PDB-7k46: Crystal Structure of a putative aspartate carbamoyltransferase Le...

ID or keywords:

Entry

Database: PDB / ID: 7k46

Title

Crystal Structure of a putative aspartate carbamoyltransferase Leishmania major Friedlin

Components

Aspartate carbamoyltransferase

Keywords

TRANSFERASE / SSGCID / Aspartate carbamoyltransferase / Leishmania major / LMJF_16_0540 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / glycosome / glutamine metabolic process / ciliary plasm / nuclear lumen / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytoplasm
Similarity search - Function

Biological species

Leishmania major (eukaryote)

Method

X-RAY DIFFRACTION /

SAD / Resolution: 1.9 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of a putative aspartate carbamoyltransferase Leishmania major Friedlin
Authors: Abendroth, J.A. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Sep 14, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 30, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 14, 2020	Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7k46.cif.gz	168.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7k46_validation.pdf.gz	431.5 KB	Display	wwPDB validaton report
Full document	7k46_full_validation.pdf.gz	431.5 KB	Display
Data in XML	7k46_validation.xml.gz	17 KB	Display
Data in CIF	7k46_validation.cif.gz	26.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k4/7k46 ftp://data.pdbj.org/pub/pdb/validation_reports/k4/7k46	HTTPS FTP

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Related structure data

Similar structure data	6jkq-1 4iv5-2 3sds-1 6jkq-2 6kj9-1 4ep1-1 3sds-3 4oh7-1 6jkr-1 3csu-d 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	TargetTrack: SSGCID-LemaA.01332.a TargetTrack: LemaA.01332.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (8) #61 - Jan 2005 Phenylalanine Hydroxylase similarity (2) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (2)

Deposited unit

A: Aspartate carbamoyltransferase

hetero molecules

36.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Aspartate carbamoyltransferase

hetero molecules

A: Aspartate carbamoyltransferase

hetero molecules

A: Aspartate carbamoyltransferase

hetero molecules

defined by author&software
Evidence: gel filtration
109 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	136.240, 136.240, 136.240
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	197
Space group name H-M	I23
Space group name Hall	I223
Symmetry operation	#1: x,y,z #2: z,x,y #3: y,z,x #4: -y,-z,x #5: z,-x,-y #6: -y,z,-x #7: -z,-x,y #8: -z,x,-y #9: y,-z,-x #10: x,-y,-z #11: -x,y,-z #12: -x,-y,z #13: x+1/2,y+1/2,z+1/2 #14: z+1/2,x+1/2,y+1/2 #15: y+1/2,z+1/2,x+1/2 #16: -y+1/2,-z+1/2,x+1/2 #17: z+1/2,-x+1/2,-y+1/2 #18: -y+1/2,z+1/2,-x+1/2 #19: -z+1/2,-x+1/2,y+1/2 #20: -z+1/2,x+1/2,-y+1/2 #21: y+1/2,-z+1/2,-x+1/2 #22: x+1/2,-y+1/2,-z+1/2 #23: -x+1/2,y+1/2,-z+1/2 #24: -x+1/2,-y+1/2,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	A-843- HOH
2	1	A-881- HOH
3	1	A-898- HOH

#1: Protein	Aspartate carbamoyltransferase / LemaA.01332.a Mass: 36269.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_16_0540 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4QEW6, aspartate carbamoyltransferase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.91 Å³/Da / Density % sol: 57.7 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Microlytic MCSG1 screen, condition G7: 25% (w/V) PEG 3350, 100mM Tris base / HCl pH 8.5: LemaA.01332.a.AE1.PS38633 (originally labelled as MyavA.00358.f.AE1.PS38633) at 13.16mg/ml; tray ...Details: Microlytic MCSG1 screen, condition G7: 25% (w/V) PEG 3350, 100mM Tris base / HCl pH 8.5: LemaA.01332.a.AE1.PS38633 (originally labelled as MyavA.00358.f.AE1.PS38633) at 13.16mg/ml; tray 315258 G7; cryo: 20% EG in 2 steps; puck: ddy3-5. For phasing a crystal from the same tray, condition D4 (200mM sodium thiocyanate, 20% (w/V) PEG 3350) was soaked for 15 sec in a mix of 90% reservoir and 10% 2.5M NaI in EG, followed by a 15sec soak in a mix of 80% reservoir and 20% 2.5m NaI in EG: tray 315258 d4: puck ddy3-3

Crystal

Density Matthews: 2.91 Å³/Da / Density % sol: 57.7 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Microlytic MCSG1 screen, condition G7: 25% (w/V) PEG 3350, 100mM Tris base / HCl pH 8.5: LemaA.01332.a.AE1.PS38633 (originally labelled as MyavA.00358.f.AE1.PS38633) at 13.16mg/ml; tray ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 18, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. obs: 33187 / % possible obs: 100 % / Redundancy: 15.975 % / B_iso Wilson estimate: 30.123 Å² / CC_1/2: 1 / R_merge(I) obs: 0.059 / R_rim(I) all: 0.061 / Χ²: 0.946 / Net I/σ(I): 32.55

