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

ID or keywords:

Entry

Database: PDB / ID: 5byd

Title

Crystal structure of human ribokinase in P21 spacegroup

Components

Ribokinase

Keywords

TRANSFERASE

Function / homology

Function and homology information

ribokinase /

ribokinase activity /

Pentose phosphate pathway / D-ribose catabolic process / pentose-phosphate shunt /

ATP binding / identical protein binding /

metal ion binding /

nucleus /

cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Park, J. / Chakrabarti, J. / Singh, B. / Gupta, R.S. / Junop, M.S.

Citation

Journal: To Be Published
Title: Crystal structure of human ribokinase in P21 spacegroup
Authors: Park, J. / Chakrabarti, J. / Singh, B. / Gupta, R.S. / Junop, M.S.

History

Deposition	Jun 10, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 15, 2016	Provider: repository / Type: Initial release
Revision 1.1	Apr 26, 2017	Group: Database references / Structure summary
Revision 1.2	Sep 27, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5byd.cif.gz	246.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5byd.ent.gz	197.9 KB	Display	PDB format
PDBx/mmJSON format	5byd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/by/5byd ftp://data.pdbj.org/pub/pdb/validation_reports/by/5byd	HTTPS FTP

-
Related structure data

Related structure data	2fv7S 5byc 5bye 5byf S: Starting model for refinement
Similar structure data	5c3y-3 7c1x-d 7c1z-d 5c40-d 5c3y-5 5c3y-2 4x8f-3 2hzb-1 6w0n-d 5wbp-d 5c3y-4 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Ribokinase

B: Ribokinase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

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 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: 0 / 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: 0 / Auth seq-ID: 15 - 325 / Label seq-ID: 15 - 325

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

#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 / Water Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.26 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M sodium HEPES, 25% PEG 6000

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection	Resolution: 2.1→44.96 Å / Num. obs: 34784 / % possible obs: 97.4 % / Redundancy: 3.7 % / B_iso Wilson estimate: 29.496 Å² / R_merge(I) obs: 0.083 / Net I/σ(I): 8.7
Reflection shell	Resolution: 2.1→2.15 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.518 / Mean I/σ(I) obs: 2.2 / % possible all: 93.4

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2FV7

2fv7

Resolution: 2.1→44.96 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21536	1762	5.1 %	RANDOM
R_work	0.17149	-	-	-
obs	0.17377	32999	97.12 %	-

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: 38.752 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.86 Å²	0 Å²	-1.02 Å²
2-	-	0.65 Å²	0 Å²
3-	-	-	0.5 Å²

Refinement step

Cycle: 1 / Resolution: 2.1→44.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4564	0	2	155	4721

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.019	4654
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	4448
X-RAY DIFFRACTION	r_angle_refined_deg	1.735	1.963	6345
X-RAY DIFFRACTION	r_angle_other_deg	1.152	3	10212
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.763	5	629
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.077	25.68	169
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.226	15	731
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.493	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	783
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	5367
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	982
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	1.636	2.17	2516
X-RAY DIFFRACTION	r_mcbond_other	1.634	2.17	2515
X-RAY DIFFRACTION	r_mcangle_it	2.358	3.249	3145
X-RAY DIFFRACTION	r_mcangle_other	2.358	3.249	3146
X-RAY DIFFRACTION	r_scbond_it	2.275	2.426	2138
X-RAY DIFFRACTION	r_scbond_other	2.274	2.426	2139
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.462	3.54	3200
X-RAY DIFFRACTION	r_long_range_B_refined	5.713	17.914	5049
X-RAY DIFFRACTION	r_long_range_B_other	5.705	17.752	5015
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: 17406 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.317	121	-
R_work	0.257	2326	-
obs	-	-	93.25 %

