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- PDB-3t61: Crystal Structure of a gluconokinase from Sinorhizobium meliloti 1021 -

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Basic information

Entry
Database: PDB / ID: 3t61
TitleCrystal Structure of a gluconokinase from Sinorhizobium meliloti 1021
ComponentsGluconokinase
KeywordsTRANSFERASE / PSI-BIOLOGY / Structural Genomics / Protein Structure Initiative / New York Structural Genomics Research Consortium / NYSGRC / Alpha/Beta / gluconokinase / Kinase / Gluconic acid
Function / homology
Function and homology information


gluconokinase / gluconokinase activity / D-gluconate metabolic process / ATP binding / cytoplasm
Similarity search - Function
Carbohydrate kinase, thermoresistant glucokinase / Shikimate kinase / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Gluconokinase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Kumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal Structure of a gluconokinase from Sinorhizobium meliloti 1021
Authors: Kumaran, D. / Almo, S.C. / Swaminathan, S.
History
DepositionJul 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Structure summary
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gluconokinase
B: Gluconokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4994
Polymers45,3102
Non-polymers1902
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-37 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.202, 68.202, 118.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsDimer

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Components

#1: Protein Gluconokinase


Mass: 22654.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: gntK, RB0698, SM_b21119 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) / References: UniProt: Q92VK3, gluconokinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2M Ammonium Phosphate Monobasic, 0.1 M Tris, 2% sucrose, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2011 / Details: mirrors
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 27740 / Num. obs: 27740 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.1 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 16.5
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 16.9 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2284 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHELXEmodel building
ARP/wARPmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→44.68 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 169839.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Extra density near the phosphate ion is not modeled.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1860 6.9 %RANDOM
Rwork0.237 ---
obs0.237 26820 97.6 %-
all-26820 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.2911 Å2 / ksol: 0.343718 e/Å3
Displacement parametersBiso mean: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2---0.75 Å20 Å2
3---1.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 10 154 2860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.94
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 281 6.9 %
Rwork0.308 3763 -
obs--89.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5po4.parpo4.top

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