PDB-1ogk: The crystal structure of Trypanosoma cruzi dUTPase in complex wit...

ID or keywords:

Entry

Database: PDB / ID: 1ogk

Title

The crystal structure of Trypanosoma cruzi dUTPase in complex with dUDP

Components

DEOXYURIDINE TRIPHOSPHATASE

Keywords

HYDROLASE / DIMER

Function / homology

Function and homology information

all-alpha NTP pyrophosphatase / Type II deoxyuridine triphosphatase / all-alpha NTP pyrophosphatases / Type II deoxyuridine triphosphatase / dUTPase/dCTP pyrophosphatase / dUTPase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology

Biological species

TRYPANOSOMA CRUZI (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.85 Å

Authors

Harkiolaki, M. / Dodson, E.J. / Bernier-Villamor, V. / Turkenburg, J.P. / Gonzalez-Pacanowska, D. / Wilson, K.S.

Citation

Journal: Structure / Year: 2004
Title: The Crystal Structure of Trypanosoma Cruzi Dutpase Reveals a Novel Dutp/Dudp Binding Fold
Authors: Harkiolaki, M. / Dodson, E.J. / Bernier-Villamor, V. / Turkenburg, J.P. / Gonzalez-Pacanowska, D. / Wilson, K.S.

History

Deposition	May 7, 2003	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 22, 2004	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	May 1, 2024	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	1ogk.cif.gz	200.4 KB	Display	PDBx/mmCIF format
PDB format	pdb1ogk.ent.gz	161.3 KB	Display	PDB format
PDBx/mmJSON format	1ogk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	1ogk_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	1ogk_full_validation.pdf.gz	1.3 MB	Display
Data in XML	1ogk_validation.xml.gz	37.8 KB	Display
Data in CIF	1ogk_validation.cif.gz	50.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/og/1ogk ftp://data.pdbj.org/pub/pdb/validation_reports/og/1ogk	HTTPS FTP

-
Related structure data

Related structure data	1oglC C: citing same article (ref.)
Similar structure data	4oqq-d 2zif-d 4ksi-d 6zvn-d 6rre-5 4beu-d 1diw-d 2je5-1 1fv0-3 5j92-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: DEOXYURIDINE TRIPHOSPHATASE

B: DEOXYURIDINE TRIPHOSPHATASE

D: DEOXYURIDINE TRIPHOSPHATASE

E: DEOXYURIDINE TRIPHOSPHATASE

hetero molecules

130 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DEOXYURIDINE TRIPHOSPHATASE

B: DEOXYURIDINE TRIPHOSPHATASE

hetero molecules

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

2

D: DEOXYURIDINE TRIPHOSPHATASE

E: DEOXYURIDINE TRIPHOSPHATASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	106.386, 50.307, 111.387
Angle α, β, γ (deg.)	90.00, 101.35, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	E
1	2	B
2	2	D
3	2	E

NCS domain segments:

Refine code: 1

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	PRO	PRO	B	B	17 - 31	17 - 31
2	1	1	SER	SER	PRO	PRO	E	D	17 - 31	17 - 31
1	2	1	ASP	ASP	LEU	LEU	B	B	41 - 53	41 - 53
2	2	1	ASP	ASP	LEU	LEU	E	D	41 - 53	41 - 53
1	3	1	ASN	ASN	SER	SER	B	B	73 - 87	73 - 87
2	3	1	ASN	ASN	SER	SER	E	D	73 - 87	73 - 87
1	4	1	TYR	TYR	ARG	ARG	B	B	194 - 204	194 - 204
2	4	1	TYR	TYR	ARG	ARG	E	D	194 - 204	194 - 204
1	1	2	DUD	DUD	DUD	DUD	B	E	1280
2	1	2	DUD	DUD	DUD	DUD	D	F	1280
3	1	2	DUD	DUD	DUD	DUD	E	G	1281

NCS ensembles :

