PDB-3fna: Crystal structure of the CBS pair of possible D-arabinose 5-phosp...

ID or keywords:

Entry

Database: PDB / ID: 3fna

Title

Crystal structure of the CBS pair of possible D-arabinose 5-phosphate isomerase yrbH from Escherichia coli CFT073

Components

Possible arabinose 5-phosphate isomerase

Keywords

ISOMERASE / CBS pair /

structural genomics / D-arabinose 5-phosphate isomerase / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG /

CBS domain / Lipopolysaccharide biosynthesis

Function / homology

CBS-domain / CBS-domain / Roll / Alpha Beta /

ADENOSINE MONOPHOSPHATE

Function and homology information

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.1 Å

Authors

Cuff, M.E. / Bigelow, L. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The CBS Pair of possible D-arabinose 5-phosphate isomerase yrbH from Escherichia coli CFT073
Authors: Cuff, M.E. / Bigelow, L. / Buck, K. / Joachimiak, A.

History

Deposition	Dec 23, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 27, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / 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	3fna.cif.gz	63.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3fna.ent.gz	49.7 KB	Display	PDB format
PDBx/mmJSON format	3fna.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/fn/3fna ftp://data.pdbj.org/pub/pdb/validation_reports/fn/3fna	HTTPS FTP

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Related structure data

Similar structure data	3kaa-2 2qv8-2 5e56-d 4wxa-4 5fe3-2 5hen-1 6v16-2 1i5n-1 5mkd-2 3i3j-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC62887.2

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: Possible arabinose 5-phosphate isomerase

B: Possible arabinose 5-phosphate isomerase

hetero molecules

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

1

A: Possible arabinose 5-phosphate isomerase

hetero molecules

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

2

B: Possible arabinose 5-phosphate isomerase

hetero molecules

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

3

A: Possible arabinose 5-phosphate isomerase

hetero molecules

B: Possible arabinose 5-phosphate isomerase

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.109, 108.458, 104.849
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Details

AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

#1: Protein	Possible arabinose 5-phosphate isomerase Mass: 16753.100 Da / Num. of mol.: 2 / Fragment: Residues 187-332 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFT073 / Gene: c3957 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Comment: AMP*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42.14 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 0.1M CHES pH 9.5, 20% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.97937, 0.97923

Detector

Type: CUSTOM-MADE / Detector: CCD / Date: Dec 13, 2008

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	0.97937	1
2	0.97923	1

Reflection

Redundancy: 9.6 % / Av σ(I) over netI: 45.14 / Number: 180513 / R_merge(I) obs: 0.093 / Χ²: 2.69 / D res high: 2.03 Å / D res low: 50 Å / Num. obs: 18777 / % possible obs: 99.2

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.51	50	91.9	1	0.103	14.033	8.5
4.37	5.51	98	1	0.076	8.17	9.2
3.82	4.37	98.5	1	0.069	5.743	9.4
3.47	3.82	99.2	1	0.086	5.116	9.5
3.22	3.47	99.5	1	0.083	3.568	9.6
3.03	3.22	99.7	1	0.094	2.86	9.7
2.88	3.03	99.8	1	0.108	2.356	9.8
2.76	2.88	99.8	1	0.125	1.957	9.8
2.65	2.76	99.9	1	0.132	1.678	9.8
2.56	2.65	99.9	1	0.149	1.38	9.9
2.48	2.56	99.9	1	0.172	1.05	9.8
2.41	2.48	100	1	0.193	0.966	9.8
2.34	2.41	100	1	0.202	0.944	9.9
2.29	2.34	100	1	0.248	0.922	9.8
2.23	2.29	100	1	0.261	0.905	9.8
2.19	2.23	100	1	0.321	0.842	9.8
2.14	2.19	100	1	0.372	0.73	9.8
2.1	2.14	100	1	0.449	0.76	9.7
2.07	2.1	99.9	1	0.534	0.679	9.4
2.03	2.07	99.8	1	0.587	0.703	9.3

Reflection

Resolution: 2.03→50 Å / Num. all: 18777 / Num. obs: 18777 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / B_iso Wilson estimate: 45.8 Å² / R_merge(I) obs: 0.093 / Χ²: 2.688 / Net I/σ(I): 45.14

Reflection shell

Resolution: 2.03→2.07 Å / Redundancy: 9.3 % / R_merge(I) obs: 0.587 / Num. unique all: 946 / Χ²: 0.703 / % possible all: 99.8

