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- PDB-6whj: Structure of Ribokinase from Giardia lamblia -

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Basic information

Entry
Database: PDB / ID: 6whj
TitleStructure of Ribokinase from Giardia lamblia
ComponentsRibokinase
KeywordsTRANSFERASE / SSGCID / Giardia lamblia / Giardia intestinalis / Ribokinase / GL50803_15297 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


ribokinase / ribokinase activity / D-ribose catabolic process / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Ribokinase / Ribokinase/fructokinase / 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
Biological speciesGiardia lamblia (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of Ribokinase from Giardia lamblia
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionApr 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Oct 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)150,3777
Polymers150,1914
Non-polymers1863
Water3,045169
1
A: Ribokinase
B: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2204
Polymers75,0962
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-6 kcal/mol
Surface area25240 Å2
MethodPISA
2
C: Ribokinase
D: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1583
Polymers75,0962
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-11 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.620, 169.920, 84.140
Angle α, β, γ (deg.)90.000, 98.360, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 4 through 6 and (name N...
21(chain B and ((resid 4 through 6 and (name N...
31(chain C and ((resid 4 through 6 and (name N...
41(chain D and (resid 4 through 28 or (resid 29...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLYSLYS(chain A and ((resid 4 through 6 and (name N...AA4 - 66 - 8
12THRTHREDOEDO(chain A and ((resid 4 through 6 and (name N...AA - E4 - 4016
13THRTHREDOEDO(chain A and ((resid 4 through 6 and (name N...AA - E4 - 4016
14THRTHREDOEDO(chain A and ((resid 4 through 6 and (name N...AA - E4 - 4016
15THRTHREDOEDO(chain A and ((resid 4 through 6 and (name N...AA - E4 - 4016
21THRTHRLYSLYS(chain B and ((resid 4 through 6 and (name N...BB4 - 66 - 8
22SERSEREDOEDO(chain B and ((resid 4 through 6 and (name N...BB - F3 - 4015
23SERSEREDOEDO(chain B and ((resid 4 through 6 and (name N...BB - F3 - 4015
24SERSEREDOEDO(chain B and ((resid 4 through 6 and (name N...BB - F3 - 4015
25SERSEREDOEDO(chain B and ((resid 4 through 6 and (name N...BB - F3 - 4015
31THRTHRLYSLYS(chain C and ((resid 4 through 6 and (name N...CC4 - 66 - 8
32THRTHRPHEPHE(chain C and ((resid 4 through 6 and (name N...CC4 - 3396 - 341
33THRTHRPHEPHE(chain C and ((resid 4 through 6 and (name N...CC4 - 3396 - 341
34THRTHRPHEPHE(chain C and ((resid 4 through 6 and (name N...CC4 - 3396 - 341
35THRTHRPHEPHE(chain C and ((resid 4 through 6 and (name N...CC4 - 3396 - 341
41THRTHRGLYGLY(chain D and (resid 4 through 28 or (resid 29...DD4 - 286 - 30
42GLNGLNGLNGLN(chain D and (resid 4 through 28 or (resid 29...DD2931
43THRTHRSERSER(chain D and (resid 4 through 28 or (resid 29...DD4 - 3376 - 339
44THRTHRSERSER(chain D and (resid 4 through 28 or (resid 29...DD4 - 3376 - 339
45THRTHRSERSER(chain D and (resid 4 through 28 or (resid 29...DD4 - 3376 - 339

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Components

#1: Protein
Ribokinase / / RK


Mass: 37547.754 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia lamblia (eukaryote) / Strain: ATCC 50803 / WB clone C6 / Gene: GL50803_15297 / Plasmid: GilaA.01141.a.AE1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: A8B6Y7, ribokinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.75
Details: Microlytic MCSG1 screen, condition A9: 200mM Magnesium chloride, 22.5% (w/V) PEG 3350, 100mM HEPES free acid / NaOH pH 6.75: GilaA.01141.a.AE1.PS38632 at 34.66mg/ml: tray: 315276a9, cryo: ...Details: Microlytic MCSG1 screen, condition A9: 200mM Magnesium chloride, 22.5% (w/V) PEG 3350, 100mM HEPES free acid / NaOH pH 6.75: GilaA.01141.a.AE1.PS38632 at 34.66mg/ml: tray: 315276a9, cryo: 15% EG in 2 steps: puck vdk2-4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 27, 2020
RadiationMonochromator: RIGAKU VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→46.83 Å / Num. obs: 35700 / % possible obs: 99.4 % / Redundancy: 6.18 % / Biso Wilson estimate: 43.921 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.11 / Χ2: 0.979 / Net I/σ(I): 15.47 / Num. measured all: 220642 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.725.2980.5293.0513521261225520.8140.58897.7
2.72-2.795.9050.4493.8415460264626180.8820.49398.9
2.79-2.876.4260.3964.4415659245324370.9250.43199.3
2.87-2.966.3620.3175.5415656248324610.9440.34599.1
2.96-3.066.3810.2746.4514739233223100.9610.29899.1
3.06-3.176.3650.237.6614583229922910.9710.25199.7
3.17-3.296.3880.16910.2913869218621710.9830.18599.3
3.29-3.426.3430.13812.613676216121560.9870.15199.8
3.42-3.576.3670.11814.9912784201520080.9910.12999.7
3.57-3.756.2790.09119.2812331197419640.9950.09999.5
3.75-3.956.2830.07922.0911460182718240.9960.08699.8
3.95-4.196.1480.06824.2710974178717850.9970.07599.9
4.19-4.486.0440.05828.3710063166616650.9970.06399.9
4.48-4.846.1920.05230.019275149614980.9980.057100
4.84-5.36.2140.0626.888948144214400.9970.06599.9
5.3-5.936.2780.07222.637986127112720.9960.079100
5.93-6.846.2510.06225.27064113111300.9980.06899.9
6.84-8.386.0490.04533.7558379699650.9990.04999.6
8.38-11.855.8540.02947.0843797497480.9990.03299.9
11.85-46.835.8720.02551.1523784184050.9990.02896.9