ID
1
2

#1: Protein	DEOXYURIDINE TRIPHOSPHATASE / DUTPASE Mass: 32104.342 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Strain: Y / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15923, dUTP diphosphatase
#2: Chemical	ChemComp-DUD / DEOXYURIDINE-5'-DIPHOSPHATE Mass: 388.162 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₁P₂

-
Experiment

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

-
Sample preparation

Crystal

Density Matthews: 2.3 Å³/Da / Density % sol: 45.7 %

Crystal grow

pH: 6.6
Details: 25% PEG 2000 MME, 0.3M SODIUM FORMATE, 50 MM SODIUM HEPES PH 7.0

Crystal grow

*PLUS

Temperature: 17 ℃ / pH: 7 / Method: vapor diffusion

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details
1	0.3 M	sodium formate	1	reservoir
2	25 %	PEG2000 MME	1	reservoir
3	50 mM	sodium HEPES	1	reservoir	pH7.0

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
Detector	Type: ADSC CCD / Detector: CCD / Date: Oct 15, 2001 / Details: MIRRORS
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 2.85→20 Å / Num. obs: 27211 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / R_merge(I) obs: 0.085 / Net I/σ(I): 9.46
Reflection shell	Resolution: 2.85→2.9 Å / Redundancy: 3 % / R_merge(I) obs: 0.442 / Mean I/σ(I) obs: 1.1 / % possible all: 97.3
Reflection	PLUS Highest resolution: 2.85 Å / Lowest resolution: 20 Å / Redundancy: 3.5 % / R_merge(I) obs*: 0.085
Reflection shell	PLUS Lowest resolution: 2.9 Å / % possible obs: 97.3 % / R_merge(I) obs: 0.442 / Mean I/σ(I) obs*: 1.1

-
Processing

Software

Name	Version	Classification
REFMAC	5.1.13	refinement
DENZO		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: NATIVE STRUCTURE

Resolution: 2.85→111.8 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.881 / SU B: 19.26 / SU ML: 0.345 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS ELEVATED B VALUES OF CHAIN D ATOMS REFLECT THE RELATIVE LACK OF STABILLISING CRYSTALLOGRAPHIC CONTACTS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.273	1362	5 %	RANDOM
R_work	0.205	-	-	-
obs	0.209	25841	99.1 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 34.97 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.7 Å²	0 Å²	1.18 Å²
2-	-	4.15 Å²	0 Å²
3-	-	-	1.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.85→111.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7712	0	72	0	7784

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.021	7960
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	7159
X-RAY DIFFRACTION	r_angle_refined_deg	1.931	1.953	10793
X-RAY DIFFRACTION	r_angle_other_deg	1.019	3	16618
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.222	5	933
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	1185
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	8715
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1648
X-RAY DIFFRACTION	r_nbd_refined	0.245	0.2	2199
X-RAY DIFFRACTION	r_nbd_other	0.25	0.2	8837
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.101	0.2	4581
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.189	0.2	153
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	0.183	0.2	13
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.257	0.2	46
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.151	0.2	4
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	0.65	1.5	4712
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.247	2	7572
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.618	3	3248
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.78	4.5	3221
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	B	841	tight positional	0.1	0.05
1	2	E	841	tight positional	0.1	0.05
2	1	B	34	tight positional	0.04	0.05
2	2	D	34	tight positional	0.05	0.05
2	3	E	34	tight positional	0.04	0.05
1	1	B	841	tight thermal	0.1	0.5
1	2	E	841	tight thermal	0.1	0.5
2	1	B	34	tight thermal	0.34	0.5
2	2	D	34	tight thermal	0.48	0.5
2	3	E	34	tight thermal	0.18	0.5

LS refinement shell

Resolution: 2.85→2.93 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.353	79
R_work	0.302	1841

