PDB-3k2v: Structure of the CBS pair of a putative D-arabinose 5-phosphate i...

ID or keywords:

Entry

Database: PDB / ID: 3k2v

Title

Structure of the CBS pair of a putative D-arabinose 5-phosphate isomerase from Klebsiella pneumoniae subsp. pneumoniae.

Components

putative D-arabinose 5-phosphate isomerase

Keywords

ISOMERASE / KpsF-like protein /

CBS domain /

Structural Genomics / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

arabinose-5-phosphate isomerase /

arabinose-5-phosphate isomerase activity / lipopolysaccharide biosynthetic process / carbohydrate derivative binding /

metal ion binding
Similarity search - Function

Biological species

Klebsiella pneumoniae subsp. pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.95 Å

Authors

Cuff, M.E. / Volkart, L. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: Structure of the CBS pair of a putative D-arabinose 5-phosphate isomerase from Klebsiella pneumoniae subsp. pneumoniae.
Authors: Cuff, M.E. / Volkart, L. / Bearden, J. / Joachimiak, A.

History

Deposition	Sep 30, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 22, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Refinement description / Source and taxonomy / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3k2v.cif.gz	75.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3k2v.ent.gz	59.7 KB	Display	PDB format
PDBx/mmJSON format	3k2v.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/k2/3k2v ftp://data.pdbj.org/pub/pdb/validation_reports/k2/3k2v	HTTPS FTP

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Related structure data

Similar structure data	4o9k-d 4g10-d 4iqa-1 2rc3-1 2rc3-2 1s1g-d 1k0o-1 1xio-d 3nqr-2 5ykv-3 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: apc63101.2

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#140 - Aug 2011 Rhomboid Protease GlpG similarity (3)

Deposited unit

A: putative D-arabinose 5-phosphate isomerase

B: putative D-arabinose 5-phosphate isomerase

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	102.151, 102.151, 214.850
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	155
Space group name H-M	H32

Details

Likely the AB dimer in the Asymmetric unit.

#1: Protein	putative D-arabinose 5-phosphate isomerase Mass: 16515.865 Da / Num. of mol.: 2 / Fragment: targeted domain 186-331 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria) Strain: MGH 78578 / Gene: KPN78578_35760, KPN_03607, yrbH / Plasmid: pMCSG19 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): modified BL21 / References: UniProt: A6TEL6
#2: Chemical	ChemComp-CMK / CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID / CMP-2-KETO-3-DEOXY-OCTULOSONIC ACID Mass: 543.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₆N₃O₁₅P
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 289 / 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: 3.27 Å³/Da / Density % sol: 62.33 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris pH8.5, 0.2M Ammonium Sulfate, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97931, 0.97945

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2009

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	0.97931	1
2	0.97945	1

Reflection

Redundancy: 12.2 % / Av σ(I) over netI: 35.55 / Number: 388844 / R_merge(I) obs: 0.108 / Χ²: 2.11 / D res high: 1.95 Å / D res low: 50 Å / Num. obs: 31947 / % possible obs: 99.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.29	50	99	1	0.102	9.026	11.1
4.2	5.29	100	1	0.075	4.685	11.4
3.67	4.2	100	1	0.08	4.197	11.5
3.33	3.67	100	1	0.086	3.453	11.8
3.1	3.33	100	1	0.094	2.931	12.1
2.91	3.1	100	1	0.101	2.366	12.3
2.77	2.91	100	1	0.112	2.147	12.3
2.65	2.77	100	1	0.122	1.652	12.3
2.54	2.65	100	1	0.137	1.512	12.4
2.46	2.54	100	1	0.162	1.334	12.4
2.38	2.46	100	1	0.161	1.164	12.4
2.31	2.38	100	1	0.184	1.07	12.4
2.25	2.31	100	1	0.202	1.026	12.4
2.2	2.25	100	1	0.221	0.918	12.4
2.15	2.2	100	1	0.267	0.883	12.4
2.1	2.15	100	1	0.316	0.873	12.4
2.06	2.1	100	1	0.395	0.823	12.4
2.02	2.06	100	1	0.473	0.849	12.4
1.98	2.02	100	1	0.526	0.887	12.4
1.95	1.98	100	1	0.676	0.983	12.4

