PDB-3kd3: Crystal structure of a phosphoserine phosphohydrolase-like protei...

ID or keywords:

Entry

Database: PDB / ID: 3kd3

Title

Crystal structure of a phosphoserine phosphohydrolase-like protein from Francisella tularensis subsp. tularensis SCHU S4

Components

Phosphoserine phosphohydrolase-like protein

Keywords

UNKNOWN FUNCTION / CSGID / Phosphoserine phosphohydrolase-like protein /

Structural Genomics / Center for Structural Genomics of Infectious Diseases

Function / homology

Function and homology information

L-phosphoserine phosphatase activity => GO:0036424 /

phosphoserine phosphatase / L-serine biosynthetic process /

metal ion binding
Similarity search - Function

Biological species

Francisella tularensis subsp. tularensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.7 Å

Authors

Nocek, B. / Zhou, M. / Peterson, S. / Anderson, W. / Joachimiak, A. / CSGID / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of a phosphoserine phosphohydrolase-like protein from Francisella tularensis subsp. tularensis SCHUS4
Authors: Nocek, B. / Zhou, M. / Peterson, S. / Anderson, W. / Joachimiak, A. / CSGID

History

Deposition	Oct 22, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 15, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Feb 8, 2017	Group: Database references / Structure summary
Revision 1.3	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3kd3.cif.gz	103.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3kd3.ent.gz	86.6 KB	Display	PDB format
PDBx/mmJSON format	3kd3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kd/3kd3 ftp://data.pdbj.org/pub/pdb/validation_reports/kd/3kd3	HTTPS FTP

-
Related structure data

Similar structure data	1vgi-d 5p95-d 5p98-d 5p9o-d 5qbv-2 1k7j-d 6ydd-1 5p9r-2 1z3s-2 3hvi-d 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 - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: IDP02448

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phosphoserine phosphohydrolase-like protein

B: Phosphoserine phosphohydrolase-like protein

hetero molecules

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

1

A: Phosphoserine phosphohydrolase-like protein

hetero molecules

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

2

B: Phosphoserine phosphohydrolase-like protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	72.574, 78.798, 87.918
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Phosphoserine phosphohydrolase-like protein Mass: 24901.771 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria) Gene: FTT0568, FTT_0568 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5NH99
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.52 Å³/Da / Density % sol: 51.26 %

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 7, 2009 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.7→40 Å / Num. all: 56050 / Num. obs: 55741 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / B_iso Wilson estimate: 26.5 Å² / R_merge(I) obs: 0.106 / Net I/σ(I): 24
Reflection shell	Resolution: 1.7→1.73 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.75 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2730 / % possible all: 99.4

-
Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
REFMAC	5.5.0102	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.7→29.34 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.956 / SU B: 3.519 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.09 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18603	2822	5.1 %	RANDOM
R_work	0.16305	-	-	-
obs	0.16423	52855	99.39 %	-
all	-	55677	-	-

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: 8.405 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.04 Å²	0 Å²	0 Å²
2-	-	0.76 Å²	0 Å²
3-	-	-	-0.8 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→29.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3437	0	20	327	3784

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	3545
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2454
X-RAY DIFFRACTION	r_angle_refined_deg	1.523	1.982	4779
X-RAY DIFFRACTION	r_angle_other_deg	0.909	3	6046
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.05	5	444
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.71	25.823	158
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.739	15	678
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.095	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	532
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3887
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	671
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.901	1.5	2167
X-RAY DIFFRACTION	r_mcbond_other	0.314	1.5	883
X-RAY DIFFRACTION	r_mcangle_it	1.673	2	3500
X-RAY DIFFRACTION	r_scbond_it	3.037	3	1378
X-RAY DIFFRACTION	r_scangle_it	5.063	4.5	1272
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→1.745 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.301	204	-
R_work	0.262	3756	-
obs	-	-	97.63 %

