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- PDB-6da0: Crystal structure of glucokinase (NfHK) from Naegleria fowleri -

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Basic information

Entry
Database: PDB / ID: 6da0
TitleCrystal structure of glucokinase (NfHK) from Naegleria fowleri
ComponentsGlucokinase
KeywordsTRANSFERASE / SSGCID / Structural Genomics / Naegleria fowleri / Glucokinase / NfHK / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glucokinase / glucokinase activity / glucose binding / glycolytic process / ATP binding
Similarity search - Function
Glucokinase / Glucokinase / ATPase, nucleotide binding domain
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / beta-D-glucopyranose / Glucokinase
Similarity search - Component
Biological speciesNaegleria fowleri (brain-eating amoeba)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Antimicrob.Agents Chemother. / Year: 2019
Title: Enzymatic and Structural Characterization of theNaegleria fowleriGlucokinase.
Authors: Milanes, J.E. / Suryadi, J. / Abendroth, J. / Van Voorhis, W.C. / Barrett, K.F. / Dranow, D.M. / Phan, I.Q. / Patrick, S.L. / Rozema, S.D. / Khalifa, M.M. / Golden, J.E. / Morris, J.C.
History
DepositionMay 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1323
Polymers50,4461
Non-polymers6862
Water6,431357
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint3 kcal/mol
Surface area17260 Å2
Unit cell
Length a, b, c (Å)202.480, 202.480, 68.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-664-

HOH

21A-792-

HOH

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Components

#1: Protein Glucokinase /


Mass: 50445.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba)
Plasmid: NafoA.19900.a.B11
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A384E136*PLUS, glucokinase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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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: 3.5 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 13.78 mg/mL NafoA.19900.a.B11.PW39443 + 2 mM magnesium chloride, AMPPNP, beta-D-glucose + Molecular Dimensions Morpheus screen, C8 (12.5% w/v PEG1000, 12.5% w/v PEG3350, 12.5% v/v MPD, 30 mM ...Details: 13.78 mg/mL NafoA.19900.a.B11.PW39443 + 2 mM magnesium chloride, AMPPNP, beta-D-glucose + Molecular Dimensions Morpheus screen, C8 (12.5% w/v PEG1000, 12.5% w/v PEG3350, 12.5% v/v MPD, 30 mM sodium nitrate, 0.3 M disodium hydrogen phosphate, 0.3 M ammonium sulfate, 100 mM bicine/Trizma base, pH 8.5), cryoprotection: direct, tray 299931c8, puck VSZ1-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→45.276 Å / Num. obs: 36362 / % possible obs: 99.6 % / Redundancy: 7.108 % / Biso Wilson estimate: 28.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.097 / Χ2: 1.009 / Net I/σ(I): 17.95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.265.2960.5723.2726420.8680.63399.7
2.26-2.326.940.5184.5625960.9420.559100
2.32-2.397.2470.455.3325330.9460.483100
2.39-2.467.2640.4065.9424630.9590.436100
2.46-2.547.2570.3476.7423740.9690.373100
2.54-2.637.2540.2748.4323070.9780.294100
2.63-2.737.2760.2319.5722140.9860.248100
2.73-2.847.3150.20210.8421410.9880.21799.9
2.84-2.977.3410.14314.4420480.9930.153100
2.97-3.117.3270.11916.5719850.9950.12899.9
3.11-3.287.3390.09220.8218890.9970.09999.7
3.28-3.487.2950.07226.2617710.9980.07799.8
3.48-3.727.3250.05931.5116680.9980.06499.7
3.72-4.027.3120.04836.4615940.9990.05299.9
4.02-4.47.2890.0441.1414370.9990.04399.5
4.4-4.927.3110.03644.4213210.9990.03999.3
4.92-5.687.2760.0440.1611600.9990.04498.8
5.68-6.967.2220.04436.739960.9990.04898.4
6.96-9.847.1640.02948.1478010.03197
9.84-45.2766.5060.02359.9544310.02592.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
MoRDaphasing
PARROTphasing
ARP/wARPmodel building
BUCCANEERmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 5BRH & 1SZ2

5brh

1sz2


Resolution: 2.2→45.276 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.76
RfactorNum. reflection% reflectionSelection details
Rfree0.1872 2015 5.54 %0
Rwork0.1539 ---
obs0.1557 36357 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.62 Å2 / Biso mean: 35.4694 Å2 / Biso min: 11.15 Å2
Refinement stepCycle: final / Resolution: 2.2→45.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 43 365 3402
Biso mean--48.97 45.2 -
Num. residues----378
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.25510.24431410.205724092550100
2.2551-2.3160.23141340.187124292563100
2.316-2.38420.2351600.177724252585100
2.3842-2.46110.22471470.169924292576100
2.4611-2.54910.19291420.172324282570100
2.5491-2.65110.22221360.164224372573100
2.6511-2.77180.22371440.171124342578100
2.7718-2.91790.19361410.162124262567100
2.9179-3.10070.19261320.158424802612100
3.1007-3.340.17871450.152124492594100
3.34-3.6760.1481390.136224732612100
3.676-4.20760.15641450.126924772622100
4.2076-5.29980.15471470.13162491263899
5.2998-45.28550.20511620.16572555271797
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)
11.68730.570.25730.9208-0.06341.1795-0.02440.1131-0.1024-0.10620.0006-0.21310.0860.25840.02540.17160.02730.02710.2165-0.00260.216370.727250.3758-2.3221
26.86180.9255-0.40611.5706-0.0221.22650.0572-0.53270.18810.0492-0.0763-0.1178-0.05860.2370.01520.1898-0.01920.01080.3579-0.030.176789.093957.227118.9861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 151 through 400 )A151 - 400
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 150 )A23 - 150

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