PDB-3esq: Crystal Structure of Calcium-bound D,D-heptose 1.7-bisphosphate p...

ID or keywords:

Entry

Database: PDB / ID: 3esq

Title

Crystal Structure of Calcium-bound D,D-heptose 1.7-bisphosphate phosphatase from E. Coli

Components

D,D-heptose 1,7-bisphosphate phosphatase

Keywords

HYDROLASE / Carbohydrate metabolism / Lipopolysaccharide biosynthesis

Function / homology

Function and homology information

D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase / D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase activity / ADP-L-glycero-beta-D-manno-heptose biosynthetic process / lipopolysaccharide core region biosynthetic process / magnesium ion binding / zinc ion binding / cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Sugiman-Marangos, S.N. / Junop, M.S.

Citation

Journal: To be Published
Title: Crystal Structure of D,D-heptose 1.7-bisphosphate phosphatase from E. Coli.
Authors: Taylor, P. / Sugiman-Marangos, S.N. / Zhang, K. / DeLeon, G. / Wright, G.D. / Junop, M.S.

History

Deposition	Oct 6, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 14, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Apr 11, 2012	Group: Other
Revision 1.3	Sep 6, 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_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3esq.cif.gz	95.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3esq.ent.gz	72.6 KB	Display	PDB format
PDBx/mmJSON format	3esq.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/es/3esq ftp://data.pdbj.org/pub/pdb/validation_reports/es/3esq	HTTPS FTP

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Related structure data

Related structure data	3esrC 2gmwS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3l8f-d 2gmw-1 2wl1-d 2gmw-2 2wv5-2 3l1v-1 3l8e-1 3l8g-d 3l1u-1 3nzd-d 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

Deposited unit

A: D,D-heptose 1,7-bisphosphate phosphatase

hetero molecules

23.6 kDa, 1 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)	63.904, 50.585, 52.638
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-383- HOH

#1: Protein	D,D-heptose 1,7-bisphosphate phosphatase / D-glycero-D-manno-heptose 1 / 7-bisphosphate phosphatase Mass: 23490.607 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0200, gmhB, JW0196, yaeD / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P63228, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 192 / 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: 1.81 Å³/Da / Density % sol: 32.08 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 25% PEG 3350, 0.1M Tris, 0.005M DTT, 0.025M sodium chloride, 0.005M calcium chloride, 11% glycerol , pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 8, 2008 / Details: mirrors
Radiation	Monochromator: Blue confocal optics mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.7→40.62 Å / Num. obs: 18244 / % possible obs: 94.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.64 % / B_iso Wilson estimate: 26.075 Å² / R_merge(I) obs: 0.047 / Net I/σ(I): 13.9
Reflection shell	Resolution: 1.7→1.76 Å / Redundancy: 2.36 % / R_merge(I) obs: 0.313 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1894 / % possible all: 80

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Processing

Software

Name	Version	Classification
CrystalClear		data collection
PHENIX		model building
REFMAC	5.2.0019	refinement
CrystalClear		data reduction
CrystalClear		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB Entry 2gmw

2gmw

Resolution: 1.7→40.62 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.932 / SU B: 7.884 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.137 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25844	944	5.2 %	RANDOM
R_work	0.20045	-	-	-
obs	0.2032	17299	94.15 %	-
all	-	17299	-	-

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: 29.588 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.22 Å²	0 Å²	0 Å²
2-	-	-0.58 Å²	0 Å²
3-	-	-	1.8 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→40.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1423	0	2	192	1617

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	1454
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.504	1.947	1973
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.729	5	181
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.501	24.714	70
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.846	15	242
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.815	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	218
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1115
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	696
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.301	0.2	999
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.197	0.2	152
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.133	0.2	3
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.248	0.2	48
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.225	0.2	15
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	0.885	1.5	905
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.376	2	1457
X-RAY DIFFRACTION	r_scbond_it	2.502	3	549
X-RAY DIFFRACTION	r_scangle_it	3.622	4.5	516
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.7→1.744 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.408	58	-
R_work	0.328	1051	-
obs	-	-	79.1 %

