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- PDB-2abq: Crystal structure of fructose-1-phosphate kinase from Bacillus ha... -

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Basic information

Entry
Database: PDB / ID: 2abq
TitleCrystal structure of fructose-1-phosphate kinase from Bacillus halodurans
Componentsfructose 1-phosphate kinase
KeywordsTRANSFERASE / kinase / dimer / T2083 / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


1-phosphofructokinase activity / lactose metabolic process / tagatose-6-phosphate kinase / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase activity / ATP binding / cytosol
Similarity search - Function
Fructose 1-phosphate kinase / Tagatose/fructose phosphokinase / pfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase ...Fructose 1-phosphate kinase / Tagatose/fructose phosphokinase / pfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Tagatose-6-phosphate kinase
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsEswaramoorthy, S. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of fructose-1-phosphate kinase from Bacillus halodurans
Authors: Eswaramoorthy, S. / Swaminathan, S.
History
DepositionJul 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _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
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: fructose 1-phosphate kinase
B: fructose 1-phosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7526
Polymers66,3722
Non-polymers3804
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-35 kcal/mol
Surface area25050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.620, 48.710, 79.050
Angle α, β, γ (deg.)82.38, 87.28, 82.14
Int Tables number1
Space group name H-MP1

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Components

#1: Protein fructose 1-phosphate kinase


Mass: 33186.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KEM5
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 3350, Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.9790, 0.9794, 0.94
SYNCHROTRONNSLS X29A20.9792
Detector
TypeIDDetectorDate
ADSC QUANTAM Q3151CCDApr 16, 2005
ADSC QUANTAM Q3152CCDFeb 3, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELMADMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97941
30.941
40.97921
ReflectionResolution: 2.1→50 Å / Num. all: 32984 / Num. obs: 32984 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 21
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.362 / Num. unique all: 2538 / % possible all: 69.7

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Processing

Software
NameVersionClassification
CBASEdata collection
SCALEPACKdata scaling
SOLVE& SHARPphasing
CNS1.1refinement
CBASSdata collection
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→39.2 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2986 1246 RANDOM
Rwork0.2549 --
obs0.2549 31234 -
all-31234 -
Refinement stepCycle: LAST / Resolution: 2.1→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4586 0 20 107 4713
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0072
X-RAY DIFFRACTIONc_angle_deg1.412

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