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- PDB-5byc: Crystal structure of human ribokinase in C2 spacegroup -

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Basic information

Entry
Database: PDB / ID: 5byc
TitleCrystal structure of human ribokinase in C2 spacegroup
ComponentsRibokinase
KeywordsTRANSFERASE
Function / homology
Function and homology information


ribokinase / ribokinase activity / Pentose phosphate pathway / D-ribose catabolic process / pentose-phosphate shunt / ATP binding / metal ion binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Ribokinase / Ribokinase/fructokinase / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPark, J. / Chakrabarti, J. / Singh, B. / Gupta, R.S. / Junop, M.S.
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Conformational flexibility of human ribokinase captured in seven crystal structures.
Authors: Akanmori, N.N. / Junop, M.S. / Gupta, R.S. / Park, J.
History
DepositionJun 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references / Structure summary
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
Revision 1.3Oct 29, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribokinase
B: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5284
Polymers70,4822
Non-polymers462
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-43 kcal/mol
Surface area27350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.920, 47.040, 80.910
Angle α, β, γ (deg.)90.00, 98.73, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 11 - 325 / Label seq-ID: 11 - 325

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ribokinase


Mass: 35241.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBKS, RBSK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H477, ribokinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / Source method: isolated from a natural source / Formula: H2O
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: 49.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M sodium HEPES, 10% isopropanol, 20% PEG 4000, 0.1M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.95→45.49 Å / Num. obs: 49417 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 13.799 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 11.5
Reflection shellResolution: 1.95→2 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.002 / Mean I/σ(I) obs: 1.9 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FV7

2fv7


Resolution: 1.95→45.49 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.361 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22044 2508 5.1 %RANDOM
Rwork0.17263 ---
obs0.17507 46908 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.526 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å2-0.49 Å2
2--1.01 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4700 0 2 511 5213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0194820
X-RAY DIFFRACTIONr_bond_other_d0.010.024623
X-RAY DIFFRACTIONr_angle_refined_deg2.1121.9626567
X-RAY DIFFRACTIONr_angle_other_deg1.641310635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4765642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.16225.585188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75615784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0561515
X-RAY DIFFRACTIONr_chiral_restr0.1260.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025563
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021030
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9071.3162559
X-RAY DIFFRACTIONr_mcbond_other0.9061.3152558
X-RAY DIFFRACTIONr_mcangle_it1.4041.9653204
X-RAY DIFFRACTIONr_mcangle_other1.4041.9663205
X-RAY DIFFRACTIONr_scbond_it1.3521.4962261
X-RAY DIFFRACTIONr_scbond_other1.3521.4972262
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.172.183364
X-RAY DIFFRACTIONr_long_range_B_refined5.86712.1095635
X-RAY DIFFRACTIONr_long_range_B_other5.68411.235389
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 35544 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.951→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 205 -
Rwork0.274 3360 -
obs--98.73 %
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)
11.15671.979-2.176611.3162-7.23995.6561-0.1206-0.06410.0042-0.40710.21820.23480.297-0.0224-0.09760.3472-0.0342-0.01620.28910.02230.342931.4828-24.191561.0846
22.97270.0888-1.49260.8801-0.31711.9544-0.03050.22960.1392-0.0980.0356-0.06360.06560.0527-0.00520.01560.01610.00090.1271-0.01040.021651.8736-3.127948.2264
32.94450.08510.41612.08350.38293.9141-0.01350.03590.35520.00590.00120.2212-0.4988-0.27580.01230.06780.04670.01190.08360.02010.069937.2766.569360.1797
410.7491-3.4032-1.71545.4971-0.75876.1692-0.1542-0.58470.44440.55430.19450.0132-0.4086-0.1682-0.04030.18310.02740.03320.0717-0.03880.065842.47428.338473.6308
53.12480.1848-0.05952.64220.55564.5881-0.0082-0.21790.06590.1683-0.016-0.1121-0.12750.33460.02420.0169-0.0128-0.00970.0560.00340.008150.2339-4.291169.1078
68.5461-2.6761-5.38319.02984.537411.9573-0.3868-0.4919-0.30540.53740.0420.36170.6543-0.02240.34480.1319-0.0305-0.02830.08460.03850.082747.5844-13.947475.8764
73.9102-3.5408-3.22873.55322.25864.0985-0.0656-0.08560.12150.11630.1016-0.1098-0.0881-0.0986-0.03610.0301-0.0121-0.04370.17930.02360.098763.0218-1.004934.1199
89.0254-3.9122-6.07683.0322.78194.10920.23450.1033-0.0561-0.1924-0.29550.3126-0.1795-0.1020.0610.04880.057-0.01420.3007-0.02850.065160.5272-1.944331.799
92.18850.3464-0.59651.4460.10343.9053-0.0861-0.1322-0.04450.0683-0.01480.05020.25460.00010.10090.0213-0.00020.00840.09230.03580.018566.6496-9.242432.0667
103.43920.67090.16042.0069-0.91144.1008-0.10450.05780.1297-0.1016-0.1083-0.1999-0.16170.39820.21280.02-0.00010.00580.18610.03420.052283.0216-2.321220.064
113.285-0.2319-0.43083.1141-0.14584.596-0.01690.30090.1934-0.0893-0.01840.0841-0.0763-0.10240.03530.0079-0.0118-0.00580.11250.01430.016167.1497-2.288912.6457
128.70583.1421-2.61634.895-1.686212.432-0.25390.5667-0.2245-0.06760.0255-0.16280.465-0.04190.22840.1336-0.033-0.01280.175-0.00830.028267.3306-8.2324-0.3614
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 15
2X-RAY DIFFRACTION2A16 - 133
3X-RAY DIFFRACTION3A134 - 228
4X-RAY DIFFRACTION4A229 - 252
5X-RAY DIFFRACTION5A253 - 313
6X-RAY DIFFRACTION6A314 - 327
7X-RAY DIFFRACTION7B11 - 45
8X-RAY DIFFRACTION8B46 - 56
9X-RAY DIFFRACTION9B57 - 135
10X-RAY DIFFRACTION10B136 - 257
11X-RAY DIFFRACTION11B258 - 318
12X-RAY DIFFRACTION12B319 - 326

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