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- PDB-8sd5: Crystal structure of HPPK from Methanocaldococcus jannaschii -

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Basic information

Entry
Database: PDB / ID: 8sd5
TitleCrystal structure of HPPK from Methanocaldococcus jannaschii
Components6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
KeywordsTRANSFERASE / HPPK / Methanocaldococcus jannaschii
Function / homology
Function and homology information


tetrahydromethanopterin biosynthetic process / thiamine diphosphokinase activity / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / thiamine diphosphate biosynthetic process / kinase activity / magnesium ion binding / ATP binding
Similarity search - Function
6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, MptE / 6-hydroxymethylpterin diphosphokinase MptE-like / 6-hydroxymethylpterin diphosphokinase MptE-like / Thiamin pyrophosphokinase, catalytic domain superfamily
Similarity search - Domain/homology
6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 Å
AuthorsShaw, G.X. / Needle, D. / Stair, N.R. / Cherry, S. / Tropea, J.E. / Waugh, D.S. / Ji, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: To be published
Title: Crystal structure of HPPK from Methanocaldococcus jannaschii
Authors: Shaw, G.X. / Needle, D. / Stair, N.R. / Cherry, S. / Tropea, J.E. / Waugh, D.S. / Ji, X.
History
DepositionApr 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
B: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
C: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
D: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,7737
Polymers110,4854
Non-polymers2883
Water1,49583
1
A: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7172
Polymers27,6211
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7172
Polymers27,6211
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7172
Polymers27,6211
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase


Theoretical massNumber of molelcules
Total (without water)27,6211
Polymers27,6211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.729, 75.744, 179.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase / HPPK / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase / 6-hydroxymethyl-7 / 8- ...HPPK / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase / 6-hydroxymethyl-7 / 8-dihydropterin diphosphokinase / 6-HMPDK / 7 / 8-dihydro-6-hydroxymethylpterin diphosphokinase / 8-dihydro-6-hydroxymethylpterin pyrophosphokinase / PPPK


Mass: 27621.184 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: mptE, MJ1634 / Production host: Escherichia coli (E. coli)
References: UniProt: Q59028, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Lithium sulphate, PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 27, 2014 / Details: Si(111)
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 22509 / % possible obs: 88.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.037 / Rrim(I) all: 0.081 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.8-2.91.80.32616010.5870.860.2450.4110.62164.1
2.9-3.0220.31118260.6280.8780.2210.3850.6672.5
3.02-3.152.20.320320.6660.8940.2050.3670.6681.3
3.15-3.322.70.24221990.8720.9650.1560.2910.6787.7
3.32-3.5330.21323380.9190.9790.1260.2490.85892.3
3.53-3.83.60.16323800.9830.9960.0890.1870.92494.6
3.8-4.184.20.10924200.9960.9990.0550.1221.00495.5
4.18-4.785.10.06525170.99810.0290.0720.99797.8
4.78-6.025.30.06425200.99810.0280.07197.7
6.02-305.80.0322676110.0140.0351.00197.7

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Processing

Software
NameVersionClassification
PHENIX(dev_3352)refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.802→29.93 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 32.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1004 4.47 %Random selection
Rwork0.2426 ---
obs0.2447 22441 88.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.802→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6905 0 15 83 7003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087033
X-RAY DIFFRACTIONf_angle_d1.1239448
X-RAY DIFFRACTIONf_dihedral_angle_d25.4692684
X-RAY DIFFRACTIONf_chiral_restr0.0921055
X-RAY DIFFRACTIONf_plane_restr0.0051202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.802-2.94920.36451060.3192256X-RAY DIFFRACTION66
2.9492-3.13380.36841180.30992662X-RAY DIFFRACTION78
3.1338-3.37550.32811430.28363019X-RAY DIFFRACTION88
3.3755-3.71460.32071420.24623231X-RAY DIFFRACTION94
3.7146-4.25080.28071600.21933299X-RAY DIFFRACTION95
4.2508-5.35060.25761670.20433411X-RAY DIFFRACTION98
5.3506-29.930.25941680.23763559X-RAY DIFFRACTION97

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