PDB-7zhi: Crystal Structure of truncated aspartate transcarbamoylase from P...

ID or keywords:

Entry

Database: PDB / ID: 7zhi

Title

Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with bound inhibitor indole

Components

Aspartate carbamoyltransferase

Keywords

TRANSFERASE / Aspartate transcarbamoylase / Plasmodium falciparum / fragment-based screening / inhibitor / malaria

Function / homology

Function and homology information

aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / membrane
Similarity search - Function

Biological species

Plasmodium falciparum 3D7 (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.946 Å

Authors

Wang, C. / Zhang, B.

Funding support

China, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2022
Title: Discovery of Small-Molecule Allosteric Inhibitors of Pf ATC as Antimalarials.
Authors: Wang, C. / Zhang, B. / Kruger, A. / Du, X. / Visser, L. / Domling, A.S.S. / Wrenger, C. / Groves, M.R.

History

Deposition	Apr 6, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 24, 2022	Provider: repository / Type: Initial release
Revision 1.1	Sep 7, 2022	Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.2	Oct 26, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	Nov 2, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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	7zhi.cif.gz	742.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7zhi.ent.gz	609.2 KB	Display	PDB format
PDBx/mmJSON format	7zhi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7zhi_validation.pdf.gz	808.7 KB	Display	wwPDB validaton report
Full document	7zhi_full_validation.pdf.gz	824.7 KB	Display
Data in XML	7zhi_validation.xml.gz	36.5 KB	Display
Data in CIF	7zhi_validation.cif.gz	49.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zh/7zhi ftp://data.pdbj.org/pub/pdb/validation_reports/zh/7zhi	HTTPS FTP

-
Related structure data

Related structure data	7zczC 7zeaC 7zgsC 7zidC 7zp2C 7zstC 5ilqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (10)

Deposited unit

A: Aspartate carbamoyltransferase

B: Aspartate carbamoyltransferase

C: Aspartate carbamoyltransferase

hetero molecules

121 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: light scattering

Unit cell

Length a, b, c (Å)	86.714, 103.822, 87.067
Angle α, β, γ (deg.)	90.000, 117.922, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	2	A
4	2	C
5	3	B
6	3	C

NCS domain segments:

End auth comp-ID: PHE / End label comp-ID: PHE

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	TYR	TYR	A	A	39 - 383	3 - 347
2	1	1	TYR	TYR	B	B	39 - 383	3 - 347
3	2	2	TYR	TYR	A	A	39 - 383	3 - 347
4	2	2	TYR	TYR	C	C	39 - 383	3 - 347
5	3	3	PHE	PHE	B	B	38 - 383	2 - 347
6	3	3	PHE	PHE	C	C	38 - 383	2 - 347

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

#1: Protein	Aspartate carbamoyltransferase Mass: 40350.762 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1344800 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A5K1K910, aspartate carbamoyltransferase
#2: Chemical	ChemComp-IND / INDOLE Mass: 117.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₇N / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 57 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200mM NaCl, 15%(w/v)PEG3350, 100mM bis-tris propane, 2%(v/v)DMSO

-
Data collection

Diffraction	Mean temperature: 291 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.946→44.8 Å / Num. obs: 28662 / % possible obs: 99 % / Redundancy: 3.3 % / CC_1/2: 0.995 / R_merge(I) obs: 0.089 / R_pim(I) all: 0.086 / R_rim(I) all: 0.123 / Net I/σ(I): 9
Reflection shell	Resolution: 2.95→3.12 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.409 / Num. unique obs: 4263 / CC_1/2: 0.857 / R_pim(I) all: 0.39 / R_rim(I) all: 0.566

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5ILQ

5ilq

Resolution: 2.946→43.54 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.915 / SU B: 44.653 / SU ML: 0.353 / Cross valid method: FREE R-VALUE / ESU R Free: 0.393
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2385	1331	4.647 %
R_work	0.1911	27314	-
all	0.193	-	-
obs	-	28645	98.888 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 69.716 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.222 Å²	0 Å²	0.636 Å²
2-	-	7.994 Å²	-0 Å²
3-	-	-	-2.847 Å²

Refinement step

Cycle: LAST / Resolution: 2.946→43.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8172	0	28	31	8231