Reflection

Resolution: 1.95→50 Å / Num. all: 31947 / Num. obs: 31947 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / B_iso Wilson estimate: 29.1 Å² / R_merge(I) obs: 0.108 / Χ²: 2.105 / Net I/σ(I): 8.7

Reflection shell

Resolution: 1.95→1.98 Å / Redundancy: 12.4 % / R_merge(I) obs: 0.676 / Num. unique all: 1582 / Χ²: 0.983 / % possible all: 100

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 1.95 Å / D res low: 50 Å / FOM : 0.45 / FOM acentric: 0.463 / FOM centric: 0.311 / Reflection: 31751 / Reflection acentric: 29151 / Reflection centric: 2600

Phasing MAD set

Highest resolution: 1.95 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	1.62	1	0.6	0.5	0	0	29151	2600
2	0.9	0.82	27.7	40.5	0.79	0.64	21926	2163

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	12.25-50	1.24	1	1.8	1.4	0	0	88	58
1	6.98-12.25	1.18	1	1.8	1.4	0	0	471	133
1	4.88-6.98	1.55	1	1.6	1	0	0	1172	208
1	3.75-4.88	1.07	1	1.2	1.1	0	0	2193	292
1	3.05-3.75	1.21	1	0.8	0.6	0	0	3525	366
1	2.57-3.05	1.91	1	0.6	0.3	0	0	5163	442
1	2.22-2.57	2.62	1	0.4	0.1	0	0	7138	503
1	1.95-2.22	4.1	1	0.2	0.1	0	0	9401	598
2	12.25-50	0.9	0.84	43.9	60.7	1.76	1.36	88	57
2	6.98-12.25	0.73	0.74	39.9	58.3	1.92	0.92	471	133
2	4.88-6.98	0.76	0.73	36.7	44.1	1.57	1.07	1172	208
2	3.75-4.88	0.87	0.76	42.3	55.3	0.98	0.7	2193	292
2	3.05-3.75	0.89	0.83	35.6	45	0.76	0.59	3524	366
2	2.57-3.05	0.92	0.85	24.4	34.4	0.72	0.46	5158	442
2	2.22-2.57	0.96	0.94	20.9	29.1	0.52	0.36	7110	503
2	1.95-2.22	0.98	1	22.1	29.8	0.35	0.25	2210	162

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	37.48775	0.144	0.443	0.145	0
2	Se	34.96555	0.003	0.44	0.074	0
3	Se	40.80559	-0.283	0.237	0.025	0
4	Se	35.52641	-0.297	0.044	-0.018	0
5	Se	54.08856	0.073	0.507	0.127	0
6	Se	36.87279	-0.268	0.115	0.035	0
7	Se	65.87883	0.16	0.381	0.098	0
8	Se	45.81907	-0.431	0.179	0.011	0
9	Se	37.54805	-0.272	0.142	-0.06	0
10	Se	35.48036	-0.534	0.029	-0.009	0
11	Se	51.31191	0.128	0.457	0.09	0
12	Se	79.22138	-0.245	0.183	-0.021	0
13	Se	68.27908	-0.239	0.17	-0.078	0
14	Se	53.67192	-0.2	0.178	-0.082	0
15	Se	116.90923	-0.513	0.065	-0.01	0
16	Se	34.07215	0.144	0.443	0.145	-0.101
17	Se	36.80737	0.003	0.439	0.074	-0.118
18	Se	42.07629	-0.282	0.237	0.024	-0.125
19	Se	36.9641	-0.296	0.044	-0.018	-0.103
20	Se	54.21249	0.073	0.506	0.127	-0.129
21	Se	59.625	-0.269	0.112	0.032	-0.133
22	Se	59.8072	0.16	0.38	0.098	-0.108
23	Se	45.21872	-0.432	0.18	0.012	-0.11
24	Se	46.25294	-0.272	0.142	-0.06	-0.099
25	Se	27.21568	-0.533	0.03	-0.009	-0.061
26	Se	67.94643	0.127	0.456	0.091	-0.116
27	Se	112.71975	-0.246	0.181	-0.021	-0.117
28	Se	82.25524	-0.24	0.169	-0.078	-0.133
29	Se	75.20015	-0.2	0.179	-0.083	-0.101
30	Se	96.68912	-0.516	0.063	-0.011	-0.072
31	Se	48.329	-0.303	0.241	0.047	0
32	Se	41.165	-0.266	0.117	0.036	0

