PDB-6wjz: Crystal structure of human ribokinase in complex with AMPCP

ID or keywords:

Entry

Database: PDB / ID: 6wjz

Title

Crystal structure of human ribokinase in complex with AMPCP

Components

Ribokinase

Keywords

TRANSFERASE / Enzyme-ligand complex

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: 1.8 Å

Authors

Park, J.

Citation

Journal: To Be Published
Title: Crystal structures of human ribokinase
Authors: Park, J.

History

Deposition	Apr 15, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 21, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6wjz.cif.gz	264.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6wjz.ent.gz	211.6 KB	Display	PDB format
PDBx/mmJSON format	6wjz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6wjz_validation.pdf.gz	2.8 MB	Display	wwPDB validaton report
Full document	6wjz_full_validation.pdf.gz	2.8 MB	Display
Data in XML	6wjz_validation.xml.gz	29.2 KB	Display
Data in CIF	6wjz_validation.cif.gz	43.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wj/6wjz ftp://data.pdbj.org/pub/pdb/validation_reports/wj/6wjz	HTTPS FTP

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Related structure data

Related structure data	5c40S 5byc 5byd 5bye 5byf 5c3y 5c3z 5c41 S: Starting model for refinement
Similar structure data	5byf-d 5c3y-2 5c3y-4 5c40-d 5c3y-5 2c4e-1 4x8f-5 5c3y-3 3in1-2 3in1-1 4x8f-6 4x8f-1 5c3y-1 5bye-d 5c41-2 3iq0-d 2g5g-1 5c3y-6 Search similar-shape structures by Omokage search (details) 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

69 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)	46.110, 71.860, 91.430
Angle α, β, γ (deg.)	90.00, 91.78, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 14 - 323 / Label seq-ID: 1 - 310

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

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Protein , 1 types, 2 molecules AB

#1: Protein	Ribokinase / RK Mass: 33740.398 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 , 5 types, 466 molecules

#2: 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
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.74 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium acetate, 20% PEG 3350

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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 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: 1.8→56.49 Å / Num. obs: 54971 / % possible obs: 99.21 % / Redundancy: 4.8 % / B_iso Wilson estimate: 26.68 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.054 / R_pim(I) all: 0.027 / R_rim(I) all: 0.06 / Net I/σ(I): 14.5
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.538 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2719 / CC_1/2: 0.855 / R_pim(I) all: 0.271 / R_rim(I) all: 0.605 / % possible all: 97.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5C40

5c40

Resolution: 1.8→56.49 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.964 / SU B: 5.585 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18632	2738	5 %	RANDOM
R_work	0.15218	-	-	-
obs	0.15384	52215	99.18 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 34.356 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.1 Å²	0 Å²	1.61 Å²
2-	-	-0.88 Å²	0 Å²
3-	-	-	0.67 Å²

Refinement step

Cycle: 1 / Resolution: 1.8→56.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4610	0	94	454	5158

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	4934
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	4617
X-RAY DIFFRACTION	r_angle_refined_deg	1.824	1.634	6745
X-RAY DIFFRACTION	r_angle_other_deg	1.524	1.565	10724
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.637	5	664
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.604	23.969	194
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.635	15	794
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.297	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	697
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	5601
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	932
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.113	1.579	2602
X-RAY DIFFRACTION	r_mcbond_other	1.113	1.579	2601
X-RAY DIFFRACTION	r_mcangle_it	1.656	2.36	3284
X-RAY DIFFRACTION	r_mcangle_other	1.656	2.361	3285
X-RAY DIFFRACTION	r_scbond_it	1.808	1.871	2332
X-RAY DIFFRACTION	r_scbond_other	1.809	1.873	2333
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.651	2.716	3462
X-RAY DIFFRACTION	r_long_range_B_refined	6.746	21.745	5369
X-RAY DIFFRACTION	r_long_range_B_other	6.644	20.479	5217
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 9700 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.226	202	-
R_work	0.226	3848	-
obs	-	-	98.25 %