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	7.2153	-0.4957	0.9058	4.6591	0.8469	2.317	0.0228	-0.0824	0.5689	0.3286	-0.036	-0.3586	-0.1984	0.3429	0.0132	0.1975	0.0066	0.0274	0.06	0.005	0.2564	48.1487	5.238	38.6064
2	5.0036	-1.4616	-3.3204	2.8735	0.8809	2.4861	0.2251	0.5578	0.159	-0.462	0.0559	-0.0117	-0.3691	-0.0873	-0.281	0.1442	0.0021	-0.0561	0.1021	0.0978	0.1171	24.1023	6.7373	37.8842
3	2.7445	1.5931	0.7356	2.4663	-0.0577	2.8159	0.0742	-0.2071	-0.1167	0.3213	-0.1556	0.4033	0.2407	-0.7517	0.0815	0.1557	-0.0518	0.0276	0.1504	-0.0254	0.2012	0.6598	-1.3768	62.1027
4	4.6078	-0.9149	-1.3696	2.7819	0.5408	2.0551	0.137	0.6999	-0.4691	-0.3037	-0.1047	0.1655	0.2996	-0.3789	-0.0324	0.2094	-0.045	-0.06	0.115	-0.0389	0.1264	11.4773	-6.6307	43.1199
5	3.2033	-0.7132	0.5578	4.0634	-0.6883	3.6424	-0.0805	-0.2879	-0.5972	0.2101	-0.0701	0.7082	0.2816	-0.7	0.1506	0.5375	-0.0736	0.1588	0.9071	0.0396	0.7183	-17.5436	7.5937	96.7272
6	4.2719	-0.6829	-2.4464	1.8376	0.0258	2.1866	0.061	-1.0277	0.4506	0.737	0.0081	0.1967	-0.5008	-0.3161	-0.0691	0.4888	-0.0482	0.0644	0.5617	-0.1093	0.4303	0.5673	20.1962	99.2669
7	6.187	-0.4445	1.2336	2.5143	-1.2101	2.98	0.1836	-0.2989	-0.0193	0.0005	-0.2706	-0.5214	0.2676	0.3475	0.0871	0.1807	-0.0215	-0.0013	0.0697	0.006	0.1489	27.1947	7.2159	81.8372
8	3.8915	-0.8978	-0.0153	2.1634	-0.639	3.048	0.0217	-0.9509	0.04	0.8623	0.0545	-0.1855	0.0572	-0.0147	-0.0762	0.4654	-0.0842	0.0344	0.5124	0.0008	0.1728	16.7314	10.135	101.2643

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 30
2	X-RAY DIFFRACTION	1	A	189 - 278
3	X-RAY DIFFRACTION	2	A	37 - 93
4	X-RAY DIFFRACTION	2	A	140 - 187
5	X-RAY DIFFRACTION	2	A	102 - 118
6	X-RAY DIFFRACTION	3	B	11 - 30
7	X-RAY DIFFRACTION	3	B	189 - 278
8	X-RAY DIFFRACTION	4	B	37 - 93
9	X-RAY DIFFRACTION	4	B	140 - 187
10	X-RAY DIFFRACTION	4	B	102 - 118
11	X-RAY DIFFRACTION	5	D	11 - 30
12	X-RAY DIFFRACTION	5	D	189 - 278
13	X-RAY DIFFRACTION	6	D	37 - 93
14	X-RAY DIFFRACTION	6	D	140 - 187
15	X-RAY DIFFRACTION	6	D	104 - 118
16	X-RAY DIFFRACTION	7	E	10 - 30
17	X-RAY DIFFRACTION	7	E	189 - 278
18	X-RAY DIFFRACTION	8	E	37 - 93
19	X-RAY DIFFRACTION	8	E	140 - 187
20	X-RAY DIFFRACTION	8	E	102 - 118

Refinement

*PLUS

Highest resolution: 2.9 Å / Lowest resolution: 20 Å / % reflection R_free: 5 %

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal	Dev ideal target
X-RAY DIFFRACTION	r_bond_d	0.02	0.02
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	1.93	2

-
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