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
12.25-50	0.68	0.773	0.538	146	88	58
6.98-12.25	0.755	0.816	0.539	604	471	133
4.88-6.98	0.75	0.787	0.54	1380	1172	208
3.75-4.88	0.686	0.714	0.474	2485	2193	292
3.05-3.75	0.631	0.653	0.422	3891	3525	366
2.57-3.05	0.573	0.591	0.363	5605	5163	442
2.22-2.57	0.426	0.439	0.237	7641	7138	503
1.95-2.22	0.208	0.219	0.034	9999	9401	598

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 31751

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.96-100	46.2	0.874	513
6.29-7.96	38.2	0.928	508
5.41-6.29	39.7	0.936	570
4.81-5.41	38.5	0.946	642
4.38-4.81	42	0.945	714
4.05-4.38	41	0.946	756
3.78-4.05	41.7	0.938	822
3.56-3.78	42.8	0.936	872
3.37-3.56	42.6	0.934	922
3.21-3.37	45.8	0.931	965
3.07-3.21	44	0.929	1017
2.95-3.07	44.4	0.932	1054
2.84-2.95	43.5	0.933	1101
2.75-2.84	43.4	0.929	1130
2.66-2.75	48.3	0.928	1163
2.58-2.66	47.2	0.934	1188
2.5-2.58	48.4	0.925	1245
2.44-2.5	51	0.929	1268
2.37-2.44	54.1	0.931	1309
2.32-2.37	51.1	0.927	1330
2.26-2.32	54.7	0.93	1357
2.21-2.26	55.4	0.934	1417
2.17-2.21	59.3	0.923	1438
2.12-2.17	63.4	0.925	1446
2.08-2.12	66.5	0.916	1502
2.04-2.08	66.6	0.909	1511
2-2.04	72.8	0.876	1520
1.95-2	74.9	0.824	2471

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6	phasing
REFMAC		refinement
PDB_EXTRACT	3.005	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: 1.95→41.58 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.962 / WR_factor R_free: 0.182 / WR_factor R_work: 0.157 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.928 / SU B: 4.702 / SU ML: 0.063 / SU R Cruickshank DPI: 0.108 / SU R_free: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.104
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.182	1604	5.1 %	RANDOM
R_work	0.156	-	-	-
obs	0.157	31749	99.84 %	-

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 max: 80.03 Å² / B_iso mean: 23.761 Å² / B_iso min: 9.91 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.48 Å²	0.24 Å²	0 Å²
2-	-	0.48 Å²	0 Å²
3-	-	-	-0.72 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→41.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1969	0	95	289	2353

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	2225
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1474
X-RAY DIFFRACTION	r_angle_refined_deg	1.532	2.027	3041
X-RAY DIFFRACTION	r_angle_other_deg	0.941	3.003	3566
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.623	5	295
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.161	22.826	92
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.565	15	404
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.492	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	376
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2450
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	427
X-RAY DIFFRACTION	r_mcbond_it	0.791	1.5	1354
X-RAY DIFFRACTION	r_mcbond_other	0.198	1.5	564
X-RAY DIFFRACTION	r_mcangle_it	1.557	2	2206
X-RAY DIFFRACTION	r_scbond_it	2.669	3	871
X-RAY DIFFRACTION	r_scangle_it	4.194	4.5	824

LS refinement shell

Resolution: 1.95→2.001 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.278	134	-
R_work	0.22	2177	-
all	-	2311	-
obs	-	-	99.36 %

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	0.9838	0.2274	-0.6476	0.3091	0.3525	3.7692	-0.064	-0.1133	-0.0024	0.0394	-0.1282	-0.0178	0.1484	-0.0418	0.1922	0.1231	0.0089	0.0004	0.067	0.0228	0.0311	-11.7055	19.2899	91.3916
2	1.7844	1.6181	-0.0381	1.7271	-0.2548	0.8076	0.1082	-0.0678	0.3018	-0.0026	-0.0976	0.3043	0.0064	-0.0684	-0.0106	0.0604	0.0247	-0.0233	0.0554	-0.03	0.1729	-20.4264	7.2301	74.9709

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-3 - 146
2	X-RAY DIFFRACTION	2	B	2 - 146

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