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	8356
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	7978
X-RAY DIFFRACTION	r_angle_refined_deg	1.715	1.64	11287
X-RAY DIFFRACTION	r_angle_other_deg	1.24	1.586	18419
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.616	5	1002
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.901	24.009	424
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.805	15	1549
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.929	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	1129
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	9322
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1900
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	1786
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	7766
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	4041
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	4059
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.188	0.2	157
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.023	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.398	0.2	47
X-RAY DIFFRACTION	r_nbd_other	0.426	0.2	67
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.246	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	2.476	4.533	4026
X-RAY DIFFRACTION	r_mcbond_other	2.477	4.533	4025
X-RAY DIFFRACTION	r_mcangle_it	4.06	6.797	5022
X-RAY DIFFRACTION	r_mcangle_other	4.059	6.797	5023
X-RAY DIFFRACTION	r_scbond_it	2.303	4.74	4330
X-RAY DIFFRACTION	r_scbond_other	2.291	4.734	4323
X-RAY DIFFRACTION	r_scangle_it	3.946	7.027	6265
X-RAY DIFFRACTION	r_scangle_other	3.935	7.018	6254
X-RAY DIFFRACTION	r_lrange_it	7.434	52.303	9122
X-RAY DIFFRACTION	r_lrange_other	7.432	52.283	9120
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.097	0.05	10707
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.097	0.05	10722
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.108	0.05	10824

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.0968	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.0968	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.09651	0.05008
2	4	C	X-RAY DIFFRACTION	Local ncs	0.09651	0.05008
3	5	B	X-RAY DIFFRACTION	Local ncs	0.10778	0.05008
3	6	C	X-RAY DIFFRACTION	Local ncs	0.10778	0.05008

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.946-3.022	0.342	98	0.333	1946	X-RAY DIFFRACTION	96.4606
3.022-3.105	0.326	96	0.312	1987	X-RAY DIFFRACTION	99.7128
3.105-3.195	0.297	78	0.284	1924	X-RAY DIFFRACTION	99.4536
3.195-3.293	0.254	69	0.24	1878	X-RAY DIFFRACTION	99.795
3.293-3.401	0.259	105	0.22	1779	X-RAY DIFFRACTION	99.7353
3.401-3.521	0.282	103	0.209	1732	X-RAY DIFFRACTION	99.7283
3.521-3.653	0.228	92	0.208	1700	X-RAY DIFFRACTION	99.7218
3.653-3.802	0.275	96	0.19	1611	X-RAY DIFFRACTION	99.3597
3.802-3.971	0.221	66	0.175	1561	X-RAY DIFFRACTION	99.1469
3.971-4.165	0.247	69	0.152	1485	X-RAY DIFFRACTION	98.9179
4.165-4.389	0.196	61	0.144	1416	X-RAY DIFFRACTION	98.3356
4.389-4.655	0.174	57	0.135	1322	X-RAY DIFFRACTION	98.3595
4.655-4.976	0.199	50	0.141	1267	X-RAY DIFFRACTION	98.2103
4.976-5.374	0.261	87	0.188	1137	X-RAY DIFFRACTION	99.2701
5.374-5.885	0.217	42	0.179	1103	X-RAY DIFFRACTION	99.3062
5.885-6.577	0.253	42	0.169	982	X-RAY DIFFRACTION	99.3211
6.577-7.589	0.184	32	0.157	885	X-RAY DIFFRACTION	98.7083
7.589-9.283	0.147	24	0.157	723	X-RAY DIFFRACTION	95.6466
9.283-13.075	0.216	45	0.195	551	X-RAY DIFFRACTION	97.7049

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	3.9065	-1.2544	-0.191	1.0975	-0.1238	1.8965	-0.0113	0.1623	-0.1432	0.0407	0.0697	-0.0444	0.152	0.1739	-0.0585	0.1974	-0.0238	0.0631	0.1957	-0.0118	0.1542	50.5511	-0.1188	13.4523
2	2.3668	0.0132	-1.0487	1.007	-1.3847	2.9005	0.0118	0.09	-0.1616	0.0714	-0.0312	0.1567	0.1616	-0.0167	0.0194	0.2845	-0.0311	0.0314	0.0106	-0.0241	0.1687	21.1086	-4.7108	45.4241
3	1.9302	0.1556	0.8458	0.7636	-0.1396	3.6432	-0.0215	0.3764	-0.0041	-0.2012	0.1007	0.2698	0.0188	-0.22	-0.0792	0.1359	-0.0277	0.017	0.3134	0.0686	0.3271	8.655	8.9129	6.2053

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	39 - 383
2	X-RAY DIFFRACTION	2	ALL	B	38 - 383
3	X-RAY DIFFRACTION	3	ALL	C	38 - 383

-
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