PDB-9cva: Crystal structure of human ribokinase in complex with K+, Mg2+, a...

ID or keywords:

Entry

Database: PDB / ID: 9cva

Title

Crystal structure of human ribokinase in complex with K+, Mg2+, and AMPCP

Components

Ribokinase

Keywords

TRANSFERASE / Ribokinase / Enzyme-ligand complex / 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 /

FOURIER SYNTHESIS / Resolution: 1.6 Å

Authors

Park, J. / Akanmori, N.

Funding support

Canada, 1items

Citation

Journal: To Be Published
Title: Crystal structure of human ribokinase in complex with K+, Mg2+, and AMPCP
Authors: Akanmori, N.N. / Park, J.

History

Deposition	Jul 29, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 13, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9cva.cif.gz	339 KB	Display	PDBx/mmCIF format
PDB format	pdb9cva.ent.gz	213.2 KB	Display	PDB format
PDBx/mmJSON format	9cva.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9cva_validation.pdf.gz	3 MB	Display	wwPDB validaton report
Full document	9cva_full_validation.pdf.gz	3 MB	Display
Data in XML	9cva_validation.xml.gz	35.6 KB	Display
Data in CIF	9cva_validation.cif.gz	49.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cv/9cva ftp://data.pdbj.org/pub/pdb/validation_reports/cv/9cva	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

72.2 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)	45.380, 70.750, 90.650
Angle α, β, γ (deg.)	90.000, 92.360, 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: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 14 - 324 / Label seq-ID: 14 - 324

Dom-ID
1
2

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

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 8 types, 518 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-A12 / PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-DIPHOSPHATE Mass: 425.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₇N₅O₉P₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#8: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.06 Å³/Da / Density % sol: 40.38 %
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: 1.6→55.76 Å / Num. obs: 74579 / % possible obs: 98.7 % / Redundancy: 5 % / B_iso Wilson estimate: 23.511 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.039 / R_pim(I) all: 0.019 / R_rim(I) all: 0.044 / Net I/σ(I): 18.1
Reflection shell	Resolution: 1.6→1.63 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.66 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3527 / CC_1/2: 0.714 / R_pim(I) all: 0.435 / R_rim(I) all: 0.737 / % possible all: 94.1

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Processing

Software

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

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.6→55.756 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.969 / SU B: 4.068 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.083
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1847	3798	5.093 %	Random
R_work	0.1528	70771	-	-
all	0.154	-	-	-
obs	0.1544	74569	98.649 %	-

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: 28.841 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.172 Å²	-0 Å²	0.831 Å²
2-	-	-1.044 Å²	0 Å²
3-	-	-	2.14 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→55.756 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4619	0	106	505	5230

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	4941
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4714
X-RAY DIFFRACTION	r_angle_refined_deg	1.681	1.799	6740
X-RAY DIFFRACTION	r_angle_other_deg	0.575	1.716	10864
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.176	5	660
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.084	5	17
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.023	5	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.65	10	775
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.579	10	180
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	820
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5762
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1036
X-RAY DIFFRACTION	r_nbd_refined	0.234	0.2	929
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	4216
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	2425
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	2618
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.221	0.2	352
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.017	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.099	0.2	10
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.245	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.206	0.2	59
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.225	0.2	21
X-RAY DIFFRACTION	r_mcbond_it	1.514	1.697	2595
X-RAY DIFFRACTION	r_mcbond_other	1.507	1.697	2595
X-RAY DIFFRACTION	r_mcangle_it	2.196	3.043	3270
X-RAY DIFFRACTION	r_mcangle_other	2.196	3.044	3271
X-RAY DIFFRACTION	r_scbond_it	2.595	2.092	2346
X-RAY DIFFRACTION	r_scbond_other	2.594	2.092	2346
X-RAY DIFFRACTION	r_scangle_it	3.908	3.68	3470
X-RAY DIFFRACTION	r_scangle_other	3.907	3.68	3471
X-RAY DIFFRACTION	r_lrange_it	6.338	20.11	5436
X-RAY DIFFRACTION	r_lrange_other	6.234	19.057	5289
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.102	0.05	9685

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	0.10246	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.10246	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
1.6-1.642	0.27	243	0.254	5052	0.255	5564	0.945	0.946	95.1653	0.226
1.642-1.687	0.262	247	0.236	5090	0.238	5444	0.941	0.954	98.0345	0.209
1.687-1.736	0.235	255	0.217	4923	0.218	5267	0.959	0.963	98.3102	0.189
1.736-1.789	0.229	265	0.2	4775	0.201	5112	0.959	0.971	98.5915	0.17
1.789-1.847	0.213	258	0.18	4623	0.182	4961	0.965	0.977	98.3874	0.154
1.847-1.912	0.211	300	0.17	4446	0.172	4829	0.971	0.98	98.2812	0.146
1.912-1.984	0.204	229	0.164	4340	0.166	4623	0.972	0.983	98.8319	0.145
1.984-2.065	0.193	229	0.156	4197	0.158	4475	0.975	0.984	98.905	0.141
2.065-2.157	0.203	204	0.158	4056	0.16	4309	0.972	0.984	98.8628	0.146
2.157-2.262	0.176	194	0.142	3862	0.143	4085	0.979	0.987	99.2901	0.134
2.262-2.384	0.183	223	0.139	3634	0.141	3882	0.979	0.988	99.356	0.135
2.384-2.529	0.205	157	0.142	3523	0.145	3704	0.975	0.987	99.3521	0.142
2.529-2.703	0.172	168	0.144	3288	0.145	3470	0.982	0.987	99.5965	0.148
2.703-2.919	0.2	187	0.153	3034	0.156	3234	0.974	0.985	99.598	0.16
2.919-3.196	0.204	160	0.155	2826	0.158	2998	0.971	0.985	99.5997	0.169
3.196-3.572	0.19	126	0.147	2575	0.149	2712	0.98	0.988	99.5944	0.167
3.572-4.122	0.144	120	0.132	2271	0.133	2403	0.987	0.99	99.5006	0.157
4.122-5.042	0.13	114	0.122	1901	0.123	2024	0.989	0.991	99.5553	0.147
5.042-7.101	0.236	78	0.171	1489	0.174	1580	0.97	0.985	99.1772	0.201
7.101-55.756	0.135	41	0.148	866	0.147	913	0.99	0.986	99.3428	0.188

