PDB-8fve: E coli. CTP synthase in complex with CTP (potassium malonate + 10...

ID or keywords:

Entry

Database: PDB / ID: 8fve

Title

E coli. CTP synthase in complex with CTP (potassium malonate + 100 mM MgCl2)

Components

CTP synthase

Keywords

CYTOSOLIC PROTEIN / LIGASE / Inhibitor complex / Metabolic enzyme

Function / homology

Function and homology information

CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutaminase activity / ATP binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Holyoak, T. / McLeod, M.J. / Tran, N.

Funding support

Canada, 2items

Citation

Journal: Protein Sci. / Year: 2023
Title: A metal-dependent conformational change provides a structural basis for the inhibition of CTP synthase by gemcitabine-5'-triphosphate.
Authors: McLeod, M.J. / Tran, N. / McCluskey, G.D. / Gillis, T.D. / Bearne, S.L. / Holyoak, T.

History

Deposition	Jan 18, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 24, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jun 14, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8fve.cif.gz	528.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8fve.ent.gz	361 KB	Display	PDB format
PDBx/mmJSON format	8fve.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8fve_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8fve_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8fve_validation.xml.gz	42 KB	Display
Data in CIF	8fve_validation.cif.gz	60 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fv/8fve ftp://data.pdbj.org/pub/pdb/validation_reports/fv/8fve	HTTPS FTP

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Related structure data

Related structure data	8fv6C 8fv7C 8fv8C 8fv9C 8fvaC 8fvbC 8fvcC 8fvdC 8sbrC 5tkvS 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 (5) #254 - Feb 2021 Cellulose Synthase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: CTP synthase

B: CTP synthase

hetero molecules

122 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CTP synthase

B: CTP synthase

hetero molecules

A: CTP synthase

B: CTP synthase

hetero molecules

defined by author&software
244 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	159.496, 109.737, 129.204
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab

#1: Protein	CTP synthase / Cytidine 5'-triphosphate synthase / Cytidine triphosphate synthetase / CTPS / UTP--ammonia ligase Mass: 60446.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pyrG, ECS88_3048 / Plasmid: pET-15B / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21(DE3) References: UniProt: B7MLA1, CTP synthase (glutamine hydrolysing)
#2: Chemical	ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID Mass: 104.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₄O₄
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₆N₃O₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 358 / 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: 4.74 Å³/Da / Density % sol: 74.04 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M TRIS-Cl pH 8.0 (room temperature), 5 mM magnesium chloride, 1.15 - 1.4 M ammonium sulfate, 15 mg/mL CTPS.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 1.1271 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 8, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1271 Å / Relative weight: 1
Reflection	Resolution: 2.4→100.4 Å / Num. obs: 89213 / % possible obs: 99.9 % / Redundancy: 12.9 % / B_iso Wilson estimate: 49.7 Å² / CC_1/2: 0.997 / CC star: 1 / R_merge(I) obs: 0.163 / R_pim(I) all: 0.047 / R_rim(I) all: 0.17 / Net I/σ(I): 6.9
Reflection shell	Resolution: 2.4→2.49 Å / Redundancy: 13.2 % / R_merge(I) obs: 1.376 / Mean I/σ(I) obs: 0.2 / Num. unique obs: 17548 / CC_1/2: 0.834 / CC star: 0.969 / R_pim(I) all: 0.39 / R_rim(I) all: 0.834 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	1.20.1_4487	refinement
DIALS		data reduction
DIALS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5TKV

5tkv

Resolution: 2.4→100.4 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.1013
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1911	4516	5.06 %
R_work	0.1665	84688	-
obs	0.1677	89204	99.77 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 61.93 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→100.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8375	0	81	358	8814

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0101	8638
X-RAY DIFFRACTION	f_angle_d	1.0735	11721
X-RAY DIFFRACTION	f_chiral_restr	0.0637	1332
X-RAY DIFFRACTION	f_plane_restr	0.0111	1529
X-RAY DIFFRACTION	f_dihedral_angle_d	14.0094	3248

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 (%)
2.4-2.43	0.2849	148	0.262	2649	X-RAY DIFFRACTION	93.67
2.43-2.45	0.2645	151	0.2416	2763	X-RAY DIFFRACTION	100
2.45-2.48	0.2618	139	0.2269	2813	X-RAY DIFFRACTION	99.97
2.48-2.52	0.2691	141	0.215	2768	X-RAY DIFFRACTION	100
2.52-2.55	0.2401	159	0.2122	2814	X-RAY DIFFRACTION	100
2.55-2.58	0.283	135	0.2173	2816	X-RAY DIFFRACTION	100
2.58-2.62	0.2379	144	0.208	2804	X-RAY DIFFRACTION	100
2.62-2.66	0.244	145	0.2092	2791	X-RAY DIFFRACTION	100
2.66-2.7	0.2829	139	0.2181	2805	X-RAY DIFFRACTION	100
2.7-2.75	0.2585	129	0.2236	2822	X-RAY DIFFRACTION	100
2.75-2.79	0.2591	159	0.2337	2783	X-RAY DIFFRACTION	100
2.79-2.84	0.2994	162	0.2508	2790	X-RAY DIFFRACTION	99.97
2.84-2.9	0.2745	153	0.2553	2819	X-RAY DIFFRACTION	100
2.9-2.96	0.2454	156	0.2317	2812	X-RAY DIFFRACTION	100
2.96-3.02	0.2533	149	0.228	2814	X-RAY DIFFRACTION	100
3.02-3.09	0.2662	141	0.2184	2795	X-RAY DIFFRACTION	100
3.09-3.17	0.256	158	0.2001	2816	X-RAY DIFFRACTION	100
3.17-3.25	0.2213	148	0.1798	2823	X-RAY DIFFRACTION	100
3.26-3.35	0.226	133	0.1743	2828	X-RAY DIFFRACTION	100
3.35-3.46	0.1871	134	0.1802	2842	X-RAY DIFFRACTION	100
3.46-3.58	0.1883	141	0.1784	2849	X-RAY DIFFRACTION	100
3.58-3.73	0.1866	176	0.1489	2790	X-RAY DIFFRACTION	100
3.73-3.9	0.1575	156	0.1306	2841	X-RAY DIFFRACTION	100
3.9-4.1	0.1618	153	0.1331	2839	X-RAY DIFFRACTION	100
4.1-4.36	0.1287	145	0.1236	2855	X-RAY DIFFRACTION	100
4.36-4.69	0.1614	158	0.1144	2856	X-RAY DIFFRACTION	100
4.69-5.17	0.1248	163	0.1216	2863	X-RAY DIFFRACTION	100
5.17-5.91	0.1708	159	0.1466	2879	X-RAY DIFFRACTION	100
5.91-7.45	0.1684	167	0.1555	2904	X-RAY DIFFRACTION	100
7.45-100.4	0.1549	175	0.1454	3045	X-RAY DIFFRACTION	99.66

