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- PDB-3ikh: Crystal structure of Ribokinase in Complex with ATP and glycerol ... -

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Basic information

Entry
Database: PDB / ID: 3ikh
TitleCrystal structure of Ribokinase in Complex with ATP and glycerol in the active site from Klebsiella pneumoniae
ComponentsCarbohydrate kinase
KeywordsTRANSFERASE / KINASE / SAD / RIBOSE / D-RIBOSE METABOLIC PROCESS / ATP / RIBOKINASE / PFKB FAMILY / 11206L1 / PSI-II / NYSGXRC / STRUCTURAL GENOMICS / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


ribokinase / ribokinase activity / D-ribose catabolic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Ribokinase / Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 1. / 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
ADENOSINE-5'-TRIPHOSPHATE / Ribokinase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsSatyanarayana, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of Ribokinase in Complex with ATP and glycerol in the active site from Klebsiella pneumoniae
Authors: Satyanarayana, L. / Burley, S.K. / Swaminathan, S.
History
DepositionAug 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbohydrate kinase
B: Carbohydrate kinase
C: Carbohydrate kinase
D: Carbohydrate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,42610
Polymers128,2134
Non-polymers2,2136
Water6,846380
1
A: Carbohydrate kinase
C: Carbohydrate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2135
Polymers64,1062
Non-polymers1,1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-17 kcal/mol
Surface area22830 Å2
MethodPISA
2
B: Carbohydrate kinase
D: Carbohydrate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2135
Polymers64,1062
Non-polymers1,1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-21 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.332, 106.352, 122.056
Angle α, β, γ (deg.)90.00, 99.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Carbohydrate kinase


Mass: 32053.193 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Top10 (Invitrogen)
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria)
Strain: ATCC700721/MGH78578) / Gene: KPN78578_16990, KPN78578_16990/5340552, KPN_01729 / Plasmid: pSGX3 (BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) Codon + RIL / References: UniProt: A6T989, ribokinase
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M LITHIUM SULFATE MONO HYDRATE, 0.1M HEPES PH 7.5, 20%PEG 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. all: 110843 / Num. obs: 110843 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 21.3 Å2 / Rsym value: 0.085 / Net I/σ(I): 13
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 8.3 / Num. unique all: 11075 / Rsym value: 0.49 / % possible all: 98.8

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I3Y

3i3y


Resolution: 1.88→37.54 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 4275 -RANDOM
Rwork0.22 ---
all0.235 106135 --
obs0.22 106135 95.3 %-
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.9 Å20 Å21.39 Å2
2--7.1 Å20 Å2
3----2.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.88→37.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8484 0 136 380 9000
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_improper_angle_deg0.83
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
LS refinement shellResolution: 1.88→1.99 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.314 562 -
Rwork0.289 --
obs-14019 78.1 %

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