Refinement TLS params.

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

ID	L11 (°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)
1	1.4426	-0.6492	0.2987	2.1177	-1.3206	3.1258	0.1341	0.0975	-0.0441	-0.1273	-0.0062	-0.0325	-0.1706	0.0372	-0.1279	0.0452	0.0064	0.0085	0.077	-0.0168	0.0198	-17.4	-10.6525	-18.5817
2	2.0401	0.6153	0.3792	2.4996	-0.5071	1.3676	0.0916	-0.151	-0.0774	0.0016	-0.0549	0.1559	-0.0106	-0.1155	-0.0367	0.0091	0.0079	-0.0086	0.1073	-0.0012	0.0192	-23.5622	-11.4327	-8.6953
3	4.6306	2.6202	-2.5962	4.6176	-2.5242	6.0454	0.2838	-0.3732	0.108	0.3977	-0.1813	-0.0948	-0.1712	-0.1244	-0.1025	0.0543	-0.0526	-0.0249	0.1858	0.0395	0.0334	-14.0633	-14.7495	4.0431
4	3.8874	-0.1081	-0.8007	2.3264	0.3134	2.2522	0.0664	-0.2037	-0.2382	0.1709	0.0092	-0.4648	0.0815	0.1023	-0.0756	0.0462	-0.0225	-0.0709	0.1244	0.0425	0.143	0.302	-16.278	-0.2558
5	4.0751	0.2855	0.23	3.0877	-0.243	2.4704	0.1791	0.2651	-0.6905	-0.2044	-0.0026	-0.3978	0.2107	0.2099	-0.1765	0.0459	0.0252	-0.0398	0.1132	-0.045	0.2207	-8.5168	-26.7247	-13.7771
6	9.6414	-0.5084	-1.6975	4.1183	0.2947	3.6434	0.2092	0.0972	0.1803	-0.1601	-0.026	-0.2616	-0.2162	0.2686	-0.1832	0.2385	-0.006	0.0034	0.2318	-0.0039	0.1927	-2.7828	-39.7893	-7.9086
7	1.324	-1.5451	2.8444	2.0269	-2.7238	7.7063	-0.0446	0.069	-0.0086	0.054	-0.0163	0.044	-0.0805	0.2925	0.061	0.0669	-0.0273	0	0.1074	0.0314	0.0292	-29.7008	8.5971	-28.6322
8	1.287	-0.9766	0.2855	1.6814	-0.6077	1.7888	-0.0024	-0.0405	-0.1135	0.0255	0.0411	0.0884	0.0495	0.051	-0.0387	0.0646	0.0003	0.015	0.0745	0.0135	0.0156	-29.2238	4.7745	-29.2103
9	1.9838	-0.0392	-0.3154	4.2568	-0.0034	2.9003	-0.0661	0.2477	-0.1606	-0.4836	0.0184	-0.0804	0.0394	-0.0148	0.0478	0.1418	-0.0022	-0.0023	0.0947	-0.0152	0.0192	-31.0482	14.453	-46.4189
10	3.0489	0.2109	-1.4296	3.9931	-0.5028	1.5843	0.0158	-0.0968	0.0802	0.0432	-0.0391	-0.2878	-0.0652	0.2142	0.0232	0.1172	-0.0223	-0.0104	0.115	0.0262	0.0301	-19.6638	27.617	-40.5497
11	1.8604	-0.1084	0.2037	3.448	-2.6318	10.4023	0.0437	-0.1437	0.2762	0.0875	0.048	0.1351	-0.6504	-0.2882	-0.0917	0.1592	-0.0144	-0.0076	0.1105	0.0018	0.0764	-26.9912	33.8975	-35.296
12	2.8718	0.6043	0.7765	2.9245	0.1052	4.0133	-0.016	-0.1627	0.2653	0.0972	0.07	0.2886	-0.3348	-0.1888	-0.054	0.0757	0.0454	0.0156	0.0895	-0.0072	0.0481	-37.7422	24.7443	-28.352

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	14 - 68
2	X-RAY DIFFRACTION	2	ALL	A	69 - 160
3	X-RAY DIFFRACTION	3	ALL	A	161 - 185
4	X-RAY DIFFRACTION	4	ALL	A	186 - 257
5	X-RAY DIFFRACTION	5	ALL	A	258 - 323
6	X-RAY DIFFRACTION	6	ALL	A	324 - 328

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