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- PDB-9zpu: Crystal Structure of a Ribokinase from Brucella suis in complex w... -

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Basic information

Entry
Database: PDB / ID: 9zpu
TitleCrystal Structure of a Ribokinase from Brucella suis in complex with ADP
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 / Ribokinase
Similarity search - Component
Biological speciesBrucella suis 1330 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 with ADP
Authors: Seibold, S. / Lovell, S. / Battaile, K.P.
History
DepositionDec 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2025Provider: 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
E: Ribokinase
F: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,71962
Polymers192,7776
Non-polymers6,94256
Water48627
1
A: Ribokinase
B: Ribokinase
C: Ribokinase
D: Ribokinase
hetero molecules

E: Ribokinase
hetero molecules

F: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,71962
Polymers192,7776
Non-polymers6,94256
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area19930 Å2
ΔGint-559 kcal/mol
Surface area71120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.093, 138.228, 80.872
Angle α, β, γ (deg.)90.00, 107.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ribokinase / RK


Mass: 32129.488 Da / Num. of mol.: 6
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.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.12 Å3/Da / Density % sol: 60.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Salt RX B6: 2.0M Ammonium citrate tribasic, 0.1M Bis-Tris Propane pH 7.0. BrsuA.01141.a.B2.PW39414 at 19.5 mg/mL. 2 mM ADP ane Ribose-5-phosphate were added prior to crystallization but only ...Details: Salt RX B6: 2.0M Ammonium citrate tribasic, 0.1M Bis-Tris Propane pH 7.0. BrsuA.01141.a.B2.PW39414 at 19.5 mg/mL. 2 mM ADP ane Ribose-5-phosphate were added prior to crystallization but only ADP was bound. plate clover plate BK 6, pg 3 position D1, Puck: PSL-0516, 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: Nov 1, 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: 2.85→45.05 Å / Num. obs: 55138 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.046 / Rrim(I) all: 0.121 / Χ2: 0.99 / Net I/σ(I): 10.6 / Num. measured all: 381045
Reflection shellResolution: 2.85→2.93 Å / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 1.273 / Num. measured all: 32877 / Num. unique obs: 4499 / CC1/2: 0.867 / Rpim(I) all: 0.504 / Rrim(I) all: 1.371 / Χ2: 0.98 / Net I/σ(I) obs: 1.6

