PDB-2rbc: Crystal structure of a putative ribokinase from Agrobacterium tum...

ID or keywords:

Entry

Database: PDB / ID: 2rbc

Title

Crystal structure of a putative ribokinase from Agrobacterium tumefaciens

Components

Sugar kinase

Keywords

TRANSFERASE / sugar kinase /

ribokinase family / ATP-binding site /

structural genomics /

Agrobacterium tumefaciens / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

kinase activity
Similarity search - Function

Biological species

Agrobacterium tumefaciens str. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.9 Å

Authors

Cuff, M.E. / Xu, X. / Zheng, H. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: Structure of a putative ribokinase from Agrobacterium tumefaciens.
Authors: Cuff, M.E. / Xu, X. / Zheng, H. / Edwards, A.M. / Savchenko, A. / Joachimiak, A.

History

Deposition	Sep 18, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 13, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2rbc.cif.gz	85.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2rbc.ent.gz	65 KB	Display	PDB format
PDBx/mmJSON format	2rbc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rb/2rbc ftp://data.pdbj.org/pub/pdb/validation_reports/rb/2rbc	HTTPS FTP

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Related structure data

Similar structure data	3in1-2 5c3y-1 6wjz-d 3nca-d 4c0e-1 5bye-d 4rni-d 6wb4-d 3nc2-d 6ils-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC6153

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Sugar kinase

hetero molecules

38.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Sugar kinase

hetero molecules

A: Sugar kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	81.024, 81.024, 139.799
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-327- CL

Details

Authors state that the biological unit of this protein is unknown, and that probably it is a dimer shown in remark 350.

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Protein , 1 types, 1 molecules A

#1: Protein	Sugar kinase / AGR_C_4560p Mass: 37365.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Species: Agrobacterium tumefaciens / Strain: C58 / Gene: RbsK, AGR_C_4560, Atu2509 / Plasmid: Modified p11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q8UCH8, UniProt: A9CHQ7*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

#1: Protein

Sugar kinase / AGR_C_4560p

Mass: 37365.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens

/ Strain: C58 / Gene: RbsK, AGR_C_4560, Atu2509 / Plasmid: Modified p11 / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8UCH8, UniProt: A9CHQ7*PLUS,

Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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Non-polymers , 5 types, 412 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 400 / 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: 3.07 Å³/Da / Density % sol: 59.94 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-Tris pH 6.5, 1.5M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.97873, 0.97886

Detector

Type: CUSTOM-MADE / Detector: CCD / Date: Apr 20, 2006

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97873	1
2	0.97886	1

Reflection

Redundancy: 13.2 % / Av σ(I) over netI: 9.9 / Number: 492007 / R_merge(I) obs: 0.073 / Χ²: 1.36 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 37345 / % possible obs: 99.7

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.68	50	98.2	1	0.052	2.933	11.8
3.72	4.68	100	1	0.047	1.82	12.9
3.25	3.72	100	1	0.054	1.742	13.5
2.95	3.25	100	1	0.059	1.329	14
2.74	2.95	100	1	0.071	1.245	14.2
2.58	2.74	100	1	0.08	1.144	14.4
2.45	2.58	100	1	0.095	1.077	14.5
2.34	2.45	100	1	0.109	0.995	14.5
2.25	2.34	100	1	0.164	1.256	14.4
2.17	2.25	100	1	0.18	1.794	14.4
2.11	2.17	100	1	0.176	0.919	14.7
2.05	2.11	99.9	1	0.203	0.929	14.6
1.99	2.05	100	1	0.244	0.918	11.8
1.94	1.99	99.8	1	0.386	0.936	9.5
1.9	1.94	97.9	1	0.25	1.302	8.5

Reflection

Resolution: 1.9→50 Å / Num. all: 69844 / Num. obs: 69844 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7 % / B_iso Wilson estimate: 30.6 Å² / R_merge(I) obs: 0.059 / Χ²: 0.993 / Net I/σ(I): 9.9

Reflection shell

Resolution: 1.9→1.94 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.235 / Mean I/σ(I) obs: 6.3 / Num. unique all: 4637 / Χ²: 1.308 / % possible all: 98.4

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 1.9 Å / D res low: 50 Å / FOM : 0.362 / FOM acentric: 0.388 / FOM centric: 0.183 / Reflection: 35714 / Reflection acentric: 31138 / Reflection centric: 4576

Phasing MAD set

Highest resolution: 1.9 Å / Lowest resolution: 50 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	2.1	1	0.1	0.1	0	0	31138	4576
2	0.97	0.93	8.8	12.4	0.32	0.28	31042	4551

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	12.01-50	1.57	1	0.4	0.2	0	0	82	84
1	6.82-12.01	1.48	1	0.4	0.3	0	0	491	241
1	4.76-6.82	1.79	1	0.4	0.2	0	0	1261	377
1	3.66-4.76	1.21	1	0.3	0.2	0	0	2404	532
1	2.97-3.66	1.47	1	0.2	0.1	0	0	3886	649
1	2.5-2.97	2.43	1	0.1	0.1	0	0	5673	804
1	2.16-2.5	3.86	1	0.1	0	0	0	7180	840
1	1.9-2.16	13.21	1	0.1	0	0	0	10161	1049
2	12.01-50	0.87	0.77	11.1	14.1	0.97	0.66	80	84
2	6.82-12.01	0.85	0.82	10	12.5	0.9	0.63	487	237
2	4.76-6.82	0.91	0.84	9.8	13.4	0.76	0.54	1260	377
2	3.66-4.76	0.95	0.9	11	15.6	0.52	0.34	2403	530
2	2.97-3.66	0.96	0.93	9.2	13.6	0.45	0.29	3883	648
2	2.5-2.97	0.97	0.94	7.5	10.1	0.38	0.28	5667	803
2	2.16-2.5	0.99	0.99	8.4	11.1	0.24	0.17	7144	834
2	1.9-2.16	1	1	9	12.2	0.14	0.1	10118	1038

