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- PDB-5bye: Crystal structure of human ribokinase in P212121 spacegroup -

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Basic information

Entry
Database: PDB / ID: 5bye
TitleCrystal structure of human ribokinase in P212121 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: 1.75 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)70,5635
Polymers70,4822
Non-polymers813
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-49 kcal/mol
Surface area26140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.250, 65.480, 180.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 15 - 324 / Label seq-ID: 15 - 324

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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris, 8% PEG 8000

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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: 1.75→47.74 Å / Num. obs: 67798 / % possible obs: 99.5 % / Redundancy: 10.6 % / Biso Wilson estimate: 22.15 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.2
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.962 / Mean I/σ(I) obs: 2.3 / % 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: 1.75→47.74 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.02 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22882 3322 4.9 %RANDOM
Rwork0.19034 ---
obs0.19221 64402 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.057 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2--1.36 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4591 0 3 437 5031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0194673
X-RAY DIFFRACTIONr_bond_other_d0.0110.024495
X-RAY DIFFRACTIONr_angle_refined_deg2.2751.9626355
X-RAY DIFFRACTIONr_angle_other_deg1.834310332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.515618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31325.33182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00915761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2751516
X-RAY DIFFRACTIONr_chiral_restr0.1360.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.025364
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021004
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_it1.4131.7212478
X-RAY DIFFRACTIONr_mcbond_other1.4131.722477
X-RAY DIFFRACTIONr_mcangle_it2.0862.5753094
X-RAY DIFFRACTIONr_mcangle_other2.0862.5763095
X-RAY DIFFRACTIONr_scbond_it1.9691.9572195
X-RAY DIFFRACTIONr_scbond_other1.9691.9582196
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9942.8423262
X-RAY DIFFRACTIONr_long_range_B_refined5.74715.1045327
X-RAY DIFFRACTIONr_long_range_B_other5.64214.3755121
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 33334 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 254 -
Rwork0.278 4625 -
obs--98.59 %
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)
12.5242-0.13851.04740.6656-0.0731.9648-0.0033-0.03140.2719-0.0156-0.01480.004-0.20540.03570.01820.0279-0.00320.0120.0553-0.00320.0359-16.4114-10.290611.1267
24.27080.22320.51422.9650.65472.9626-0.0148-0.2510.51750.3322-0.02780.1255-0.492-0.08650.04260.15660.0170.02590.0739-0.05560.1076-25.8896-2.12920.6662
30.685-0.11050.05961.3181-1.29052.1601-0.0048-0.0724-0.08810.0872-0.125-0.2313-0.01690.3010.12980.04040.0161-0.00490.1020.02120.0828.4619-29.501336.6265
42.935-0.41380.81753.35490.49713.30080.05410.3284-0.242-0.4167-0.0487-0.74780.26070.7703-0.00540.21490.17320.1560.32940.09510.354920.1424-44.362931.7674
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 259
2X-RAY DIFFRACTION2A260 - 324
3X-RAY DIFFRACTION3B15 - 234
4X-RAY DIFFRACTION4B235 - 330

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