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

ID or keywords:

Entry

Database: PDB / ID: 9cvb

Title

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

Components

Ribokinase

Keywords

TRANSFERASE / Ribokinase / enzyme-substrate 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: 1.45 Å

Authors

Park, J. / Akanmori, N.N.

Funding support

Canada, 1items

Citation

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

History

Deposition	Jul 29, 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	9cvb.cif.gz	366.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	9cvb_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	9cvb_full_validation.pdf.gz	2.9 MB	Display
Data in XML	9cvb_validation.xml.gz	35.9 KB	Display
Data in CIF	9cvb_validation.cif.gz	51.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cv/9cvb ftp://data.pdbj.org/pub/pdb/validation_reports/cv/9cvb	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
Related items in Molecule of the Month	#108 - Dec 2008 Hsp90 similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

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Related items in Molecule of the Month

#108 - Dec 2008
Hsp90
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: Ribokinase

B: Ribokinase

hetero molecules

72.1 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)	45.410, 70.930, 90.920
Angle α, β, γ (deg.)	90.000, 92.490, 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: LEU / End label comp-ID: LEU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 14 - 323 / Label seq-ID: 14 - 323

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 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 , 7 types, 592 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#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-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#7: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 582 / 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: 2.08 Å³/Da / Density % sol: 40.74 %
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→70.93 Å / Num. obs: 101613 / % possible obs: 99.6 % / Redundancy: 4.8 % / B_iso Wilson estimate: 20.117 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.048 / R_pim(I) all: 0.024 / R_rim(I) all: 0.054 / Net I/σ(I): 13.9
Reflection shell	Resolution: 1.45→1.48 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.632 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4997 / CC_1/2: 0.67 / R_pim(I) all: 0.329 / R_rim(I) all: 0.716 / % possible all: 96.9

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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: 1.45→55.967 Å / Cor.coef. F_o:F_c: 0.981 / Cor.coef. F_o:F_c free: 0.969 / SU B: 2.707 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.062
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1763	5067	4.988 %	Random
R_work	0.1296	96521	-	-
all	0.132	-	-	-
obs	0.1319	101588	99.534 %	-

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: 24.795 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.261 Å²	0 Å²	0.457 Å²
2-	-	0.077 Å²	-0 Å²
3-	-	-	1.139 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→55.967 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4608	0	97	582	5287

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	4968
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4724
X-RAY DIFFRACTION	r_angle_refined_deg	1.655	1.801	6796
X-RAY DIFFRACTION	r_angle_other_deg	0.581	1.717	10897
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.886	5	670
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.354	5	15
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.013	5	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.999	10	788
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.833	10	180
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	824
X-RAY DIFFRACTION	r_chiral_restr_other	0.074	0.2	2
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5823
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1039
X-RAY DIFFRACTION	r_nbd_refined	0.233	0.2	937
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.195	0.2	4164
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	2423
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	2610
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.185	0.2	374
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.09	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.078	0.2	10
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.179	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.187	0.2	55
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.104	0.2	26
X-RAY DIFFRACTION	r_mcbond_it	6.935	2.479	2617
X-RAY DIFFRACTION	r_mcbond_other	6.91	2.479	2617
X-RAY DIFFRACTION	r_mcangle_it	9.365	4.452	3308
X-RAY DIFFRACTION	r_mcangle_other	9.367	4.454	3309
X-RAY DIFFRACTION	r_scbond_it	8.85	2.897	2351
X-RAY DIFFRACTION	r_scbond_other	8.849	2.897	2352
X-RAY DIFFRACTION	r_scangle_it	12.346	5.166	3488
X-RAY DIFFRACTION	r_scangle_other	12.344	5.167	3489
X-RAY DIFFRACTION	r_lrange_it	16.093	27.235	5496
X-RAY DIFFRACTION	r_lrange_other	15.197	25.853	5331
X-RAY DIFFRACTION	r_rigid_bond_restr	3.775	3	9692
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.105	0.05	9744

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	0.10534	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.10534	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	0.267	377	0.224	6974	0.226	7522	0.958	0.968	97.7267	0.203
1.488-1.528	0.207	349	0.175	6944	0.176	7322	0.972	0.98	99.6039	0.152
1.528-1.573	0.204	358	0.15	6783	0.152	7145	0.972	0.985	99.944	0.126
1.573-1.621	0.196	337	0.134	6627	0.137	6974	0.974	0.988	99.8566	0.112
1.621-1.674	0.169	305	0.122	6334	0.124	6651	0.981	0.991	99.8196	0.102
1.674-1.733	0.182	333	0.123	6118	0.126	6461	0.976	0.991	99.8452	0.105
1.733-1.798	0.179	310	0.115	5975	0.119	6295	0.981	0.992	99.8411	0.101
1.798-1.872	0.175	318	0.107	5709	0.11	6040	0.981	0.993	99.7848	0.096
1.872-1.955	0.16	300	0.109	5474	0.112	5796	0.984	0.993	99.6204	0.104
1.955-2.05	0.169	322	0.115	5168	0.119	5506	0.983	0.992	99.7094	0.115
2.05-2.161	0.153	266	0.115	5029	0.117	5326	0.986	0.993	99.4179	0.118
2.161-2.292	0.16	219	0.108	4714	0.11	4954	0.985	0.994	99.5761	0.115
2.292-2.449	0.169	236	0.111	4436	0.114	4687	0.983	0.992	99.68	0.123
2.449-2.645	0.166	189	0.114	4142	0.116	4353	0.984	0.992	99.4946	0.131
2.645-2.897	0.173	211	0.129	3801	0.131	4029	0.98	0.989	99.5781	0.15
2.897-3.238	0.209	169	0.139	3496	0.143	3686	0.972	0.988	99.4303	0.166
3.238-3.737	0.158	160	0.133	3042	0.135	3221	0.984	0.99	99.4101	0.161
3.737-4.572	0.168	147	0.124	2577	0.126	2736	0.984	0.991	99.5614	0.157
4.572-6.444	0.189	107	0.162	2030	0.163	2151	0.985	0.988	99.3491	0.209
6.444-55.967	0.208	54	0.164	1149	0.165	1209	0.975	0.984	99.5037	0.221

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