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	0.4177	-0.789	0.5339	3.2886	-1.3561	3.5033	0.0905	0.1521	-0.017	-0.2551	-0.0202	-0.1116	-0.3751	0.1198	-0.0703	0.1189	0.018	0.0318	0.1215	-0.0119	0.141	-17.4027	-10.2682	-18.5819
2	1.3271	0.3583	-0.1266	2.8948	-0.1407	1.2679	0.0497	0.0989	-0.1431	-0.2047	-0.0149	0.1925	-0.105	-0.1353	-0.0348	0.0322	0.0359	-0.0219	0.122	-0.004	0.15	-27.3811	-11.8172	-12.5034
3	1.6585	-0.2446	0.668	2.4146	-0.01	1.2278	0.0705	-0.0731	-0.0667	0.0753	-0.0773	-0.0458	-0.177	-0.063	0.0068	0.0552	0.0145	-0.0036	0.0878	-0.0268	0.1604	-20.3782	-11.1462	-3.6136
4	3.7127	1.0756	-0.7477	2.4713	-0.7672	3.1251	0.0409	-0.2406	0.1969	0.1679	-0.0257	-0.0595	-0.144	-0.032	-0.0152	0.0168	-0.0035	-0.0203	0.1083	-0.0049	0.1484	-11.9252	-14.4119	4.3027
5	1.653	0.4104	-0.367	3.6601	0.3902	1.6828	0.0409	-0.0303	-0.0025	0.0316	-0.0497	-0.1512	-0.1428	0.0957	0.0088	0.014	-0.0153	-0.0122	0.1054	0.0184	0.1963	1.8492	-13.1654	-0.2192
6	4.202	-0.6637	-1.1934	3.6795	-1.9833	12.9173	-0.0437	0.0656	-0.2149	-0.0447	-0.0113	-0.1859	0.4882	0.462	0.0549	0.0442	0.0035	0.0075	0.0891	0.0192	0.2714	3.64	-23.55	-2.249
7	2.9932	0.6995	-1.1086	4.701	-2.0071	3.4936	0.0232	0.172	-0.0938	-0.2773	-0.0576	-0.273	0.0262	0.1947	0.0344	0.0215	0.0059	0.0042	0.0797	-0.0358	0.1671	-6.993	-25.0543	-11.8471
8	1.5775	-2.0205	0.3715	8.9688	-2.9931	2.6203	0.2362	0.2313	-0.1677	-0.493	-0.2313	0.0091	0.3641	0.2365	-0.0049	0.1139	0.0279	0.0232	0.1392	-0.042	0.1767	-10.5764	-32.6445	-15.4158
9	0.6951	-1.9963	1.655	5.8189	-4.2564	7.8166	0.0221	-0.0615	-0.2657	-0.0944	0.1525	0.7712	0.0933	-0.2711	-0.1746	0.2439	-0.0596	0.0028	0.2936	-0.0003	0.294	-37.5089	9.5372	-36.7238
10	7.3199	0.4872	0.7316	4.6652	0.6951	7.0582	-0.0809	-0.2992	0.4752	0.1795	0.16	-0.2217	-1.0294	0.4226	-0.0791	0.387	-0.0043	0.0699	0.1941	-0.0104	0.1694	-15.9574	4.8348	-14.9484
11	1.5044	-1.1698	-0.3995	4.2407	-0.4357	2.1317	-0.1374	-0.0381	-0.3438	-0.1023	0.1107	0.488	0.2975	-0.3501	0.0267	0.2181	-0.0461	0.038	0.2614	-0.0035	0.2354	-37.2217	6.0617	-30.6225
12	1.5396	-1.5067	0.4302	1.8926	-1.5995	3.605	-0.049	0.0198	-0.1078	0.0524	-0.0221	0.1152	-0.0791	0.0584	0.0711	0.342	-0.0158	0.1025	0.1392	-0.0076	0.1803	-26.3948	3.4659	-31.5545
13	1.8136	-0.7804	-0.5482	4.5289	-0.2793	2.8763	0.0619	0.3477	-0.1435	-0.6447	-0.0614	0.1705	0.1986	-0.2673	-0.0005	0.4344	0.0176	-0.0117	0.283	-0.0078	0.1728	-32.6326	12.3024	-46.5474
14	1.613	-0.0329	-1.0849	2.8886	-0.9811	3.2858	0.0753	-0.0754	0.0102	-0.1098	-0.1773	-0.2645	-0.1421	0.1765	0.102	0.3484	0.0355	0.0469	0.1962	0.0566	0.1717	-22.1551	26.3098	-41.7506
15	0.5044	-0.1784	0.2685	1.3991	-0.9723	6.2893	-0.0327	0.0119	0.1173	0.0342	-0.0427	-0.0054	-0.297	-0.09	0.0753	0.2942	0.0164	0.0096	0.2432	0.0218	0.2415	-28.1265	34.7914	-39.5802
16	3.0916	0.2113	0.8853	2.3686	-0.3803	5.0646	0.0355	0.0138	0.2117	-0.058	-0.0092	0.345	-0.3828	-0.4199	-0.0263	0.2137	0.0772	0.0407	0.2614	-0.0005	0.1897	-37.7718	24.7754	-28.077

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	14 - 68
2	X-RAY DIFFRACTION	2	A	69 - 114
3	X-RAY DIFFRACTION	3	A	115 - 161
4	X-RAY DIFFRACTION	4	A	162 - 200
5	X-RAY DIFFRACTION	5	A	201 - 238
6	X-RAY DIFFRACTION	6	A	239 - 257
7	X-RAY DIFFRACTION	7	A	258 - 307
8	X-RAY DIFFRACTION	8	A	308 - 328
9	X-RAY DIFFRACTION	9	B	14 - 27
10	X-RAY DIFFRACTION	10	B	28 - 48
11	X-RAY DIFFRACTION	11	B	49 - 92
12	X-RAY DIFFRACTION	12	B	93 - 133
13	X-RAY DIFFRACTION	13	B	134 - 188
14	X-RAY DIFFRACTION	14	B	189 - 238
15	X-RAY DIFFRACTION	15	B	239 - 255
16	X-RAY DIFFRACTION	16	B	256 - 324

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