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	3.495	0.3139	-1.1015	3.445	-2.7889	4.4707	-0.0572	-0.1651	-0.0567	0.1839	0.0674	0.073	-0.0782	-0.21	-0.0102	0.0631	-0.0156	0.0256	0.079	-0.0042	0.0385	10.8145	38.5589	18.7477
2	0.8772	-0.8526	0.6399	0.9592	-0.7981	3.296	-0.0034	0.021	0.0237	-0.0128	-0.0176	-0.004	-0.2231	0.159	0.0209	0.066	-0.0132	0.0057	0.06	-0.0064	0.0658	21.8977	46.2045	2.7228
3	0.2084	0.133	-0.1548	2.5355	-0.3831	3.2726	-0.0377	-0.0058	0.0062	-0.2254	-0.0218	-0.2765	0.0218	0.2496	0.0595	0.0699	0.0009	0.0213	0.0524	0.0181	0.1011	22.6087	57.108	-0.841
4	0.165	-0.2625	-0.2229	1.7535	1.1384	3.3058	-0.0417	0.0237	0.0263	-0.09	-0.0403	0.1048	-0.1011	-0.2004	0.082	0.0839	0.0102	-0.0032	0.0407	-0.007	0.0762	12.445	57.6272	0.837
5	4.7108	-2.4085	4.2473	1.169	-2.1957	4.854	0.1504	0.0877	-0.1121	-0.0892	-0.0667	0.0507	0.1294	0.1358	-0.0836	0.0829	0.0081	-0.01	0.0845	-0.0067	0.0446	19.4679	40.6359	-6.5465
6	1.5407	0.201	-1.5101	0.0423	-0.2793	2.7506	-0.0303	-0.0008	-0.1743	0.0124	-0.0223	-0.0048	0.1262	0.0488	0.0526	0.081	0.0106	0.0121	0.0558	0.005	0.0674	21.8336	32.937	13.1757
7	0.8377	-0.5337	-0.0433	0.9982	-0.5734	1.2207	0.0388	0.0324	-0.1199	-0.0354	-0.0481	0.0856	0.061	-0.0929	0.0093	0.0467	-0.0163	-0.0028	0.0593	-0.0047	0.0681	11.4573	36.9456	8.0549
8	0.6908	-0.2778	-0.6137	0.608	-0.3808	3.1475	0.0035	-0.0054	-0.041	0.0129	0.035	0.1355	-0.165	-0.2472	-0.0385	0.0242	0.0056	0.0093	0.0701	-0.0043	0.0665	3.9127	46.1454	3.5002
9	2.923	-0.3338	-0.1667	1.4304	-0.2442	3.2802	-0.0028	-0.1192	0.0719	0.0837	0.0505	0.0504	-0.1779	-0.1782	-0.0477	0.0565	0.0258	0.0173	0.055	-0.0068	0.0461	11.3987	49.359	20.0931
10	0.9851	-0.6923	-0.1396	2.0949	-0.5044	1.4394	-0.024	-0.1082	0.0853	0.1168	0.0119	-0.1	-0.1326	0.0968	0.0121	0.0692	0.0008	-0.0085	0.0577	-0.0107	0.0372	22.834	47.4615	21.2147
11	9.3288	3.9925	-1.6309	6.166	-1.9289	2.6942	-0.1584	-0.2236	-0.0796	-0.0867	0.1188	0.2116	0.0364	-0.0343	0.0395	0.0438	0.0075	0.0215	0.0548	-0.0156	0.0532	37.528	28.7624	2.0218
12	2.8288	0.8424	-2.8916	0.8124	-0.8803	3.9004	0.052	-0.1452	0.0789	0.046	0.0703	-0.0515	-0.086	0.2234	-0.1223	0.0367	0.0043	-0.0073	0.0685	-0.0031	0.077	57.0684	34.8897	-2.5978
13	2.977	-0.2748	-1.5193	0.3743	0.0865	1.2208	0.0263	-0.0474	0.04	0.1182	-0.0001	-0.0643	0.0049	0.1274	-0.0262	0.0462	-0.0037	-0.0173	0.0671	-0.0071	0.0836	59.8741	46.2623	-4.2308
14	2.9815	-0.4312	-2.0096	1.1857	0.3292	1.7632	-0.0061	0.107	-0.0193	-0.0373	-0.0091	0.0611	-0.0449	-0.0277	0.0153	0.0518	-0.0048	-0.0029	0.0507	-0.0069	0.0792	52.0617	46.5706	-10.6664
15	0.9538	0.4469	-1.4503	1.5529	-1.791	4.8916	-0.0895	-0.0679	-0.1058	-0.1561	0.0118	-0.0892	0.365	0.2664	0.0778	0.0603	0.0364	-0.0012	0.0412	-0.0011	0.0549	58.4805	27.4738	-5.7813
16	1.5094	-0.2222	0.2636	1.0237	-0.5692	1.0851	-0.0383	0.0616	-0.2296	-0.0201	0.0115	0.033	0.1346	0.0066	0.0268	0.0777	-0.0041	0.0226	0.0177	-0.0063	0.0839	44.4148	24.8288	-2.725
17	6.8493	-1.462	-4.9729	0.3553	0.6863	5.3875	-0.0339	0.2082	-0.0161	-0.0332	-0.0453	-0.0043	0.1771	-0.1408	0.0793	0.0856	-0.0251	0.018	0.0578	-0.0109	0.0327	52.7282	36.5563	-20.834
18	2.9491	1.225	-1.9493	2.7445	-1.4024	2.7351	0.0987	0.2848	0.0717	0.1861	0.0465	0.1026	-0.2239	-0.3077	-0.1452	0.0567	0.0093	-0.0004	0.0796	-0.0041	0.038	36.7771	37.1579	-9.5737
19	3.5596	0.2555	-0.2499	1.322	0.1896	0.3882	-0.0233	-0.0242	0.1214	0.0008	-0.0322	0.0403	0.0002	-0.0481	0.0554	0.0389	0.0021	0.0031	0.0614	-0.0169	0.058	36.7749	38.3874	3.3031
20	1.9128	0.1648	0.3316	3.162	0.5502	1.4093	-0.0477	-0.2118	0.0944	0.1801	-0.0149	0.0123	0.0411	-0.0097	0.0627	0.0507	0.0117	0.0028	0.0769	0.0077	0.0189	45.8624	37.1544	11.9188

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 7
2	X-RAY DIFFRACTION	2	A	8 - 24
3	X-RAY DIFFRACTION	3	A	25 - 46
4	X-RAY DIFFRACTION	4	A	47 - 62
5	X-RAY DIFFRACTION	5	A	63 - 75
6	X-RAY DIFFRACTION	6	A	76 - 93
7	X-RAY DIFFRACTION	7	A	94 - 127
8	X-RAY DIFFRACTION	8	A	128 - 163
9	X-RAY DIFFRACTION	9	A	164 - 187
10	X-RAY DIFFRACTION	10	A	188 - 216
11	X-RAY DIFFRACTION	11	B	1 - 7
12	X-RAY DIFFRACTION	12	B	8 - 24
13	X-RAY DIFFRACTION	13	B	25 - 47
14	X-RAY DIFFRACTION	14	B	48 - 62
15	X-RAY DIFFRACTION	15	B	63 - 85
16	X-RAY DIFFRACTION	16	B	86 - 125
17	X-RAY DIFFRACTION	17	B	126 - 140
18	X-RAY DIFFRACTION	18	B	141 - 160
19	X-RAY DIFFRACTION	19	B	161 - 186
20	X-RAY DIFFRACTION	20	B	187 - 216

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi