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- PDB-3h49: Crystal structure of a putative Ribokinase (Apo Form) from E.coli... -

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Basic information

Entry
Database: PDB / ID: 3h49
TitleCrystal structure of a putative Ribokinase (Apo Form) from E.coli at 1.8A resolution
ComponentsRibokinase
KeywordsTRANSFERASE / Ribokinase / pfkB family / Sugar kinase ydjH / NYSGXRC / 11206A / PSI2 / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / Kinase
Function / homology
Function and homology information


carbohydrate kinase activity / D-galacturonate catabolic process / 2-dehydro-3-deoxygluconokinase activity / D-glucuronate catabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / DNA damage response / cytosol
Similarity search - Function
Ribokinase/fructokinase / 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
Uncharacterized sugar kinase YdjH
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsSatyanarayana, L. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative Ribokinase (Apo Form) from E.coli at 1.8A resolution.
Authors: Satyanarayana, L. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionApr 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribokinase
B: Ribokinase


Theoretical massNumber of molelcules
Total (without water)71,3992
Polymers71,3992
Non-polymers00
Water5,603311
1
A: Ribokinase


Theoretical massNumber of molelcules
Total (without water)35,7001
Polymers35,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribokinase


Theoretical massNumber of molelcules
Total (without water)35,7001
Polymers35,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Ribokinase

B: Ribokinase


Theoretical massNumber of molelcules
Total (without water)71,3992
Polymers71,3992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3290 Å2
ΔGint-23 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.088, 73.718, 82.153
Angle α, β, γ (deg.)90.00, 96.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribokinase /


Mass: 35699.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: TOP10 (Invitrogen) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b1772, JW5289, ydjH / Plasmid: pSGX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon+RIL
References: UniProt: P77493, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.03 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M Ammonium Acetate,30% PEG 4K,Sodium Citrate 5.6pH, 10%Isopropanol., 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 315r / Detector: CCD / Date: Apr 8, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 51641 / Num. obs: 51641 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 10.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 7.7 / Num. unique all: 5073 / Rsym value: 0.48 / % possible all: 96.7

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXCDphasing
SHARPphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→34.71 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The main chain oxygen of Ser141 shows anisotropic effect.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1984 -RANDOM
Rwork0.213 ---
all0.229 49918 --
obs0.213 49918 94.5 %-
Displacement parametersBiso mean: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å2-0.53 Å2
2--3.77 Å20 Å2
3----2.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.8→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4590 0 0 311 4901
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_improper_angles_deg0.82
X-RAY DIFFRACTIONc_dihedral_angle_d23
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.259 292 -
Rwork0.265 --
obs-7217 85.4 %

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