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.03 Å / D res low: 50 Å / FOM : 0.424 / FOM acentric: 0.441 / FOM centric: 0.285 / Reflection: 18727 / Reflection acentric: 16730 / Reflection centric: 1997

Phasing MAD set

Highest resolution: 2.03 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	0.3	0.3	0	0	16730	1997
2	0.85	0.78	11.4	16.4	0.84	0.77	13128	1660

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	12.65-50	1.17	1	1.3	0.9	0	0	45	32
1	7.24-12.65	1.15	1	1.5	0.9	0	0	242	91
1	5.07-7.24	1.93	1	1.4	0.8	0	0	665	151
1	3.9-5.07	1.04	1	0.8	0.7	0	0	1242	215
1	3.17-3.9	1.29	1	0.5	0.4	0	0	2022	276
1	2.67-3.17	2.07	1	0.3	0.1	0	0	2984	359
1	2.31-2.67	3.48	1	0.2	0	0	0	4107	397
1	2.03-2.31	9.82	1	0.1	0	0	0	5423	476
2	12.65-50	0.92	0.69	24.7	32.6	1.97	1.61	45	32
2	7.24-12.65	0.7	0.74	22.7	27.8	1.97	1.4	241	86
2	5.07-7.24	0.65	0.66	17.5	22.1	1.84	1.27	665	150
2	3.9-5.07	0.77	0.66	17.5	21.6	1.21	0.95	1241	213
2	3.17-3.9	0.85	0.78	14.4	18.7	0.88	0.7	2019	269
2	2.67-3.17	0.89	0.88	10	13.5	0.7	0.5	2978	353
2	2.31-2.67	0.96	0.98	8.4	10.9	0.42	0.27	4097	394
2	2.03-2.31	0.99	0.98	8.7	11.6	0.25	0.18	1842	163

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	39.83596	-0.225	-0.126	-0.061	0
2	Se	42.47618	-0.547	-0.235	-0.102	0
3	Se	41.90104	-0.513	-0.129	-0.064	0
4	Se	57.7012	-0.475	-0.092	0.019	0
5	Se	42.06295	-0.626	-0.144	-0.153	0
6	Se	55.33124	-0.585	-0.283	-0.082	0
7	Se	42.52646	-0.686	-0.339	-0.048	0
8	Se	43.8018	-0.651	-0.057	-0.08	0
9	Se	70.44505	-0.498	-0.033	-0.103	0
10	Se	56.92918	-0.094	-0.067	-0.112	0
11	Se	68.30847	-0.119	-0.161	-0.046	0
12	Se	47.27854	-0.115	-0.063	0.004	0
13	Se	58.82204	-0.267	-0.168	-0.14	0
14	Se	46.7346	-0.578	-0.177	-0.045	0
15	Se	73.0979	-0.65	-0.297	-0.075	0
16	Se	67.17161	-0.252	-0.038	-0.117	0
17	Se	55.03701	-0.623	-0.164	-0.043	0
18	Se	63.19827	-0.298	-0.056	-0.146	0
19	Se	51.54322	-0.449	-0.021	-0.072	0
20	Se	44.18999	-0.225	-0.126	-0.061	-0.172
21	Se	47.73014	-0.548	-0.236	-0.101	-0.146
22	Se	46.87647	-0.514	-0.129	-0.064	-0.123
23	Se	65.73748	-0.474	-0.092	0.019	-0.107
24	Se	46.4326	-0.627	-0.143	-0.154	-0.098
25	Se	66.8315	-0.585	-0.283	-0.082	-0.152
26	Se	48.33464	-0.685	-0.339	-0.047	-0.135
27	Se	47.53928	-0.651	-0.059	-0.08	-0.126
28	Se	74.57764	-0.497	-0.033	-0.103	-0.095
29	Se	63.95687	-0.092	-0.067	-0.112	-0.135
30	Se	68.37031	-0.12	-0.161	-0.047	-0.096
31	Se	53.05678	-0.115	-0.063	0.004	-0.091
32	Se	61.79441	-0.268	-0.168	-0.14	-0.1
33	Se	66.63028	-0.579	-0.177	-0.045	-0.109
34	Se	71.60002	-0.65	-0.298	-0.074	-0.125
35	Se	66.88232	-0.252	-0.038	-0.119	-0.076
36	Se	70.19363	-0.623	-0.164	-0.043	-0.051
37	Se	89.027	-0.298	-0.054	-0.145	-0.065
38	Se	62.11614	-0.451	-0.021	-0.073	-0.037

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
12.65-50	0.664	0.748	0.546	77	45	32
7.24-12.65	0.694	0.771	0.488	333	242	91
5.07-7.24	0.776	0.818	0.59	816	665	151
3.9-5.07	0.711	0.739	0.546	1457	1242	215
3.17-3.9	0.651	0.68	0.445	2298	2022	276
2.67-3.17	0.551	0.58	0.31	3343	2984	359
2.31-2.67	0.368	0.391	0.128	4504	4107	397
2.03-2.31	0.168	0.18	0.034	5899	5423	476

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 18727

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
6.76-100	58.5	0.775	513
5.38-6.76	39.4	0.915	513
4.72-5.38	35.7	0.939	503
4.28-4.72	37.3	0.937	511
3.97-4.28	41.2	0.928	512
3.74-3.97	39.2	0.934	506
3.54-3.74	38.3	0.94	540
3.37-3.54	39.9	0.937	571
3.22-3.37	43.8	0.914	603
3.09-3.22	44.7	0.922	613
2.98-3.09	48	0.917	645
2.87-2.98	45.5	0.902	663
2.78-2.87	48.9	0.892	687
2.69-2.78	46.3	0.907	708
2.62-2.69	46.8	0.903	737
2.55-2.62	57.1	0.871	761
2.48-2.55	55.6	0.861	754
2.42-2.48	59.6	0.856	788
2.36-2.42	62.5	0.868	817
2.31-2.36	63.6	0.876	823
2.26-2.31	63.7	0.867	825
2.22-2.26	65.4	0.862	865
2.17-2.22	72.3	0.844	879
2.13-2.17	74	0.839	889
2.09-2.13	74.6	0.851	903
2.03-2.09	78.5	0.763	1598

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MLPHARE		phasing
DM	6	phasing
REFMAC		refinement
PDB_EXTRACT	3.006	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: 2.1→50 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.95 / WR_factor R_free: 0.252 / WR_factor R_work: 0.219 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.881 / SU B: 10.769 / SU ML: 0.134 / SU R Cruickshank DPI: 0.236 / SU R_free: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.186
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.243	863	5.1 %	RANDOM
R_work	0.211	-	-	-
all	0.213	16930	-	-
obs	0.213	16930	99.08 %	-

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: 77.2 Å² / B_iso mean: 37.11 Å² / B_iso min: 20.28 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.22 Å²	0 Å²	0 Å²
2-	-	-0.15 Å²	0 Å²
3-	-	-	2.37 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1860	0	36	66	1962

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.021	2017
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1351
X-RAY DIFFRACTION	r_angle_refined_deg	1.562	2.007	2736
X-RAY DIFFRACTION	r_angle_other_deg	0.874	3.001	3279
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.597	5	258
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.618	22.561	82
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.355	15	379
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.125	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	333
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2213
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	384
X-RAY DIFFRACTION	r_mcbond_it	0.817	1.5	1256
X-RAY DIFFRACTION	r_mcbond_other	0.169	1.5	518
X-RAY DIFFRACTION	r_mcangle_it	1.531	2	2038
X-RAY DIFFRACTION	r_scbond_it	2.363	3	761
X-RAY DIFFRACTION	r_scangle_it	3.776	4.5	698

LS refinement shell

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

	R_factor	Num. reflection	% reflection
R_free	0.291	59	-
R_work	0.24	1179	-
all	-	1238	-
obs	-	-	99.44 %

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	1.759	-0.2973	0.0536	2.8728	-0.3091	3.8337	0.1702	-0.1363	-0.1704	-0.102	-0.0849	-0.1276	0.0464	-0.1808	-0.0854	0.0194	-0.0127	-0.0123	0.0688	0.075	0.1046	21.138	17.3508	5.717
2	3.5897	1.516	0.2015	6.0158	0.3375	2.7614	0.2262	-0.292	-0.7356	0.0835	-0.13	-0.8126	-0.1451	0.0688	-0.0962	0.026	-0.0084	-0.03	0.1137	0.1611	0.3719	42.2132	16.593	4.5023

Refinement TLS group

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

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