2.687-2.850.325550.2289370.23415580.9380.96863.67140.205
2.85-3.0460.268580.2489900.24914650.950.96171.53580.226
3.046-3.2890.26420.22910590.2313490.9510.96781.6160.214
3.289-3.6020.248630.21811080.2212700.9540.97292.20470.207
3.602-4.0260.241610.19310700.19511360.9610.97799.55990.189
4.026-4.6460.211540.1679600.1710140.9690.9841000.171
4.646-5.6830.202230.1718370.1728600.9740.9831000.183
5.683-8.0080.267260.2076500.2096760.9630.9761000.224
8.008-66.180.125190.1833680.183870.9840.9751000.218
Refinement TLS params.Method: refined / Origin x: 3.568 Å / Origin y: -0.3138 Å / Origin z: 13.4425 Å
111213212223313233
T0.0018 Å2-0.0038 Å2-0.0011 Å2-0.0283 Å2-0.0099 Å2--0.0339 Å2
L0.1141 °20.1549 °2-0.0985 °2-0.7191 °2-0.5713 °2--0.7986 °2
S0.0124 Å °-0.0082 Å °-0.012 Å °0.0245 Å °-0.0458 Å °-0.1182 Å °-0.026 Å °0.1292 Å °0.0334 Å °
Refinement TLS groupSelection: ALL

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