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

ID or keywords:

Entry

Database: PDB / ID: 7zcz

Title

Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with bound inhibitor 1-(4-chlorophenyl)methanamine

Components

Aspartate carbamoyltransferase

Keywords

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

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: 2.45 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	Mar 29, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 31, 2022	Provider: repository / Type: Initial release
Revision 1.1	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 1.2	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 1.3	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

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PDBx/mmCIF format	7zcz.cif.gz	749.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7zcz.ent.gz	611.3 KB	Display	PDB format
PDBx/mmJSON format	7zcz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7zcz_validation.pdf.gz	880.1 KB	Display	wwPDB validaton report
Full document	7zcz_full_validation.pdf.gz	903.2 KB	Display
Data in XML	7zcz_validation.xml.gz	38.6 KB	Display
Data in CIF	7zcz_validation.cif.gz	53.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zc/7zcz ftp://data.pdbj.org/pub/pdb/validation_reports/zc/7zcz	HTTPS FTP

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Related structure data

Related structure data	7zeaC 7zgsC 7zhiC 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

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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

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

1

Idetical with deposited unit
defined by author
Evidence: light scattering

Unit cell

Length a, b, c (Å)	86.659, 103.628, 86.864
Angle α, β, γ (deg.)	90.000, 117.455, 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:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	TYR	TYR	PHE	PHE	1	A	A	39 - 383	3 - 347
2	1	TYR	TYR	SER	SER	2	B	B	39 - 379	3 - 343
3	2	TYR	TYR	PHE	PHE	3	A	A	39 - 383	3 - 347
4	2	TYR	TYR	PHE	PHE	4	C	C	39 - 383	3 - 347
5	3	PHE	PHE	GLN	GLN	5	B	B	38 - 382	2 - 346
6	3	PHE	PHE	GLN	GLN	6	C	C	38 - 382	2 - 346

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 (E. coli) References: UniProt: A0A5K1K910, aspartate carbamoyltransferase
#2: Chemical	ChemComp-C2B / 1-(4-CHLOROPHENYL)METHANAMINE Mass: 141.598 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₈ClN / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO₄
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.99 Å³/Da / Density % sol: 58.85 %
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

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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: 2.45→45.04 Å / Num. obs: 49863 / % possible obs: 99.1 % / Redundancy: 3.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.045 / R_pim(I) all: 0.043 / R_rim(I) all: 0.062 / Net I/σ(I): 12.2
Reflection shell	Resolution: 2.45→2.53 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.521 / Num. unique obs: 49863 / CC_1/2: 0.797 / R_pim(I) all: 0.482 / R_rim(I) all: 0.712

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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: 2.45→43.425 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.947 / SU B: 19.321 / SU ML: 0.193 / Cross valid method: FREE R-VALUE / ESU R: 0.339 / ESU R Free: 0.228
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2177	2384	4.783 %
R_work	0.1757	47458	-
all	0.178	-	-
obs	-	49842	99.113 %

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: 60.676 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.022 Å²	-0 Å²	0.623 Å²
2-	-	3.461 Å²	-0 Å²
3-	-	-	-1.354 Å²

Refinement step

Cycle: LAST / Resolution: 2.45→43.425 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8161	0	34	163	8358

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	8346
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	7971
X-RAY DIFFRACTION	r_angle_refined_deg	1.83	1.641	11273
X-RAY DIFFRACTION	r_angle_other_deg	1.336	1.587	18403
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.506	5	1001
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.735	24.019	423
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.956	15	1548
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.337	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	1128
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	9294
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1888
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	1712
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	7732
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	4144
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	4060
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.195	0.2	218
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.075	0.2	7
X-RAY DIFFRACTION	r_metal_ion_refined	0.063	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.216	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.285	0.2	43
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.154	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	2.821	4.248	4022
X-RAY DIFFRACTION	r_mcbond_other	2.821	4.247	4021
X-RAY DIFFRACTION	r_mcangle_it	4.386	6.367	5017
X-RAY DIFFRACTION	r_mcangle_other	4.386	6.368	5018
X-RAY DIFFRACTION	r_scbond_it	3.144	4.5	4324
X-RAY DIFFRACTION	r_scbond_other	3.023	4.494	4313
X-RAY DIFFRACTION	r_scangle_it	4.652	6.63	6256
X-RAY DIFFRACTION	r_scangle_other	4.613	6.621	6239
X-RAY DIFFRACTION	r_lrange_it	6.894	49.168	9189
X-RAY DIFFRACTION	r_lrange_other	6.875	49.149	9180
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.098	0.05	10568
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.088	0.05	10804
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.102	0.05	10798