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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: 2.85→45.05 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 2822 5.13 %
Rwork0.1945 --
obs0.1977 54983 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→45.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13001 0 384 27 13412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413529
X-RAY DIFFRACTIONf_angle_d0.69718448
X-RAY DIFFRACTIONf_dihedral_angle_d18.184664
X-RAY DIFFRACTIONf_chiral_restr0.0462164
X-RAY DIFFRACTIONf_plane_restr0.0052391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.90.46551130.42742617X-RAY DIFFRACTION99
2.9-2.950.40261610.36382550X-RAY DIFFRACTION99
2.95-3.010.36461580.31342591X-RAY DIFFRACTION99
3.01-3.070.3541360.2962592X-RAY DIFFRACTION99
3.07-3.140.36551550.28552606X-RAY DIFFRACTION99
3.14-3.210.34921540.26842537X-RAY DIFFRACTION99
3.21-3.290.30631480.2512578X-RAY DIFFRACTION99
3.29-3.380.28951420.2412617X-RAY DIFFRACTION99
3.38-3.480.32131380.24822615X-RAY DIFFRACTION100
3.48-3.590.3271450.23762563X-RAY DIFFRACTION100
3.59-3.720.26231450.19672614X-RAY DIFFRACTION100
3.72-3.870.2271420.1772619X-RAY DIFFRACTION100
3.87-4.040.25021320.17012633X-RAY DIFFRACTION100
4.04-4.260.22571480.16332597X-RAY DIFFRACTION100
4.26-4.520.20591500.14922592X-RAY DIFFRACTION100
4.52-4.870.21681280.14472620X-RAY DIFFRACTION100
4.87-5.360.21641150.16032663X-RAY DIFFRACTION100
5.36-6.130.28711420.18792623X-RAY DIFFRACTION100
6.14-7.720.22251330.17742657X-RAY DIFFRACTION100
7.72-45.050.20191370.16122677X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.6725-1.12171.38531.804-0.5472.6597-0.8871-0.19040.34930.73850.4061-0.0371-0.5589-0.14920.52410.67210.1059-0.080.4250.0590.492664.86071.336736.7166
22.5216-0.72190.04212.6348-1.2420.6675-0.00130.2075-0.10650.14350.0121-0.0449-0.21010.17070.04530.69280.0463-0.19570.6639-0.03980.690870.748-2.31837.8096
35.06710.35-0.04843.6031-0.04143.2570.3009-0.8373-0.34450.4525-0.2860.0981-0.21990.0767-0.11430.73260.2062-0.06110.9272-0.05750.562562.51180.772845.8833
45.8918-2.11941.28763.8177-1.17242.23430.14640.1669-0.4610.1348-0.0343-0.0047-0.01570.0679-0.14020.72320.0172-0.11240.67260.02920.50662.1475-5.256635.4323
55.5341.2190.29172.2113-0.81551.7664-0.4274-0.32190.2498-0.44050.3780.34020.1004-0.28250.08160.70320.0475-0.22070.50990.08850.776852.82130.907626.7611
60.3681-0.02220.76054.0620.40544.53390.07230.442-0.0496-0.0791-0.053-0.08210.0840.4697-0.00030.66330.0551-0.11660.6176-0.04520.646159.62130.693613.7822
75.09240.64740.35674.25711.22653.9743-0.3333-0.0667-0.38530.05110.2374-0.7493-0.34920.6978-0.260.5021-0.00590.01670.57880.01190.681670.544410.0316.1897
87.8158-2.6534-0.18811.48420.81180.995-0.3607-0.86341.00820.02780.4821-0.7501-0.28870.1273-0.04130.71810.036-0.15380.59060.06260.810765.288614.587424.0664
95.7423-3.41643.48028.6176-1.62127.9716-0.4761-0.70480.88220.002-0.1365-0.3635-0.3089-0.2250.54770.80140.1221-0.22850.82050.05620.992474.588316.80230.1054
107.13492.40881.05242.77750.01523.0226-0.62720.4764-0.3457-0.56710.4776-0.62370.1665-0.02090.26910.7682-0.033-0.28820.5368-0.0630.57627.2646-1.4755-2.4135
113.71970.2560.00031.3378-0.52451.2906-0.18540.5501-0.41590.06550.2085-0.0579-0.0807-0.14630.0190.7899-0.016-0.21470.69050.00140.857524.6203-3.7459-7.1028
123.62411.50512.00811.7357-0.13272.86530.43010.0301-0.60640.3151-0.0999-0.37960.1914-0.1442-0.16990.80990.0178-0.19070.49720.00240.758834.54-4.2683.7271
133.1616-0.86590.42823.6611-1.38015.6665-0.05-0.4797-0.52940.12860.40060.48020.0663-0.7506-0.2310.49860.0029-0.07040.51210.1060.613628.16897.933115.2824
146.81952.4424-0.04042.0673-2.23734.148-0.04740.70090.0184-1.01550.84371.11880.3522-0.7621-0.72311.0403-0.128-0.27660.75720.12250.945318.088314.91480.7074
154.21291.40091.8852.4822.78833.12910.1897-0.3745-0.64050.42740.1144-0.36910.01190.0369-0.12580.9081-0.0784-0.27620.5724-0.03570.962314.1672-19.0176-11.4676
161.24520.1147-0.77362.64211.29683.58980.0047-0.03120.02830.0548-0.1839-0.4731-0.72650.31950.37120.8109-0.1372-0.28920.7860.07490.995811.2006-16.2279-18.5192
174.49590.91192.11293.58941.1613.4129-0.3401-0.29970.54910.1101-0.20940.5668-0.5101-0.35950.50840.7131-0.0206-0.13470.6226-0.1270.7979-4.3145-20.5024-24.0367
186.8094-0.67380.70062.7337-0.1262.5-0.0863-0.7075-0.33020.26090.1137-0.03440.09560.26940.05050.59890.0095-0.01140.67020.04080.42744.619-38.2272-22.9117
192.6451-0.36012.55051.2144-1.38123.3803-0.2125-0.35010.16350.25-0.09340.0255-0.2072-0.21390.35520.66850.1632-0.03570.7697-0.02260.64380.8695-15.707253.3804
