PDB-5c3z: Crystal structure of human ribokinase in complex with AMPPCP in C...

ID or keywords:

Entry

Database: PDB / ID: 5c3z

Title

Crystal structure of human ribokinase in complex with AMPPCP in C2 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 /

metal ion binding / identical protein binding /

nucleus /

cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 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 complex with AMPPCP in C2 spacegroup
Authors: Park, J. / Chakrabarti, J. / Singh, B. / Gupta, R.S. / Junop, M.S.

History

Deposition	Jun 17, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5c3z.cif.gz	260.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5c3z.ent.gz	218.3 KB	Display	PDB format
PDBx/mmJSON format	5c3z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5c3z_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	5c3z_full_validation.pdf.gz	1 MB	Display
Data in XML	5c3z_validation.xml.gz	32 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c3/5c3z ftp://data.pdbj.org/pub/pdb/validation_reports/c3/5c3z	HTTPS FTP

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Related structure data

Related structure data	2fv7S 5byc 5byd 5bye 5byf 5c3y 5c40 5c41 S: Starting model for refinement
Similar structure data	6xk2-1 7c1y-d 2jg1-2 6wjz-d 3ie7-1 2fv7-2 5m89-d 5bye-d 5byf-d 4xck-2 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
Related items in Molecule of the Month	#118 - Oct 2009 Sodium-Potassium Pump similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1)

Deposited unit

A: Ribokinase

B: Ribokinase

hetero molecules

71.7 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)	142.557, 72.943, 91.864
Angle α, β, γ (deg.)	90.00, 114.81, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	0	1	0	A	11 - 324
2	0	1	0	B	11 - 324

#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-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₈N₅O₁₂P₃ / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.08 Å³/Da / Density % sol: 60.01 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M sodium HEPES, 10% PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.1 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 29, 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: 1.9→50 Å / Num. obs: 67611 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / R_merge(I) obs: 0.051 / Net I/σ(I): 18.464
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.429 / Mean I/σ(I) obs: 2.875 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0123	refinement
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2FV7

2fv7

Resolution: 1.9→50 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.96 / SU B: 5.181 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18766	3427	5.1 %	RANDOM
R_work	0.14934	-	-	-
obs	0.15125	64182	99.15 %	-

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: 36.267 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.62 Å²	0 Å²	-0.11 Å²
2-	-	1.16 Å²	0 Å²
3-	-	-	-1.17 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4651	0	69	508	5228

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.028	0.019	4892
X-RAY DIFFRACTION	r_bond_other_d	0.012	0.02	4636
X-RAY DIFFRACTION	r_angle_refined_deg	2.435	1.981	6694
X-RAY DIFFRACTION	r_angle_other_deg	1.817	3	10666
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.011	5	655
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.016	25.611	180
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.136	15	778
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.558	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.154	0.2	812
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.02	5638
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	1037
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	1.71	1.932	2590
X-RAY DIFFRACTION	r_mcbond_other	1.71	1.931	2589
X-RAY DIFFRACTION	r_mcangle_it	2.307	2.882	3255
X-RAY DIFFRACTION	r_mcangle_other	2.307	2.883	3256
X-RAY DIFFRACTION	r_scbond_it	2.823	2.319	2302
X-RAY DIFFRACTION	r_scbond_other	2.823	2.32	2303
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.244	3.356	3440
X-RAY DIFFRACTION	r_long_range_B_refined	7.585	18.23	5762
X-RAY DIFFRACTION	r_long_range_B_other	7.585	18.234	5763
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: 35892 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-ID	Auth asym-ID
1	A
2	B

LS refinement shell

Resolution: 1.894→1.943 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.256	242	-
R_work	0.227	4446	-
obs	-	-	93.8 %