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Processing

Software
NameVersionClassification
PHENIX1.18rc4refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MR-Rosettaphasing
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MR-rosetta starting from hhpred hit 1rkd

1rkd


Resolution: 2.65→46.83 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 1954 5.47 %0
Rwork0.1789 ---
obs0.1814 35692 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.31 Å2 / Biso mean: 46.9772 Å2 / Biso min: 18.59 Å2
Refinement stepCycle: final / Resolution: 2.65→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9527 0 12 169 9708
Biso mean--36.24 37.37 -
Num. residues----1304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059727
X-RAY DIFFRACTIONf_angle_d0.77613185
X-RAY DIFFRACTIONf_dihedral_angle_d21.7273463
X-RAY DIFFRACTIONf_chiral_restr0.0511547
X-RAY DIFFRACTIONf_plane_restr0.0051719
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5385X-RAY DIFFRACTION11.288TORSIONAL
12B5385X-RAY DIFFRACTION11.288TORSIONAL
13C5385X-RAY DIFFRACTION11.288TORSIONAL
14D5385X-RAY DIFFRACTION11.288TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.720.27091310.21792330246197
2.72-2.790.30021410.23262447258899
2.79-2.870.31681470.22262333248099
2.87-2.960.30111420.23292434257699
2.96-3.070.22931270.21392365249299
3.07-3.190.26361470.203424542601100
3.19-3.340.23981240.198523882512100
3.34-3.510.23071290.200424372566100
3.51-3.730.2421370.188324452582100
3.73-4.020.20291250.160724092534100
4.02-4.430.16781490.144924352584100
4.43-5.070.20611400.13724102550100
5.07-6.380.22361660.178224262592100
6.38-46.830.18411490.15332425257499
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.82781.84870.33764.17810.4991.1236-0.1257-0.0922-0.0153-0.04730.1377-0.0805-0.1457-0.01160.08520.18860.0510.0280.28770.02630.296710.912633.96743.8629
21.10731.3770.19933.41820.95551.25620.05160.0571-0.2365-0.1766-0.1822-0.65210.29070.21750.03790.18390.07310.02010.30270.08230.419815.432118.77371.5783
31.83230.4212-0.74093.51240.09440.43560.16890.17780.0504-0.5484-0.1654-1.04330.00090.490.02240.32290.02780.19360.44210.0690.586218.268221.5051-7.3322
41.39480.2773-0.46014.60110.24561.29920.07160.12660.1167-0.17670.1159-0.12650.1095-0.0179-0.12880.1556-0.0102-0.04240.32940.11190.30887.128528.7983-2.1443
52.96841.05110.01053.61190.13014.3002-0.1440.2449-0.0005-0.24910.2233-0.10120.1396-0.13090.01340.19510.00530.00910.24120.0110.2753-0.068412.8056-2.9559
63.15770.8599-0.44491.2503-1.57322.40590.1069-0.17660.4617-0.14380.03080.4011-0.4258-0.40270.00810.26710.03790.03370.3282-0.03450.4662-7.763519.85338.2158
72.85170.9795-0.54393.60490.74833.80230.0939-0.44550.2720.433-0.34560.60160.1026-0.60360.09310.2467-0.03480.03580.3704-0.08240.3367-8.283313.478215.0952
83.70870.8795-0.05493.3947-0.07544.54550.101-0.4549-0.30330.68280.0771-0.9390.10570.4827-0.04850.25970.02-0.07490.40330.02450.40568.324512.128415.5279
92.6785-0.3664-1.48040.88511.45432.68370.2633-0.7730.33130.19940.2192-1.06760.03051.2864-0.32550.41040.0333-0.19150.8105-0.08991.105618.823717.177716.4831
101.72050.2372-0.05242.81950.06361.11930.0446-0.0258-0.0813-0.0692-0.0337-0.1945-0.06370.0879-0.03790.15270.0109-0.01430.2240.0220.210621.257256.3938-3.4458
112.1419-0.3092-0.31572.70710.30873.666-0.03820.11570.0306-0.24020.00280.2579-0.0249-0.18310.050.22480.0055-0.04350.22830.0510.313810.219670.8797-7.5047
122.5167-0.79410.06522.4040.00213.4575-0.1705-0.1230.1260.06670.1975-0.30160.33480.22430.02580.4037-0.13580.00160.3466-0.01120.202920.327276.177738.5447
132.7704-1.0857-0.81262.7199-0.78383.4308-0.0363-0.271-0.01020.48070.11690.21010.0609-0.3009-0.12970.368-0.08610.02810.33180.01830.238110.028778.771143.3563
142.6645-0.3949-0.55911.8859-0.27276.77550.17930.2167-0.16910.0018-0.01810.01930.982-0.8557-0.20010.3399-0.0471-0.02170.41030.07490.39190.526778.13228.6635
152.9596-0.10150.04513.38040.20094.01290.01140.0950.1013-0.1548-0.00930.393-0.0254-0.5155-0.02740.2498-0.0179-0.01230.35960.02130.25557.40884.955924.0147
164.593-1.3617-0.52435.34732.27525.12070.3140.21330.5511-0.0118-0.1871-0.5756-0.64460.2967-0.16370.3976-0.05830.05190.2920.09430.454818.084691.375927.2424
171.5292-1.32420.15962.258-1.13850.8286-0.412-0.09340.12430.45710.2312-0.01290.0382-0.27260.04011.0454-0.0823-0.06890.4206-0.05670.320823.972252.625343.0352
184.69490.1218-0.77480.00220.00071.1835-0.1076-1.22210.63320.4850.0943-0.07430.02550.33980.16841.2667-0.0247-0.13980.6277-0.1650.357735.970845.591454.6312
191.7886-1.41080.29071.2089-0.44570.6193-0.2445-0.58120.8090.46580.0479-0.7159-0.1402-0.1477-0.0721.2738-0.1678-0.08320.4347-0.19310.528832.184355.234544.9909
203.1372-1.3039-0.83462.99220.05813.2973-0.18710.1485-0.11420.3074-0.0786-0.119-0.24590.15520.29280.5055-0.1079-0.00870.34-0.02470.288939.278535.286836.6944
214.4922-0.3468-1.82193.38732.02854.2527-0.3704-0.7466-0.74570.7025-0.04330.11280.84950.08610.36690.73-0.03490.16260.3670.09750.465631.042928.09646.666
221.50020.17510.57651.7364-1.04920.9473-0.267-0.5534-0.36891.38570.00660.36610.4858-0.58890.34941.08970.07120.34590.75780.1370.699220.522535.148955.2796
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 33 )A4 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 69 )A34 - 69
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 97 )A70 - 97
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 128 )A98 - 128
5X-RAY DIFFRACTION5chain 'A' and (resid 129 through 181 )A129 - 181
6X-RAY DIFFRACTION6chain 'A' and (resid 182 through 213 )A182 - 213
7X-RAY DIFFRACTION7chain 'A' and (resid 214 through 256 )A214 - 256
8X-RAY DIFFRACTION8chain 'A' and (resid 257 through 318 )A257 - 318
9X-RAY DIFFRACTION9chain 'A' and (resid 319 through 336 )A319 - 336
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 195 )B3 - 195
11X-RAY DIFFRACTION11chain 'B' and (resid 196 through 340 )B196 - 340
12X-RAY DIFFRACTION12chain 'C' and (resid 4 through 69 )C4 - 69
13X-RAY DIFFRACTION13chain 'C' and (resid 70 through 181 )C70 - 181
14X-RAY DIFFRACTION14chain 'C' and (resid 182 through 213 )C182 - 213
15X-RAY DIFFRACTION15chain 'C' and (resid 214 through 285 )C214 - 285
16X-RAY DIFFRACTION16chain 'C' and (resid 286 through 339 )C286 - 339
17X-RAY DIFFRACTION17chain 'D' and (resid 4 through 53 )D4 - 53
18X-RAY DIFFRACTION18chain 'D' and (resid 54 through 69 )D54 - 69
19X-RAY DIFFRACTION19chain 'D' and (resid 70 through 126 )D70 - 126
20X-RAY DIFFRACTION20chain 'D' and (resid 127 through 247 )D127 - 247
21X-RAY DIFFRACTION21chain 'D' and (resid 248 through 315 )D248 - 315
22X-RAY DIFFRACTION22chain 'D' and (resid 316 through 337 )D316 - 337

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