PDB-3esr: Crystal Structure of D,D-heptose1.7-bisphosphate phosphatase from...

ID or keywords:

Entry

Database: PDB / ID: 3esr

Title

Crystal Structure of D,D-heptose1.7-bisphosphate phosphatase from E. coli in complex with calcium and phosphate

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: 1.95 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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	3esr.cif.gz	92.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3esr.ent.gz	69.8 KB	Display	PDB format
PDBx/mmJSON format	3esr.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3esr_validation.pdf.gz	430.5 KB	Display	wwPDB validaton report
Full document	3esr_full_validation.pdf.gz	433.4 KB	Display
Data in XML	3esr_validation.xml.gz	10.5 KB	Display
Data in CIF	3esr_validation.cif.gz	14.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/es/3esr ftp://data.pdbj.org/pub/pdb/validation_reports/es/3esr	HTTPS FTP

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Related structure data

Related structure data	3esqC 2gmwS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1yd9-1 2y2b-2 2ht6-1 4lhw-5 4qgl-d 4dm4-1 3uid-1 5xr6-2 1ohu-1 2y8e-1 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

23.7 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)	64.183, 50.446, 52.018
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-256- 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: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 108 / 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: 1.79 Å³/Da / Density % sol: 31.38 %
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, 0.005M sodium phosphate, 11% glycerol , pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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 5, 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: 1.95→39.65 Å / Num. all: 11271 / Num. obs: 11271 / % possible obs: 88.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.79 % / B_iso Wilson estimate: 31.76 Å² / R_merge(I) obs: 0.055 / Net I/σ(I): 13.5
Reflection shell	Resolution: 1.95→2.02 Å / Redundancy: 3.33 % / R_merge(I) obs: 0.34 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1245 / % possible all: 98.2

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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: 1.95→39.65 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.925 / SU B: 13.015 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.25 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27598	540	4.8 %	RANDOM
R_work	0.20843	-	-	-
obs	0.21149	10728	87.9 %	-
all	-	10728	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 34.351 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.89 Å²	0 Å²	0 Å²
2-	-	-0.18 Å²	0 Å²
3-	-	-	1.07 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→39.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1423	0	7	108	1538

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	1458
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.791	1.95	1979
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	14.649	5	181
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.937	24.714	70
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.1	15	242
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.706	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.118	0.2	218
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1115
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	667
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.305	0.2	963
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.197	0.2	96
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.215	0.2	3
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.272	0.2	43
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.246	0.2	9
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	1.025	1.5	905
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.559	2	1457
X-RAY DIFFRACTION	r_scbond_it	2.812	3	553
X-RAY DIFFRACTION	r_scangle_it	4.135	4.5	522
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.95→2.002 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.383	39	-
R_work	0.295	794	-
obs	-	-	89.38 %

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	2.315	1.0424	-0.1159	2.633	-0.7937	2.2756	0.2793	-0.197	-0.2231	0.2004	-0.0548	0.019	0.1794	-0.1051	-0.2245	0.0085	0.0017	0.0271	0.135	-0.0272	0.1078	17.992	8.646	18.287
2	2.6435	0.2584	-1.1534	0.4117	-0.02	2.0132	0.0661	0.1625	-0.1008	-0.0207	0.0419	0.0123	-0.0362	0.0702	-0.108	0.0511	-0.03	0.0069	0.1033	0.005	0.1575	18.092	11.413	15.026
3	11.338	5.5151	-9.6138	3.8955	-9.124	24.4624	0.7805	-0.4629	0.6811	0.67	-0.2005	0.4638	-1.2527	0.2312	-0.58	0.1358	-0.0876	0.0597	-0.0425	-0.025	0.0671	18.735	16.016	26.77
4	15.6008	1.4855	0.0929	1.7776	1.7117	4.5223	0.2434	-0.0848	0.3249	0.007	-0.0853	-0.0167	-0.4057	0.3866	-0.1581	0.0358	-0.0631	0.0324	0.0485	0.0296	0.1377	21.442	20.594	14.198
5	2.9292	0.3914	-1.2445	1.2875	-3.2561	8.2573	0.0578	-0.3128	-0.0276	0.1964	0.0844	0.3739	-0.3596	-0.0867	-0.1422	0.0121	0.0114	0.0413	0.0844	0.0045	0.1468	4.298	8.151	29.451
6	4.0814	-1.6364	0.2035	11.3428	-4.5814	4.4142	0.1238	-0.0043	0.2762	0.1658	0.0004	0.7669	-0.0975	0.0114	-0.1242	-0.0271	0.0069	0.0301	0.1009	-0.0107	0.1747	2.431	13.889	15.228
7	17.3663	-1.4112	-3.4411	1.3888	3.6463	9.5773	-0.259	0.8992	0.5467	-0.5761	0.5421	0.1066	-0.3769	-0.4328	-0.2832	0.0151	-0.0088	-0.006	0.1608	0.0718	0.1888	4.528	15.135	4.17
8	11.9633	0.8885	0.5455	4.6336	0.4994	0.071	-0.1242	0.1537	-0.5551	0.0773	0.107	0.1365	0.0367	0.0545	0.0172	-0.0079	-0.0095	0.0218	0.1076	-0.0205	0.1555	6.706	2.84	12.397
9	7.5354	1.0635	-0.3828	3.1202	-0.4668	0.4668	-0.1355	0.151	-0.5653	-0.0191	0.0978	-0.3332	0.1403	-0.1339	0.0377	-0.0042	-0.0317	0.0364	0.1257	-0.0866	0.1295	12.831	0.068	6.65
10	78.5396	-12.2364	16.3401	16.3768	-4.4677	20.1728	-0.8581	3.1741	-1.4897	-2.1869	-0.1263	0.9929	0.2288	2.4269	0.9844	0.0668	-0.0702	0.0727	0.301	-0.063	-0.088	17.575	8.198	-4.306
11	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0.0114	0.022	0.0016	0.0105	-0.0048	0.0222	3.4291	9.6279	25.2589
12	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	-0.0954	-0.0624	-0.0155	0.0638	-0.0015	0.1063	14.2225	3.098	17.3609
13	292.4738	-120.2172	-2.933	49.4136	1.2056	0.0294	-4.9385	8.8793	-6.9695	1.5989	2.7179	-0.1367	-2.3981	-1.7617	2.2206	0.0061	-0.2858	0.1703	0.2023	-0.1842	0.1695	13.3293	5.2864	19.7089
14	0.4767	0.3649	-0.311	0.5857	-0.4756	0.4697	0.0281	0.057	-0.0763	0.0204	-0.0001	-0.0426	-0.1	-0.0272	-0.0279	-0.0555	0.0148	-0.0176	0.0275	-0.0212	0.0278	12.8488	8.8369	17.0754

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	24 - 48
2	X-RAY DIFFRACTION	2	A	49 - 83
3	X-RAY DIFFRACTION	3	A	84 - 95
4	X-RAY DIFFRACTION	4	A	96 - 109
5	X-RAY DIFFRACTION	5	A	110 - 130
6	X-RAY DIFFRACTION	6	A	131 - 144
7	X-RAY DIFFRACTION	7	A	145 - 152
8	X-RAY DIFFRACTION	8	A	153 - 167
9	X-RAY DIFFRACTION	9	A	168 - 200
10	X-RAY DIFFRACTION	10	A	201 - 205
11	X-RAY DIFFRACTION	11	A	212
12	X-RAY DIFFRACTION	12	A	213
13	X-RAY DIFFRACTION	13	A	214
14	X-RAY DIFFRACTION	14	A	215 - 322

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