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	2.3852	2.7502	2.5926	5.0025	2.1418	3.2593	-0.149	-0.0434	0.0758	-0.0087	-0.0003	-0.1837	-0.28	-0.0799	0.1493	0.081	0.0411	0.0358	0.038	0.0209	0.1218	5.2605	2.3684	-25.7648
2	5.6525	1.6335	3.3594	2.1027	2.1473	4.3004	-0.2319	-0.2636	0.4248	-0.0782	-0.0932	0.0517	-0.4468	-0.1861	0.325	0.0809	0.0256	-0.0287	0.032	0.0041	0.077	1.2188	5.9829	-26.6119
3	4.6334	0.8092	1.5829	4.4329	0.4567	4.5753	-0.0446	-0.3762	-0.0449	0.1623	0.0461	0.1934	-0.1102	-0.4955	-0.0015	0.0465	0.0369	0.0493	0.1283	0.0332	0.0616	-6.1106	-4.0883	-20.173
4	4.513	2.869	0.3247	5.8168	0.3776	2.3287	-0.1353	-0.0511	-0.0268	-0.1393	0.0909	-0.1829	-0.0822	0.006	0.0445	0.0544	0.0327	0.0013	0.0412	0.0182	0.0462	6.6467	-3.8836	-22.1257
5	0.4964	-1.0291	0.3048	2.3087	-1.0982	5.1004	0.0055	-0.0481	-0.1311	-0.0259	0.1075	0.1306	0.4318	-0.2474	-0.113	0.123	-0.0363	-0.0167	0.0181	0.0252	0.197	-2.3058	-14.6825	-31.3231
6	6.0745	0.8984	-1.0468	4.8975	-0.7708	2.8482	0.0227	0.1221	-0.5266	0.1565	-0.005	-0.2287	0.6823	0.208	-0.0178	0.2358	0.0272	-0.0429	0.0536	-0.0125	0.1315	2.7841	-17.1406	-37.0481
7	4.6153	-1.1072	1.0188	3.6183	-1.1638	4.5626	0.0918	0.5958	0.0111	-0.3609	-0.1624	-0.1503	0.1901	0.3267	0.0706	0.1189	0.0076	0.0299	0.1651	-0.038	0.1265	6.1577	-7.4871	-49.7911
8	5.0225	0.2249	0.5867	3.7035	-0.3091	4.8561	-0.1571	0.3627	0.1502	-0.1092	0.1116	0.1082	-0.3669	-0.4478	0.0455	0.0396	0.0256	-0.0095	0.0893	0.0232	0.0252	-9.2085	1.7672	-42.7754
9	0.6202	-0.214	0.7875	2.9264	1.8113	3.2392	0.0364	0.0441	0.0837	-0.1569	0.006	0.1376	0.2256	-0.1249	-0.0424	0.1196	-0.0809	-0.0893	0.0675	0.0604	0.1742	12.6468	10.0223	-5.738
10	1.9539	-0.4628	-0.4768	2.8116	1.4573	4.095	-0.058	0.0317	0.1036	-0.1151	0.0778	0.2308	0.0737	-0.3009	-0.0198	0.0151	-0.0181	-0.0373	0.0373	0.0256	0.1519	8.3133	17.035	-3.4906
11	3.2953	-1.3575	0.1302	4.5083	1.77	8.1145	-0.1038	0.031	0.3714	0.0279	0.0799	0.0785	-0.3126	0.1225	0.0239	0.0183	-0.0089	0.0084	0.0107	-0.0215	0.1733	15.1365	28.7954	2.9714
12	0.5851	0.6355	-0.2125	10.3972	-1.0511	0.148	-0.0659	0.4419	0.1598	-0.477	0.0781	-0.2634	0.0404	-0.1289	-0.0123	0.2654	-0.0403	-0.046	0.3898	0.0669	0.2092	23.1638	28.673	-8.1362
13	7.9811	0.8831	-1.5691	3.8093	0.4759	4.5428	-0.2913	0.4149	0.1103	-0.1618	0.2508	-0.1658	-0.1043	0.3815	0.0406	0.0494	-0.0687	-0.0114	0.1461	-0.0481	0.1396	32.0874	25.9296	2.6529
14	0.2132	-1.2251	0.0777	7.4631	-0.5341	0.0483	-0.0042	0.0102	-0.0233	-0.1549	-0.0772	-0.3508	0.0634	0.0206	0.0814	0.5229	0.0903	0.0668	0.4398	-0.0986	0.6233	30.5651	5.3022	1.6126
15	4.9179	-0.3221	-1.5009	4.4011	-0.262	7.0965	-0.0249	-0.142	-0.275	0.2467	0.0049	-0.3508	0.2618	0.6355	0.0201	0.0295	0.0304	-0.0093	0.0638	0.0173	0.0949	23.9583	12.8624	10.3559
16	4.2378	0.7671	4.0588	0.8471	-0.72	9.0019	0.0579	-0.2763	-0.4237	0.0633	-0.0766	-0.1468	0.5759	-0.1118	0.0187	0.2139	0.0378	0.0328	0.0549	0.0347	0.1586	20.37	5.7983	14.6683

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	15 - 39
2	X-RAY DIFFRACTION	2	A	40 - 68
3	X-RAY DIFFRACTION	3	A	69 - 97
4	X-RAY DIFFRACTION	4	A	98 - 140
5	X-RAY DIFFRACTION	5	A	141 - 161
6	X-RAY DIFFRACTION	6	A	162 - 192
7	X-RAY DIFFRACTION	7	A	193 - 257
8	X-RAY DIFFRACTION	8	A	258 - 329
9	X-RAY DIFFRACTION	9	B	15 - 77
10	X-RAY DIFFRACTION	10	B	78 - 153
11	X-RAY DIFFRACTION	11	B	154 - 179
12	X-RAY DIFFRACTION	12	B	180 - 186
13	X-RAY DIFFRACTION	13	B	187 - 254
14	X-RAY DIFFRACTION	14	B	255 - 266
15	X-RAY DIFFRACTION	15	B	267 - 307
16	X-RAY DIFFRACTION	16	B	308 - 326

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi