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- PDB-11bl: Crystal Structure of a Ribokinase from Brucella suis in complex A... -

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Basic information

Entry
Database: PDB / ID: 11bl
TitleCrystal Structure of a Ribokinase from Brucella suis in complex ADP (P21 form)
ComponentsRibokinase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / ribokinase
Function / homology
Function and homology information


ribokinase / ribokinase activity / D-ribose catabolic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Ribokinase / 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-like
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Ribokinase
Similarity search - Component
Biological speciesBrucella suis 1330 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of a Ribokinase from Brucella suis in complex ADP (P21 form)
Authors: Seibold, S. / Lovell, S. / Battaile, K.P.
History
DepositionFeb 16, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribokinase
B: Ribokinase
C: Ribokinase
D: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,80014
Polymers128,5184
Non-polymers2,28210
Water19811
1
A: Ribokinase
C: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3036
Polymers64,2592
Non-polymers1,0444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-43 kcal/mol
Surface area23310 Å2
MethodPISA
2
B: Ribokinase
D: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4978
Polymers64,2592
Non-polymers1,2386
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-65 kcal/mol
Surface area22890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.363, 81.851, 100.634
Angle α, β, γ (deg.)90.00, 106.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribokinase / RK


Mass: 32129.488 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella suis 1330 (bacteria) / Gene: rbsK, BS1330_II0005 / Plasmid: BrsuA.01141.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3GDY9, ribokinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Grid Salt screen B1: 2.4 M AmSO4 + 0.3 M Tri-Sodium Citrate pH 4.0. BrsuA.01141.a.B2.PW39414 at 19.5 mg/mL. 2 mM ATP and MgCl2 were added prior to crystallization but only ADP was bound. ...Details: Grid Salt screen B1: 2.4 M AmSO4 + 0.3 M Tri-Sodium Citrate pH 4.0. BrsuA.01141.a.B2.PW39414 at 19.5 mg/mL. 2 mM ATP and MgCl2 were added prior to crystallization but only ADP was bound. Clover_Plate B6, BK 6, pg 3, Puck: PSL-1507, Cryo: 2.5M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 4, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.9→47.09 Å / Num. obs: 27251 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.079 / Rrim(I) all: 0.206 / Χ2: 0.99 / Net I/σ(I): 7.8 / Num. measured all: 183528
Reflection shellResolution: 2.9→3.08 Å / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 1.129 / Num. measured all: 28869 / Num. unique obs: 4355 / CC1/2: 0.8 / Rpim(I) all: 0.473 / Rrim(I) all: 1.227 / Χ2: 1.01 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(2.0_5904: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→47.09 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.286 1381 5.09 %
Rwork0.2449 --
obs0.247 27156 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8044 0 138 11 8193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058284
X-RAY DIFFRACTIONf_angle_d0.73111315
X-RAY DIFFRACTIONf_dihedral_angle_d17.2392723
X-RAY DIFFRACTIONf_chiral_restr0.0471381
X-RAY DIFFRACTIONf_plane_restr0.0051474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-30.45191340.38152534X-RAY DIFFRACTION100
3-3.120.41471440.32122573X-RAY DIFFRACTION100
3.12-3.270.34161330.31312563X-RAY DIFFRACTION100
3.27-3.440.37221230.26822588X-RAY DIFFRACTION100
3.44-3.650.34071390.24592542X-RAY DIFFRACTION100
3.65-3.940.31251440.23912587X-RAY DIFFRACTION99
3.94-4.330.25841460.21592573X-RAY DIFFRACTION100
4.33-4.960.2361490.19992560X-RAY DIFFRACTION99
4.96-6.240.26111330.24512614X-RAY DIFFRACTION100
6.24-47.090.21471360.22022641X-RAY DIFFRACTION99

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