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.9-1.95	9.661	0.563	4.21	2436	0.933	0.595	100
1.95-2	9.981	0.438	5.44	2363	0.956	0.462	100
2-2.06	10.347	0.359	6.78	2324	0.971	0.378	100
2.06-2.12	10.998	0.267	9.4	2229	0.984	0.28	100
2.12-2.19	13.1	0.207	13.97	2181	0.992	0.215	100
2.19-2.27	14.151	0.181	16.8	2098	0.995	0.187	99.9
2.27-2.36	14.676	0.149	20.23	2045	0.996	0.155	100
2.36-2.45	15.312	0.129	23.32	1958	0.998	0.133	99.7
2.45-2.56	16.097	0.114	26.29	1861	0.998	0.117	100
2.56-2.69	17.169	0.097	31.07	1801	0.999	0.1	100
2.69-2.83	18.985	0.082	36.84	1722	0.999	0.084	100
2.83-3	22.085	0.07	45.22	1606	0.999	0.072	99.9
3-3.21	22.186	0.058	53.28	1543	0.999	0.06	100
3.21-3.47	22.13	0.048	62.91	1427	1	0.049	100
3.47-3.8	21.999	0.04	74.93	1324	1	0.041	100
3.8-4.25	21.827	0.036	83.37	1179	1	0.037	100
4.25-4.91	21.773	0.033	87.5	1068	1	0.034	100
4.91-6.01	21.969	0.035	77.37	897	1	0.036	100
6.01-8.5	21.68	0.034	78.44	715	1	0.035	100
8.5-50	19.637	0.024	93.4	410	1	0.025	99.3

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2	refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.25	data extraction
PHASER		phasing
PARROT		phasing
ARP/wARP		model building
CRANK2		phasing
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.9→48.17 Å / SU ML: 0.1763 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.5641
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1758	1954	5.89 %	0
R_work	0.1523	31224	-	-
obs	0.1538	33178	99.96 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 26.42 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→48.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2314	0	8	421	2743

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0062	2408
X-RAY DIFFRACTION	f_angle_d	0.7942	3270
X-RAY DIFFRACTION	f_chiral_restr	0.0529	398
X-RAY DIFFRACTION	f_plane_restr	0.0074	418
X-RAY DIFFRACTION	f_dihedral_angle_d	11.6174	897

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 (%)
1.9-1.95	0.2753	121	0.1927	2234	X-RAY DIFFRACTION	99.92
1.95-2	0.2365	129	0.166	2214	X-RAY DIFFRACTION	100
2-2.06	0.1882	126	0.1628	2211	X-RAY DIFFRACTION	100
2.06-2.13	0.1811	126	0.1557	2218	X-RAY DIFFRACTION	99.96
2.13-2.2	0.1839	141	0.1517	2233	X-RAY DIFFRACTION	100
2.2-2.29	0.1893	162	0.1626	2180	X-RAY DIFFRACTION	100
2.29-2.39	0.206	121	0.1495	2232	X-RAY DIFFRACTION	100
2.39-2.52	0.2216	153	0.1687	2226	X-RAY DIFFRACTION	99.96
2.52-2.68	0.1932	123	0.1613	2224	X-RAY DIFFRACTION	100
2.68-2.89	0.1923	137	0.1665	2237	X-RAY DIFFRACTION	100
2.89-3.17	0.1946	138	0.1568	2240	X-RAY DIFFRACTION	99.96
3.18-3.63	0.1676	180	0.1456	2205	X-RAY DIFFRACTION	100
3.64-4.58	0.139	114	0.1215	2282	X-RAY DIFFRACTION	100
4.58-48.17	0.1452	183	0.1579	2288	X-RAY DIFFRACTION	99.76

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	1.73109147232	-0.163223106119	-0.0689501057106	1.98441262284	0.981139647451	1.94707683683	-0.0303634062119	0.146542564251	0.00350050960699	-0.237247215953	0.0041684233146	-0.0819215806387	-0.0246620166242	0.128491972566	0.0265690589577	0.16895115081	0.0210323753622	0.0155818835777	0.148090993658	0.00949350015545	0.134765493616	44.246252425	32.9174781243	77.685269822
2	2.25015559763	-0.723815333114	0.302801231715	2.24434387854	0.42513863124	0.912720383772	0.00361884294111	-0.0182047359766	-0.170367917613	0.0458743622083	-0.0485274815436	0.270218051632	0.0426150351536	-0.138577423115	0.0497417977466	0.129184926089	0.00880572158766	0.00658041846188	0.149316373676	-0.0250484770642	0.113846713792	30.9724972811	32.8197914419	85.6308929046
3	0.329259578642	0.0479688573094	0.349071793113	1.54025509497	0.185417194333	0.940806930227	0.0503313186877	0.0881273626833	-0.133411760649	-0.230957498701	-0.0308938622737	0.0578054280924	0.133170199975	-0.00461168894034	-0.0181109831115	0.23288933484	0.0275491074094	-0.00365924691949	0.155463953162	-0.0472004916592	0.194315947497	42.1751060585	8.25050724559	76.7393020356
4	1.04569556934	1.64064692645	0.388022266457	4.90732452752	-1.81266269335	3.30307386601	0.181912166711	-0.120361997473	0.0189745321638	0.408933033811	0.0417400296753	0.0960652666418	0.150014848385	-0.246862403622	-0.205150883881	0.257329167504	0.00994221399033	-0.0320304027042	0.181624645248	-0.0231595060325	0.204659313542	45.744175863	3.13351616984	91.0210711455
5	1.27257030965	-1.20886795643	0.328126041636	4.07660741398	-0.547593737526	0.759493250705	0.0454250215874	0.0454569052193	-0.0500368404554	0.0640820144005	-0.0548643741801	-0.266336070885	0.0659061276338	0.115935014398	0.0214190412453	0.141003197584	-0.00170063333825	-0.00117904743711	0.162560761494	-0.0468749323055	0.164269004483	50.3349108701	18.883673306	86.3514616979

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Selection details	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 3 through 62 )	3 - 62	1 - 60
2	2	chain 'A' and (resid 63 through 141 )	63 - 141	61 - 133
3	3	chain 'A' and (resid 142 through 234 )	142 - 234	134 - 226
4	4	chain 'A' and (resid 235 through 278 )	235 - 278	227 - 257
5	5	chain 'A' and (resid 279 through 328 )	279 - 328	258 - 307

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