204.8935-0.7810.7645.997-0.9211.76010.02140.752-0.408-0.18550.0689-0.4440.0212-0.4806-0.07970.61760.0371-0.01750.79460.01720.615196.92-29.803153.4104
214.9828-0.37631.36573.48050.73291.17120.08530.0835-1.0719-0.0820.06090.83060.2221-0.6628-0.25760.6701-0.0791-0.00480.9323-0.01460.849883.9862-38.459357.1558
225.6296-0.45280.74212.89432.25892.24210.4869-0.1131-0.44890.26230.28170.4871-0.4799-0.7536-0.11441.1318-0.0834-0.09911.30760.091.161272.0517-33.470258.9348
234.34350.7580.64260.22470.29591.2913-0.22520.00431.1750.03050.0370.0134-0.34610.00240.17380.64440.08550.04370.6104-0.02651.021949.0175-32.134927.9715
244.70721.1253-1.00880.9262-0.38752.9056-0.27770.0812-0.95410.13870.2264-0.24420.41580.32030.00280.65140.0602-0.10380.7782-0.10280.997540.3837-42.809631.2504
253.25421.1875-0.01213.3175-0.60871.9546-0.15240.7263-0.79990.03890.3004-0.73970.31360.02110.05640.57950.13560.04750.8515-0.1590.985844.8336-39.81524.9289
263.2369-1.2171-1.64083.13290.20866.7860.10510.9385-0.9092-0.4795-0.24290.13850.1915-0.6657-0.10460.5971-0.0398-0.10360.6611-0.08170.954226.6967-42.856325.2232
273.10610.41510.67850.73110.88334.0968-0.10410.43560.01050.0422-0.1683-0.5185-0.42960.02330.11940.65470.05870.08010.69550.05090.809724.6746-33.758724.6065
284.8507-2.2668-0.57122.7402-0.16192.96540.25970.09580.4669-0.0087-0.4835-0.1132-0.46850.09330.10580.7282-0.0154-0.10880.55480.03620.792924.106-22.805633.9496
293.8947-0.68961.22282.2039-0.65432.8773-0.2917-0.1763-0.0270.20420.1589-0.6514-0.44110.38290.17660.6047-0.0465-0.12290.6148-0.03410.768430.5046-31.436945.171
307.35231.35550.85316.6828-0.90543.2360.0118-0.2796-0.7555-0.32450.3436-0.3810.17650.3153-0.39410.6899-0.0247-0.06570.6832-0.02220.989839.539-38.935149.0783
315.37580.10430.4610.18740.59321.7681-0.08710.45751.0702-0.0343-0.0942-0.1501-0.1488-0.44220.18670.6937-0.01110.04480.593-0.04680.67260.1283-34.181417.9191
322.40410.1829-0.67421.7978-0.98335.20650.03630.0015-0.0092-0.32070.22590.22930.4652-0.5911-0.22460.5748-0.1027-0.050.5028-0.04710.882372.3168-43.906716.116
333.7565-1.0009-0.02610.97460.01842.65090.1347-0.41-0.540.00470.04350.25070.20720.0529-0.17030.5986-0.080.00810.4864-0.03320.7474.0081-38.24421.7499
342.37120.4280.89432.06470.38293.2183-0.16030.2270.283-0.3310.03840.5776-0.4787-0.04840.1410.6035-0.0355-0.09840.4941-0.02270.744181.6492-28.50495.2721
358.42450.359-5.40395.2634-1.93139.6430.08640.5547-0.13750.23640.46050.37730.2472-1.022-0.69390.8228-0.0121-0.08660.7454-0.05011.049969.1007-40.6919-1.8583
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 70 )
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 99 )
4X-RAY DIFFRACTION4chain 'A' and (resid 100 through 136 )
5X-RAY DIFFRACTION5chain 'A' and (resid 137 through 177 )
6X-RAY DIFFRACTION6chain 'A' and (resid 178 through 228 )
7X-RAY DIFFRACTION7chain 'A' and (resid 229 through 257 )
8X-RAY DIFFRACTION8chain 'A' and (resid 258 through 292 )
9X-RAY DIFFRACTION9chain 'A' and (resid 293 through 312 )
10X-RAY DIFFRACTION10chain 'B' and (resid 8 through 24 )
11X-RAY DIFFRACTION11chain 'B' and (resid 25 through 98 )
12X-RAY DIFFRACTION12chain 'B' and (resid 99 through 179 )
13X-RAY DIFFRACTION13chain 'B' and (resid 180 through 291 )
14X-RAY DIFFRACTION14chain 'B' and (resid 292 through 311 )
15X-RAY DIFFRACTION15chain 'C' and (resid 7 through 45 )
16X-RAY DIFFRACTION16chain 'C' and (resid 46 through 116 )
17X-RAY DIFFRACTION17chain 'C' and (resid 117 through 179 )
18X-RAY DIFFRACTION18chain 'C' and (resid 180 through 312 )
19X-RAY DIFFRACTION19chain 'D' and (resid 5 through 136 )
20X-RAY DIFFRACTION20chain 'D' and (resid 137 through 228 )
21X-RAY DIFFRACTION21chain 'D' and (resid 229 through 291 )
22X-RAY DIFFRACTION22chain 'D' and (resid 292 through 310 )
23X-RAY DIFFRACTION23chain 'E' and (resid 8 through 37 )
24X-RAY DIFFRACTION24chain 'E' and (resid 38 through 70 )
25X-RAY DIFFRACTION25chain 'E' and (resid 71 through 124 )
26X-RAY DIFFRACTION26chain 'E' and (resid 125 through 148 )
27X-RAY DIFFRACTION27chain 'E' and (resid 149 through 179 )
28X-RAY DIFFRACTION28chain 'E' and (resid 180 through 228 )
29X-RAY DIFFRACTION29chain 'E' and (resid 229 through 292 )
30X-RAY DIFFRACTION30chain 'E' and (resid 293 through 312 )
31X-RAY DIFFRACTION31chain 'F' and (resid 7 through 45 )
32X-RAY DIFFRACTION32chain 'F' and (resid 46 through 70 )
33X-RAY DIFFRACTION33chain 'F' and (resid 71 through 177 )
34X-RAY DIFFRACTION34chain 'F' and (resid 178 through 292 )
35X-RAY DIFFRACTION35chain 'F' and (resid 293 through 312 )

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