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	38.51506	-0.875	-0.645	-0.074	0
2	Se	36.64563	-0.862	-0.665	-0.18	0
3	Se	39.58156	-1.119	-0.574	-0.079	0
4	Se	34.83258	-0.849	-0.552	-0.158	0
5	Se	58.77821	-0.825	-0.61	-0.12	0
6	Se	39.0239	-1.064	-0.753	-0.132	0
7	Se	39.12199	-0.914	-0.528	-0.205	0
8	Se	59.43863	-0.962	-0.898	-0.149	0
9	Se	66.28204	-1.203	-0.697	-0.251	0
10	Se	42.91651	-0.875	-0.645	-0.074	-0.054
11	Se	37.70619	-0.861	-0.665	-0.18	-0.044
12	Se	42.29323	-1.119	-0.574	-0.079	-0.054
13	Se	37.93235	-0.849	-0.552	-0.158	-0.046
14	Se	65.09966	-0.825	-0.609	-0.12	-0.056
15	Se	42.81662	-1.064	-0.753	-0.132	-0.047
16	Se	46.25343	-0.914	-0.528	-0.205	-0.025
17	Se	61.77279	-0.963	-0.899	-0.149	-0.027
18	Se	69.5309	-1.203	-0.697	-0.251	-0.026

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
12.01-50	0.524	0.678	0.375	166	82	84
6.82-12.01	0.589	0.704	0.354	732	491	241
4.76-6.82	0.606	0.682	0.353	1638	1261	377
3.66-4.76	0.541	0.601	0.273	2936	2404	532
2.97-3.66	0.529	0.577	0.24	4535	3886	649
2.5-2.97	0.463	0.502	0.184	6477	5673	804
2.16-2.5	0.315	0.34	0.106	8020	7180	840
1.9-2.16	0.169	0.182	0.045	11210	10161	1049

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 35714

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
8.25-100	47.9	0.831	505
6.44-8.25	36.8	0.923	562
5.46-6.44	42.9	0.906	652
4.82-5.46	45.1	0.924	747
4.37-4.82	44	0.933	820
4.02-4.37	46.5	0.929	883
3.75-4.02	46.5	0.91	952
3.52-3.75	46.8	0.925	995
3.33-3.52	47.2	0.895	1069
3.17-3.33	51.2	0.888	1112
3.03-3.17	50.3	0.886	1172
2.91-3.03	48.9	0.898	1211
2.8-2.91	47.7	0.887	1244
2.7-2.8	51	0.888	1291
2.61-2.7	50.5	0.891	1339
2.53-2.61	53.2	0.88	1372
2.46-2.53	51.9	0.874	1404
2.39-2.46	55.1	0.868	1460
2.33-2.39	56.9	0.844	1463
2.27-2.33	58.2	0.836	1181
2.22-2.27	64	0.852	1573
2.17-2.22	63	0.817	1234
2.12-2.17	62.2	0.832	1595
2.08-2.12	66.6	0.832	1681
2.04-2.08	69.6	0.832	1746
2-2.04	69.5	0.823	1764
1.96-2	74.4	0.749	1672
1.9-1.96	77.1	0.613	3015

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	3	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

MAD / Resolution: 1.9→32.17 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.933 / SU B: 6.809 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.129
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: The Bijvoet differences were used in phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.228	1802	5 %	RANDOM
R_work	0.188	-	-	-
all	0.19	35713	-	-
obs	0.19	35713	95.51 %	-

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: 20.905 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.83 Å²	0 Å²	0 Å²
2-	-	0.83 Å²	0 Å²
3-	-	-	-1.67 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→32.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2295	0	52	400	2747

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	2480
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1648
X-RAY DIFFRACTION	r_angle_refined_deg	1.49	1.978	3379
X-RAY DIFFRACTION	r_angle_other_deg	0.944	3	4015
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.106	5	325
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.518	23.2	100
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.603	15	391
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.459	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	385
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2800
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	496
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	523
X-RAY DIFFRACTION	r_nbd_other	0.201	0.2	1838
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	1215
X-RAY DIFFRACTION	r_nbtor_other	0.088	0.2	1332
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.189	0.2	298
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.148	0.2	12
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.193	0.2	53
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.127	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	1.304	1.5	1885
X-RAY DIFFRACTION	r_mcbond_other	0.231	1.5	643
X-RAY DIFFRACTION	r_mcangle_it	1.327	2	2541
X-RAY DIFFRACTION	r_scbond_it	2.678	3	979
X-RAY DIFFRACTION	r_scangle_it	3.575	4.5	838

LS refinement shell

Resolution: 1.9→1.95 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.407	131	-
R_work	0.362	2417	-
all	-	2548	-
obs	-	-	93.99 %

Refinement TLS params.

Method: refined / Origin x: 22.4041 Å / Origin y: 0.1285 Å / Origin z: 19.7446 Å

	11	12	13	21	22	23	31	32	33
T	-0.0755 Å²	0.0051 Å²	0.0019 Å²	-	-0.0828 Å²	0.0248 Å²	-	-	-0.0735 Å²
L	0.952 °²	0.3421 °²	-0.3958 °²	-	0.6633 °²	-0.3053 °²	-	-	1.5371 °²
S	0.0458 Å °	-0.0107 Å °	0.0536 Å °	0.0214 Å °	0.008 Å °	0.0279 Å °	0.0215 Å °	-0.0294 Å °	-0.0538 Å °

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