PDB-4e0c: 1.8 Angstrom Resolution Crystal Structure of Transaldolase from F...

ID or keywords:

Entry

Database: PDB / ID: 4e0c

Title

1.8 Angstrom Resolution Crystal Structure of Transaldolase from Francisella tularensis (phosphate-free)

Components

Transaldolase

Keywords

TRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / Alpha-Beta Barrel/TIM Barrel

Function / homology

Function and homology information

transaldolase / transaldolase activity / pentose-phosphate shunt, non-oxidative branch / carbohydrate metabolic process / cytoplasm
Similarity search - Function

Biological species

Francisella tularensis subsp. tularensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Light, S.H. / Minasov, G. / Halavaty, A.S. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Adherence to Burgi-Dunitz stereochemical principles requires significant structural rearrangements in Schiff-base formation: insights from transaldolase complexes.
Authors: Light, S.H. / Minasov, G. / Duban, M.E. / Anderson, W.F.

History

Deposition	Mar 2, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 14, 2012	Provider: repository / Type: Initial release
Revision 1.1	Mar 5, 2014	Group: Database references
Revision 1.2	Sep 13, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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

-
Download

PDBx/mmCIF format	4e0c.cif.gz	274.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4e0c.ent.gz	220.3 KB	Display	PDB format
PDBx/mmJSON format	4e0c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4e0c_validation.pdf.gz	449 KB	Display	wwPDB validaton report
Full document	4e0c_full_validation.pdf.gz	452.4 KB	Display
Data in XML	4e0c_validation.xml.gz	31.4 KB	Display
Data in CIF	4e0c_validation.cif.gz	49.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e0/4e0c ftp://data.pdbj.org/pub/pdb/validation_reports/e0/4e0c	HTTPS FTP

-
Related structure data

Related structure data	3te9C 3tk7C 3tkfC 3tnoC 3igxS 3upb S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3upb-d 3tkf-d 3sls-d 1za3-2 4gll-d 3u0j-d 2awh-d 3et2-d 2j14-d 6kyt-2 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	TargetTrack: IDP02095

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Transaldolase

B: Transaldolase

hetero molecules

77 kDa, 2 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)	54.761, 87.019, 140.688
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Transaldolase Mass: 38476.074 Da / Num. of mol.: 2 / Fragment: Transaldolase (TalA) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria) Strain: SCHU S4 / Schu 4 / Gene: FTT_1093c, talA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5NFX0, transaldolase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 753 / 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: 2.18 Å³/Da / Density % sol: 43.53 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein: 11.2 mg/ml, 0.5 M sodium chloride, 0.01 M Tris-HCl (pH 8.3), Screen: Pegs G1 (Qiagen), 0.2 M magnesium chloride, 20% (w/v) Peg 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 9, 2012 / Details: Beryllium lenses
Radiation	Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.8→30 Å / Num. all: 62204 / Num. obs: 62204 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / R_merge(I) obs: 0.077 / Net I/σ(I): 20.5
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 6.5 % / R_merge(I) obs: 0.491 / Mean I/σ(I) obs: 4 / % possible all: 99.4

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.6.0117	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IGX

3igx

Resolution: 1.8→29.59 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.952 / SU B: 3.961 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18917	3147	5.1 %	RANDOM
R_work	0.15062	-	-	-
obs	0.15254	58978	98.31 %	-
all	-	58978	-	-

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: 24.577 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.35 Å²	0 Å²	0 Å²
2-	-	-0.35 Å²	0 Å²
3-	-	-	-0.99 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→29.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4872	0	5	753	5630

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.02	5056
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.948	1.975	6856
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.74	5	656
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.827	26.15	213
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.073	15	991
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.105	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.153	0.2	823
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	3662
X-RAY DIFFRACTION	r_gen_planes_other
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.8→1.846 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.22	215	-
R_work	0.191	3922	-
obs	-	-	96.39 %

