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- PDB-5byd: Crystal structure of human ribokinase in P21 spacegroup -

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Basic information

Entry
Database: PDB / ID: 5byd
TitleCrystal structure of human ribokinase in P21 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: 2.1 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)70,5444
Polymers70,4822
Non-polymers622
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-17 kcal/mol
Surface area25540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.590, 89.910, 75.140
Angle α, β, γ (deg.)90.00, 98.80, 90.00
Int Tables number4
Space group name H-MP1211
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: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 15 - 325 / Label seq-ID: 15 - 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.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M sodium HEPES, 25% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→44.96 Å / Num. obs: 34784 / % possible obs: 97.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 29.496 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.7
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.2 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FV7

2fv7


Resolution: 2.1→44.96 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.871 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21536 1762 5.1 %RANDOM
Rwork0.17149 ---
obs0.17377 32999 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.752 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å2-1.02 Å2
2--0.65 Å20 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 2.1→44.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4564 0 2 155 4721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194654
X-RAY DIFFRACTIONr_bond_other_d0.0060.024448
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.9636345
X-RAY DIFFRACTIONr_angle_other_deg1.152310212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7635629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07725.68169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22615731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4931511
X-RAY DIFFRACTIONr_chiral_restr0.0980.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025367
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02982
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_it1.6362.172516
X-RAY DIFFRACTIONr_mcbond_other1.6342.172515
X-RAY DIFFRACTIONr_mcangle_it2.3583.2493145
X-RAY DIFFRACTIONr_mcangle_other2.3583.2493146
X-RAY DIFFRACTIONr_scbond_it2.2752.4262138
X-RAY DIFFRACTIONr_scbond_other2.2742.4262139
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4623.543200
X-RAY DIFFRACTIONr_long_range_B_refined5.71317.9145049
X-RAY DIFFRACTIONr_long_range_B_other5.70517.7525015
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17406 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 121 -
Rwork0.257 2326 -
obs--93.25 %
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)
12.38522.75022.59265.00252.14183.2593-0.149-0.04340.0758-0.0087-0.0003-0.1837-0.28-0.07990.14930.0810.04110.03580.0380.02090.12185.26052.3684-25.7648
25.65251.63353.35942.10272.14734.3004-0.2319-0.26360.4248-0.0782-0.09320.0517-0.4468-0.18610.3250.08090.0256-0.02870.0320.00410.0771.21885.9829-26.6119
34.63340.80921.58294.43290.45674.5753-0.0446-0.3762-0.04490.16230.04610.1934-0.1102-0.4955-0.00150.04650.03690.04930.12830.03320.0616-6.1106-4.0883-20.173
44.5132.8690.32475.81680.37762.3287-0.1353-0.0511-0.0268-0.13930.0909-0.1829-0.08220.0060.04450.05440.03270.00130.04120.01820.04626.6467-3.8836-22.1257
50.4964-1.02910.30482.3087-1.09825.10040.0055-0.0481-0.1311-0.02590.10750.13060.4318-0.2474-0.1130.123-0.0363-0.01670.01810.02520.197-2.3058-14.6825-31.3231
66.07450.8984-1.04684.8975-0.77082.84820.02270.1221-0.52660.1565-0.005-0.22870.68230.208-0.01780.23580.0272-0.04290.0536-0.01250.13152.7841-17.1406-37.0481
74.6153-1.10721.01883.6183-1.16384.56260.09180.59580.0111-0.3609-0.1624-0.15030.19010.32670.07060.11890.00760.02990.1651-0.0380.12656.1577-7.4871-49.7911
85.02250.22490.58673.7035-0.30914.8561-0.15710.36270.1502-0.10920.11160.1082-0.3669-0.44780.04550.03960.0256-0.00950.08930.02320.0252-9.20851.7672-42.7754
90.6202-0.2140.78752.92641.81133.23920.03640.04410.0837-0.15690.0060.13760.2256-0.1249-0.04240.1196-0.0809-0.08930.06750.06040.174212.646810.0223-5.738
101.9539-0.4628-0.47682.81161.45734.095-0.0580.03170.1036-0.11510.07780.23080.0737-0.3009-0.01980.0151-0.0181-0.03730.03730.02560.15198.313317.035-3.4906
113.2953-1.35750.13024.50831.778.1145-0.10380.0310.37140.02790.07990.0785-0.31260.12250.02390.0183-0.00890.00840.0107-0.02150.173315.136528.79542.9714
120.58510.6355-0.212510.3972-1.05110.148-0.06590.44190.1598-0.4770.0781-0.26340.0404-0.1289-0.01230.2654-0.0403-0.0460.38980.06690.209223.163828.673-8.1362
137.98110.8831-1.56913.80930.47594.5428-0.29130.41490.1103-0.16180.2508-0.1658-0.10430.38150.04060.0494-0.0687-0.01140.1461-0.04810.139632.087425.92962.6529
140.2132-1.22510.07777.4631-0.53410.0483-0.00420.0102-0.0233-0.1549-0.0772-0.35080.06340.02060.08140.52290.09030.06680.4398-0.09860.623330.56515.30221.6126
154.9179-0.3221-1.50094.4011-0.2627.0965-0.0249-0.142-0.2750.24670.0049-0.35080.26180.63550.02010.02950.0304-0.00930.06380.01730.094923.958312.862410.3559
164.23780.76714.05880.8471-0.729.00190.0579-0.2763-0.42370.0633-0.0766-0.14680.5759-0.11180.01870.21390.03780.03280.05490.03470.158620.375.798314.6683
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 39
2X-RAY DIFFRACTION2A40 - 68
3X-RAY DIFFRACTION3A69 - 97
4X-RAY DIFFRACTION4A98 - 140
5X-RAY DIFFRACTION5A141 - 161
6X-RAY DIFFRACTION6A162 - 192
7X-RAY DIFFRACTION7A193 - 257
8X-RAY DIFFRACTION8A258 - 329
9X-RAY DIFFRACTION9B15 - 77
10X-RAY DIFFRACTION10B78 - 153
11X-RAY DIFFRACTION11B154 - 179
12X-RAY DIFFRACTION12B180 - 186
13X-RAY DIFFRACTION13B187 - 254
14X-RAY DIFFRACTION14B255 - 266
15X-RAY DIFFRACTION15B267 - 307
16X-RAY DIFFRACTION16B308 - 326

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