PDB-9cwu: Crystal structure of human ribokinase in complex with K+

ID or keywords:

Entry

Database: PDB / ID: 9cwu

Title

Crystal structure of human ribokinase in complex with K+

Components

Ribokinase

Keywords

TRANSFERASE / Ribokinase / Ribose metabolism

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

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

Park, J. / Akanmori, N.N.

Funding support

Canada, 1items

Citation

Journal: To Be Published
Title: To be published
Authors: Park, J. / Akanmori, N.N.

History

Deposition	Jul 30, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 6, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9cwu.cif.gz	356.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9cwu.ent.gz	222.5 KB	Display	PDB format
PDBx/mmJSON format	9cwu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9cwu_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	9cwu_full_validation.pdf.gz	1.3 MB	Display
Data in XML	9cwu_validation.xml.gz	35.2 KB	Display
Data in CIF	9cwu_validation.cif.gz	50.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cw/9cwu ftp://data.pdbj.org/pub/pdb/validation_reports/cw/9cwu	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Ribokinase

B: Ribokinase

hetero molecules

70.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	45.560, 70.870, 91.120
Angle α, β, γ (deg.)	90.000, 93.060, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 15 - 321 / Label seq-ID: 15 - 321

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Ribokinase / RK 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.09 Å³/Da / Density % sol: 41.21 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M TrisHCl (pH 8.5), 25% (w/v) PEG 2000 MME

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 1.45→55.95 Å / Num. obs: 102166 / % possible obs: 99.7 % / Redundancy: 4.9 % / B_iso Wilson estimate: 18.379 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.046 / R_pim(I) all: 0.023 / R_rim(I) all: 0.051 / Net I/σ(I): 15.5
Reflection shell	Resolution: 1.45→1.48 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.651 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5087 / CC_1/2: 0.741 / R_pim(I) all: 0.32 / R_rim(I) all: 0.728 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
pointless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.45→55.912 Å / Cor.coef. F_o:F_c: 0.979 / Cor.coef. F_o:F_c free: 0.966 / SU B: 4.018 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.066
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1891	5096	4.989 %	Random
R_work	0.1471	97052	-	-
all	0.149	-	-	-
obs	0.1491	102148	99.681 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 23.818 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.365 Å²	-0 Å²	0.833 Å²
2-	-	-1.822 Å²	-0 Å²
3-	-	-	-0.628 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→55.912 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4607	0	20	635	5262

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	4826
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4652
X-RAY DIFFRACTION	r_angle_refined_deg	1.743	1.802	6578
X-RAY DIFFRACTION	r_angle_other_deg	0.619	1.727	10734
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.408	5	653
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	16.997	5	15
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.31	10	800
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.97	10	178
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	800
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	5664
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1012
X-RAY DIFFRACTION	r_nbd_refined	0.236	0.2	918
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	4204
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	2388
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	2592
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.19	0.2	417
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.034	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.107	0.2	8
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.171	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.225	0.2	53
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.161	0.2	29
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.119	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	7.146	2.431	2570
X-RAY DIFFRACTION	r_mcbond_other	7.142	2.431	2570
X-RAY DIFFRACTION	r_mcangle_it	9.351	4.373	3237
X-RAY DIFFRACTION	r_mcangle_other	9.353	4.373	3238
X-RAY DIFFRACTION	r_scbond_it	8.31	2.79	2256
X-RAY DIFFRACTION	r_scbond_other	8.308	2.79	2257
X-RAY DIFFRACTION	r_scangle_it	11.499	4.995	3341
X-RAY DIFFRACTION	r_scangle_other	11.498	4.995	3342
X-RAY DIFFRACTION	r_lrange_it	14.735	27.455	5427
X-RAY DIFFRACTION	r_lrange_other	14.019	25.729	5221
X-RAY DIFFRACTION	r_rigid_bond_restr	5.379	3	9478
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.106	0.05	9648

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.10605	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.10605	0.05008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.45-1.488	0.268	394	0.243	7134	0.244	7550	0.964	0.969	99.7086	0.216
1.488-1.528	0.252	345	0.235	6976	0.236	7358	0.961	0.969	99.4971	0.204
1.528-1.573	0.232	360	0.208	6808	0.209	7180	0.967	0.971	99.8329	0.179
1.573-1.621	0.215	335	0.182	6579	0.184	6925	0.979	0.978	99.8412	0.155
1.621-1.674	0.21	312	0.174	6428	0.176	6750	0.974	0.981	99.8519	0.149
1.674-1.733	0.217	341	0.17	6136	0.172	6488	0.973	0.982	99.8305	0.145
1.733-1.798	0.228	302	0.158	5993	0.162	6301	0.966	0.984	99.9048	0.136
1.798-1.872	0.218	322	0.156	5715	0.16	6050	0.969	0.987	99.7851	0.137
1.872-1.955	0.196	293	0.147	5514	0.15	5831	0.975	0.988	99.5884	0.135
1.955-2.05	0.175	328	0.135	5193	0.137	5534	0.982	0.99	99.7651	0.129
2.05-2.161	0.16	266	0.131	5046	0.133	5337	0.984	0.991	99.5316	0.13
2.161-2.292	0.203	225	0.13	4748	0.133	4995	0.974	0.99	99.5596	0.133
2.292-2.449	0.182	235	0.132	4422	0.135	4682	0.978	0.989	99.466	0.139
2.449-2.645	0.201	189	0.135	4202	0.138	4399	0.972	0.989	99.8181	0.148
2.645-2.897	0.186	215	0.138	3826	0.141	4054	0.981	0.988	99.6793	0.156
2.897-3.238	0.188	164	0.139	3504	0.141	3684	0.977	0.988	99.5657	0.164
3.238-3.737	0.169	163	0.142	3053	0.143	3232	0.982	0.988	99.5049	0.169
3.737-4.572	0.171	147	0.128	2595	0.13	2757	0.984	0.99	99.4559	0.162
4.572-6.444	0.15	106	0.155	2022	0.155	2148	0.987	0.988	99.0689	0.2
6.444-55.912	0.228	55	0.159	1158	0.162	1220	0.962	0.982	99.4262	0.199

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