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	2.7994	-1.5542	-0.4606	2.0707	0.6993	1.4858	-0.1335	-0.1808	-0.2443	0.2024	0.0673	0.0842	0.2483	0.0034	0.0662	0.0957	0.0066	0.0172	0.0537	0.0345	0.0902	2.1274	-23.9577	15.0799
2	13.2207	6.0334	-3.3266	6.1333	-1.2253	6.2124	-0.08	-0.3965	-0.6595	0.047	-0.1225	-0.1118	0.8555	-0.3035	0.2025	0.1894	-0.0266	-0.006	0.1414	0.0248	0.1385	-17.6739	-18.1982	15.3316
3	6.4496	-2.4727	0.0151	2.0159	-0.4919	2.7849	-0.2039	-0.3788	0.0343	0.306	0.2477	0.0966	-0.2225	-0.5595	-0.0438	0.1349	0.0527	0.0256	0.2258	0.0174	0.0726	-17.0619	-9.2114	25.471
4	0.813	-0.2093	0.1617	1.0372	-0.4644	1.2588	-0.0431	-0.0792	0.0765	0.1119	0.0304	-0.0361	-0.1545	-0.0398	0.0126	0.0761	0.0042	-0.0133	0.0554	-0.0059	0.0714	-4.6303	-0.8462	16.4668
5	0.976	-0.3482	0.0171	1.8742	0.1458	1.2709	0.0431	0.095	-0.0102	-0.2129	-0.04	-0.0631	0.0433	0.1162	-0.0031	0.0819	0.0128	0.0201	0.0726	0.0136	0.0898	3.7647	-11.6081	0.5003
6	4.3023	0.0882	-0.8638	4.1196	-1.0088	2.2975	0.0208	0.0096	-0.1323	-0.258	-0.1286	-0.1037	0.1815	0.1468	0.1079	0.1101	0.0402	0.0049	0.0573	0.0043	0.0638	6.09	-25.8895	6.0368
7	0.8609	0.3378	-0.4141	0.9889	-0.6503	2.2337	-0.0225	0.0211	0.0323	-0.0138	0.0616	0.0124	0.0664	-0.0837	-0.0392	0.0683	0.0248	-0.0147	0.0529	0.0062	0.0878	-8.7364	-0.8382	2.053
8	42.6833	1.6804	-10.069	12.9826	-0.9911	29.8961	-0.4535	-0.2347	-0.7855	0.387	0.1373	0.7538	0.0768	-2.5349	0.3162	0.102	0.0129	0.0541	0.5194	0.0919	0.176	-29.3887	-8.9888	19.7593
9	5.0853	0.24	-0.8068	1.2619	0.4947	2.1213	0.0264	0.4324	0.232	-0.1901	-0.0294	0.0477	-0.211	-0.1287	0.0029	0.0969	0.0211	-0.012	0.1235	0.0283	0.0682	-24.7652	20.3967	-30.2175
10	4.0288	-1.5779	0.3865	1.8728	0.1912	0.4853	-0.0183	0.3461	0.1283	-0.001	-0.0817	-0.2826	0.0219	0.1042	0.1001	0.0627	0.0165	0.0199	0.1422	0.0252	0.1115	-9.9181	17.1933	-26.429
11	3.1767	1.3282	2.2586	2.5403	2.0482	4.5911	-0.0306	0.2242	0.2714	-0.1271	-0.0067	-0.1937	-0.2093	0.136	0.0373	0.0913	-0.0249	0.0371	0.1711	0.0482	0.2054	5.7883	25.4988	-25.3542
12	1.0391	0.0245	0.3004	0.6517	0.0087	1.1422	-0.0218	0.0755	0.1186	0.0146	-0.0135	-0.0753	-0.1143	0.0631	0.0353	0.0474	0.003	0.0033	0.064	0.0056	0.0921	-9.5605	23.9193	-13.581
13	0.3947	0.1879	0.1261	2.5371	0.6246	0.846	-0.0175	-0.0184	-0.0392	-0.0342	0.0472	0.0446	0.0915	-0.0388	-0.0297	0.054	0.0021	-0.0103	0.0929	0.0021	0.0673	-19.858	7.333	-12.3236
14	0.6298	-0.1017	-0.055	0.6057	-0.109	1.582	0.0299	0.0601	-0.0344	-0.0742	0.0026	0.0646	0.1182	-0.1313	-0.0325	0.0509	-0.0031	-0.0143	0.0994	-0.0055	0.078	-27.1149	10.8763	-19.3201
15	6.1335	0.3057	11.1777	0.9523	2.9676	26.6291	0.001	-0.3015	-0.2316	0.1456	0.0229	0.1712	0.3694	-0.4708	-0.0239	0.1209	-0.0019	0.0254	0.2032	0.0025	0.1444	-35.6925	13.3569	-19.5589
16	0.8886	0.2517	-0.3147	0.7497	-0.6174	1.4318	-0.0139	0.0684	-0.0118	-0.0341	0.0131	-0.104	0.0974	0.0764	0.0009	0.0549	0.0209	-0.0056	0.067	-0.0096	0.0838	-6.7171	9.0282	-11.6652

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 35
2	X-RAY DIFFRACTION	2	A	36 - 50
3	X-RAY DIFFRACTION	3	A	51 - 96
4	X-RAY DIFFRACTION	4	A	97 - 166
5	X-RAY DIFFRACTION	5	A	167 - 247
6	X-RAY DIFFRACTION	6	A	248 - 269
7	X-RAY DIFFRACTION	7	A	278 - 316
8	X-RAY DIFFRACTION	8	A	317 - 321
9	X-RAY DIFFRACTION	9	B	2 - 29
10	X-RAY DIFFRACTION	10	B	30 - 46
11	X-RAY DIFFRACTION	11	B	47 - 77
12	X-RAY DIFFRACTION	12	B	78 - 166
13	X-RAY DIFFRACTION	13	B	167 - 195
14	X-RAY DIFFRACTION	14	B	196 - 260
15	X-RAY DIFFRACTION	15	B	261 - 279
16	X-RAY DIFFRACTION	16	B	280 - 321

-
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