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	2.7228	0.0647	0.5689	1.8849	-1.0368	3.2314	0.0509	0.0219	-0.3055	0.1449	0.0191	0.0287	-0.1588	0.1512	-0.07	0.0601	-0.0173	0.0205	0.0351	-0.0223	0.0744	20.243	9.777	15.472
2	1.8429	0.2012	-0.7507	1.2136	-1.8795	3.5687	0.1222	-0.0672	-0.0877	0.2809	0.0196	0.1501	-0.4696	0.0445	-0.1418	0.1483	-0.0139	0.0522	0.0017	0.0085	-0.0095	15.504	13.229	22.049
3	9.5947	1.2618	-0.5762	13.5716	1.2042	8.0553	0.0101	0.1202	0.1416	0.0011	0.0502	-0.2241	-0.183	0.3853	-0.0603	0.0724	-0.0729	0.0003	0.0219	0.0047	-0.0373	23.909	21.156	14.396
4	0.0634	-0.075	0.2108	0.3099	0.3911	2.5583	0.1793	0.0757	0.0441	0.2185	0.2629	0.4396	-0.4285	-0.325	-0.4422	0.0858	0.0051	0.0384	0.0576	0.0757	0.0054	8.054	11.293	24.039
5	1.9479	-2.5446	0.7834	3.4535	0.3966	15.879	-0.0772	-0.2586	-0.063	0.1022	0.2443	0.0406	-0.4684	-0.5062	-0.1671	0.0145	0.0682	0.0924	0.1117	0.1013	0.0362	2.902	8.079	31.389
6	3.5839	-5.6564	2.432	23.3503	-8.3175	5.5456	-0.0867	-0.142	-0.2198	0.3327	0.274	0.9366	-0.3093	-0.1314	-0.1873	0.0063	0.0291	0.0712	0.0123	0.0484	0.1344	2.119	13.29	15.644
7	4.2307	0.0877	-1.9483	8.3164	6.2027	13.3506	0.0698	0.713	0.3604	-0.4022	0.1328	0.2888	-0.5617	-0.4536	-0.2026	0.0003	0.0488	-0.0077	0.0863	0.1021	0.1014	3.519	17.339	5.516
8	4.1522	0.9796	0.1095	2.8692	0.0508	1.2565	-0.0317	0.3196	-0.7554	0.0787	0.0793	0.3037	-0.0169	-0.033	-0.0476	-0.0021	-0.0098	0.0177	0.0317	-0.0373	0.1986	8.644	3.352	9.749
9	31.041	-6.4942	-2.9132	22.557	-6.7967	2.8609	0.2728	-1.0087	-0.9631	-0.0553	0.0317	-0.5939	0.0045	0.3487	-0.3045	0.0498	-0.0378	0.0218	-0.0218	-0.0232	0.2115	10.969	-7.029	11.371
10	3.5958	4.7594	0.368	7.3295	-0.7411	1.5024	-0.2644	0.7171	-0.4972	-0.5285	0.3113	-0.0304	-0.0221	0.0417	-0.0469	0.0005	-0.0035	0.0273	0.1332	-0.1542	0.0927	16.242	4.676	1.317
11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0.0099	0.0729	0.0432	0.027	0.0794	-0.0122	3.3189	9.5951	25.4224
12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0.0159	-0.0315	0.0043	-0.0304	0.0173	0.0946	14.2566	2.832	17.4673
13	0.8704	0.4645	-0.1134	0.7112	-0.1967	0.8087	0.0013	0.0562	-0.0634	0.0382	0.0489	-0.0223	-0.0943	0.0411	-0.0501	-0.0074	0.0152	0.0075	-0.0255	0.0098	-0.0291	14.8523	9.0612	15.3024

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	24 - 62
2	X-RAY DIFFRACTION	2	A	63 - 95
3	X-RAY DIFFRACTION	3	A	96 - 105
4	X-RAY DIFFRACTION	4	A	106 - 118
5	X-RAY DIFFRACTION	5	A	119 - 130
6	X-RAY DIFFRACTION	6	A	131 - 143
7	X-RAY DIFFRACTION	7	A	144 - 151
8	X-RAY DIFFRACTION	8	A	152 - 178
9	X-RAY DIFFRACTION	9	A	179 - 187
10	X-RAY DIFFRACTION	10	A	188 - 205
11	X-RAY DIFFRACTION	11	A	212
12	X-RAY DIFFRACTION	12	A	213
13	X-RAY DIFFRACTION	13	A	214 - 405

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