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	0.09776	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.09776	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.0884	0.05008
2	4	C	X-RAY DIFFRACTION	Local ncs	0.0884	0.05008
3	5	B	X-RAY DIFFRACTION	Local ncs	0.10191	0.05008
3	6	C	X-RAY DIFFRACTION	Local ncs	0.10191	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 (%)
2.45-2.512	0.322	129	0.297	3465	X-RAY DIFFRACTION	96.9779
2.512-2.581	0.303	167	0.277	3394	X-RAY DIFFRACTION	98.4245
2.581-2.656	0.286	201	0.258	3285	X-RAY DIFFRACTION	98.8656
2.656-2.737	0.26	159	0.231	3200	X-RAY DIFFRACTION	99.2612
2.737-2.827	0.253	178	0.208	3087	X-RAY DIFFRACTION	99.5123
2.827-2.926	0.281	149	0.204	3040	X-RAY DIFFRACTION	99.4697
2.926-3.036	0.263	149	0.2	2908	X-RAY DIFFRACTION	99.4146
3.036-3.16	0.24	129	0.189	2830	X-RAY DIFFRACTION	99.2287
3.16-3.301	0.235	116	0.18	2730	X-RAY DIFFRACTION	99.6848
3.301-3.462	0.174	107	0.175	2625	X-RAY DIFFRACTION	99.6353
3.462-3.649	0.248	92	0.177	2485	X-RAY DIFFRACTION	99.7677
3.649-3.87	0.226	122	0.181	2320	X-RAY DIFFRACTION	99.3087
3.87-4.136	0.216	127	0.162	2170	X-RAY DIFFRACTION	99.3942
4.136-4.467	0.169	109	0.129	2020	X-RAY DIFFRACTION	99.3467
4.467-4.893	0.132	97	0.112	1887	X-RAY DIFFRACTION	99.5984
4.893-5.469	0.219	101	0.161	1712	X-RAY DIFFRACTION	99.725
5.469-6.312	0.216	107	0.182	1459	X-RAY DIFFRACTION	99.7452
6.312-7.723	0.239	59	0.156	1293	X-RAY DIFFRACTION	99.2658
7.723-10.892	0.139	51	0.124	1000	X-RAY DIFFRACTION	99.5265

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	4.0889	-0.9503	-0.2226	1.013	0.1033	1.9263	-0.066	0.1708	-0.186	-0.003	0.0728	-0.0518	0.195	0.2141	-0.0067	0.0558	-0.0208	0.0147	0.1316	-0.0253	0.0248	50.7976	-0.1768	13.4424
2	2.3405	0.0344	-1.0611	1.3264	-1.4745	2.9754	-0.0559	0.053	-0.1929	0.0737	-0.0143	0.0812	0.1982	-0.0757	0.0702	0.1038	-0.0422	0.0365	0.0223	-0.0159	0.0287	21.5672	-4.7105	45.5539
3	2.0293	0.2926	0.7816	1.0665	-0.261	3.8146	-0.0209	0.4064	-0.0199	-0.1492	0.1097	0.3297	0.0791	-0.2667	-0.0888	0.0309	-0.0354	-0.0355	0.2834	0.0359	0.1465	8.9558	8.9477	6.3044

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	1	ALL	A	501 - 523
3	X-RAY DIFFRACTION	2	ALL	B	38 - 382
4	X-RAY DIFFRACTION	2	ALL	B	501 - 538
5	X-RAY DIFFRACTION	3	ALL	C	38 - 383
6	X-RAY DIFFRACTION	3	ALL	C	401
7	X-RAY DIFFRACTION	3	ALL	C	501 - 522

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