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- PDB-8sbu: Crystal structure of MBP fusion with HPPK from Methanocaldococcus... -

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Basic information

Entry
Database: PDB / ID: 8sbu
TitleCrystal structure of MBP fusion with HPPK from Methanocaldococcus jannaschii
ComponentsMaltose/maltodextrin-binding periplasmic protein,6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
KeywordsTRANSFERASE / MBP fusion / 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 / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding ...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 / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / kinase activity / outer membrane-bounded periplasmic space / periplasmic space / phosphorylation / DNA damage response / magnesium ion binding / ATP binding / membrane
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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 MBP fusion with 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 4, 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: Maltose/maltodextrin-binding periplasmic protein,6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
B: Maltose/maltodextrin-binding periplasmic protein,6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,1284
Polymers137,4432
Non-polymers6852
Water6,107339
1
A: Maltose/maltodextrin-binding periplasmic protein,6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0642
Polymers68,7221
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltose/maltodextrin-binding periplasmic protein,6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0642
Polymers68,7221
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.170, 69.827, 73.121
Angle α, β, γ (deg.)67.44, 74.63, 78.13
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / HPPK / 2-amino-4-hydroxy-6- ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / 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: 68721.578 Da / Num. of mol.: 2
Mutation: D89A,K90A,E179A,N180A,K246A,E366A,K369A,D370A,R374N,I375A,T376A,K377A,I376A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Gene: malE, b4034, JW3994, mptE, MJ1634 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RIL
References: UniProt: P0AEX9, UniProt: Q59028, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 1.91 Å3/Da / Density % sol: 35.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: Lithium sulphate, PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 18, 2018
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 51068 / % possible obs: 98.5 % / Redundancy: 3.9 % / Rpim(I) all: 0.105 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.283.51.82250570.40.7561.1312.1490.94197.6
2.28-2.373.81.78950730.4770.8031.0652.0840.94597.7
2.37-2.483.91.55350640.560.8470.9041.7980.97197.8
2.48-2.6141.10651000.7240.9170.6421.2791.0198.1
2.61-2.7740.80350940.8260.9510.4650.9281.01398.2
2.77-2.9940.50651050.9150.9780.2930.5851.04698.6
2.99-3.2940.29551220.9620.990.1710.3411.03998.8
3.29-3.7640.15151360.9860.9960.0880.1751.01798.9
3.76-4.7340.08751450.9940.9980.0510.1011.01299.3
4.73-3040.06251720.9970.9990.0360.0711.03799.7

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Processing

Software
NameVersionClassification
PHENIXv1.16refinement
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.279 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 35.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1002 1.96 %Random selection
Rwork0.2212 ---
obs0.2222 51029 97.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→29.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9107 0 46 339 9492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059353
X-RAY DIFFRACTIONf_angle_d0.70412669
X-RAY DIFFRACTIONf_dihedral_angle_d16.9843425
X-RAY DIFFRACTIONf_chiral_restr0.0611410
X-RAY DIFFRACTIONf_plane_restr0.0041626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30920.38761300.32956884X-RAY DIFFRACTION94
2.3092-2.45380.36831490.30177117X-RAY DIFFRACTION98
2.4538-2.64310.33521400.27797146X-RAY DIFFRACTION98
2.6431-2.90890.33371450.25247205X-RAY DIFFRACTION98
2.9089-3.32930.3151460.24057185X-RAY DIFFRACTION99
3.3293-4.19260.24231510.19747224X-RAY DIFFRACTION99
4.1926-29.2790.22391410.18347266X-RAY DIFFRACTION100

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