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	9.409	5.8745	3.6612	3.7066	2.3049	1.4855	0.1349	0.1078	0.0237	0.1405	0.0096	-0.0651	0.0374	0.0822	-0.1445	0.228	-0.0356	-0.0051	0.2742	-0.019	0.4203	61.7855	9.3421	17.2885
2	7.1406	-2.784	-6.502	1.7784	1.8024	6.6957	-0.1816	0.7415	-0.1046	0.1506	0.0271	-0.0136	0.0911	-1.0038	0.1545	0.1078	0.059	0.0063	0.2395	-0.0357	0.0273	30.3511	11.821	19.8977
3	1.8861	-1.4394	-0.9806	1.9296	-0.0762	2.3019	-0.0895	-0.0908	0.2224	0.129	0.1155	-0.055	-0.0988	-0.0521	-0.0261	0.0948	0.0675	-0.0212	0.0485	-0.0164	0.0842	35.2532	14.4136	18.5665
4	2.2101	0.647	0.6031	3.49	0.8406	1.8888	-0.1013	0.2241	0.051	-0.2836	0.0292	0.0785	0.0042	0.0985	0.0721	0.1045	0.0464	0.0161	0.0592	0.0199	0.0095	40.9259	0.5258	3.4457
5	4.9285	-1.2288	-3.8178	2.9083	2.4371	10.4046	-0.1841	-0.1213	-0.6179	0.0443	-0.1212	-0.029	0.704	0.0248	0.3053	0.1725	0.0267	0.0296	0.0248	0.0169	0.1294	37.9818	-14.3023	10.4456
6	6.206	0.8617	-0.9303	2.3844	0.3371	3.2567	-0.0257	-0.3817	-0.3075	0.1977	-0.0461	-0.1493	0.4412	0.1258	0.0717	0.1282	0.0796	0.0134	0.1056	0.0377	0.025	43.8308	-5.3727	22.6457
7	5.2305	-0.8094	1.1649	3.2542	6.1151	13.2403	-0.057	0.2638	0.1162	0.0159	0.0215	-0.0517	0.1869	0.296	0.0355	0.1863	-0.0284	0.0153	0.1804	0.0137	0.2164	22.1508	54.6769	45.8448
8	2.4862	-2.5673	-3.9328	2.9814	3.331	7.8568	-0.0615	0.1533	0.0006	0.0045	-0.1319	-0.0692	0.252	-0.2679	0.1934	0.0437	0.0476	0.0224	0.1134	0.0066	0.1199	19.0044	29.6441	26.1235
9	1.6634	-1.0381	-1.1781	2.5474	0.3856	3.1227	0.1372	0.012	0.1113	-0.1199	-0.0485	-0.3117	-0.1034	0.1694	-0.0887	0.0433	0.0392	0.0365	0.0649	0.041	0.0906	22.9098	29.1707	27.4552
10	2.7514	-1.0622	-0.7302	2.364	0.4115	2.1833	0.1316	-0.1382	0.0259	0.1519	0.006	-0.0375	-0.0698	-0.2004	-0.1376	0.0923	0.0425	0.0216	0.073	0.0327	0.0276	10.0549	30.7855	38.5526
11	4.2725	0.3619	0.8941	3.578	-0.039	4.1296	0.0772	0.2207	0.118	0.0773	0.0249	0.2671	-0.1985	-0.4396	-0.1021	0.0969	0.1507	0.045	0.2475	0.0724	0.0765	-6.3595	34.1724	29.1656
12	4.0273	0.8425	0.9354	3.0176	0.2565	4.2484	-0.0269	0.4838	0.5422	-0.2169	0.0929	0.0408	-0.5805	-0.1928	-0.066	0.2144	0.1172	0.0683	0.1393	0.1221	0.1308	8.8884	44.749	23.2122

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	11 - 18
2	X-RAY DIFFRACTION	2	A	19 - 34
3	X-RAY DIFFRACTION	3	A	35 - 135
4	X-RAY DIFFRACTION	4	A	136 - 233
5	X-RAY DIFFRACTION	5	A	234 - 257
6	X-RAY DIFFRACTION	6	A	258 - 326
7	X-RAY DIFFRACTION	7	B	10 - 14
8	X-RAY DIFFRACTION	8	B	15 - 34
9	X-RAY DIFFRACTION	9	B	35 - 114
10	X-RAY DIFFRACTION	10	B	115 - 200
11	X-RAY DIFFRACTION	11	B	201 - 257
12	X-RAY DIFFRACTION	12	B	258 - 325

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