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	2.15573763065	0.969635123517	0.0499893854802	1.72718631759	-0.308925270143	1.86611510678	0.118615448646	-0.405735901459	0.143307849758	0.19542127461	-0.236849447811	-0.0427190861067	-0.252041989929	0.210901594608	0.117174071728	0.362498571013	-0.0868257301139	-0.0097182711305	0.327063935274	-0.03729438086	0.320474989396	-70.4992013649	13.309815134	-39.2440963949
2	1.87828124739	0.236197128896	-0.0489507655597	1.76041433753	0.637480299686	2.55849632059	-0.0184746486198	0.175023945202	0.273657359756	-0.167262577999	-0.0454789681249	-0.14769862151	-0.413614640861	0.182981395048	0.0324778883153	0.344863395136	-0.0423743852372	-0.0296320060121	0.303088586233	0.0737387057603	0.344771419481	-66.3962865541	16.5068142938	-58.4132330862
3	1.58195097443	-0.533897374205	-0.1914467669	1.9314803135	-1.26953132808	3.38040753214	-0.173035985986	-0.511080043668	-0.255435705612	0.428133215595	-0.349006654707	-0.443311643953	-0.261663907973	1.09566955888	0.317921771478	0.515082780748	-0.218133683386	-0.155867264769	0.957314600859	0.25209746689	0.647454361004	-43.2802608235	9.86239124644	-23.9673917112
4	2.9247704047	-1.24033144931	0.350417871341	1.60906931455	-0.38720255878	1.93571825863	0.0333911344278	0.204296813306	-0.158900378019	-0.123294603524	-0.114779934322	-0.0915079907652	0.382796147681	0.285803028769	0.0917604543143	0.434610819877	0.101524950318	0.0695940476584	0.331473058897	0.0145035760925	0.35451955085	-64.0227012523	-15.4014756811	-77.7813311895
5	4.99715788748	-1.65312724981	0.00541130279315	1.65037536537	-0.127330391669	1.8483563416	-0.0403205943387	0.40459278954	0.1645810914	-0.13015802348	-0.100813220251	-0.234902564096	0.253079490061	0.188149298752	0.0954084940053	0.4114972166	0.0923354542074	0.0563483825616	0.408231890173	-0.0116679168207	0.367245406382	-65.7437037734	-8.52115689857	-89.0771096891
6	3.22659199297	-0.854213588139	1.07267001992	1.58614065888	-0.751199292403	1.40157340798	0.173224546968	0.138319399341	-0.362181994521	-0.206298739435	-0.184147790369	0.260166304264	0.31275665013	-0.0345840145821	0.0399378846596	0.41787099012	0.0302574144749	0.0383337870129	0.343407661891	-0.0510237950702	0.380711278451	-78.0723142608	-12.2485706144	-80.3193370472
7	2.28788842683	-0.273166948602	-0.404054072654	2.41109824072	0.994755146668	2.45547067445	-0.0675617548085	-0.191376479432	-0.197296882356	0.215488722515	0.0537299086448	-0.19580993975	0.515537290651	0.335451700074	-0.0100525402023	0.399985618869	0.0885118273842	0.021794565279	0.365708286116	0.0772259251122	0.346776407913	-61.7464604407	-14.6541700743	-63.0365304006
8	2.18008010821	0.0764948628109	0.662488294705	2.24625060253	-0.519527024428	2.73575684272	-0.200963530644	0.415526717737	0.620941760559	-0.274830023884	0.0660804215672	-0.275573267454	-0.327402889207	0.445364158648	0.128477578916	0.420701819837	0.0507855179608	0.106969514226	0.591934623602	0.106024144699	0.645005117724	-42.8224244032	-0.3173717692	-97.2899926526
9	2.32101193228	0.281848972381	0.183246805593	3.27871223891	-1.13658413608	3.81370468834	0.0527221868311	0.564682907213	0.314535604444	-0.504056175202	-0.0834178763827	-0.279833086985	0.112476114958	0.420118264189	0.0273583839142	0.593577997321	0.131668423333	0.17354647994	0.74836554647	0.120034810286	0.467415904825	-45.8639966588	-8.84847376557	-106.64788915
10	2.1208925923	-0.154167307695	0.0955499262539	3.20084373138	-0.861330800549	3.61433878168	-0.293869325472	1.21065721821	0.209765537357	-0.927680867805	0.0230227028017	-0.16026985712	0.259467300622	0.977926921392	0.0316757960909	0.671756986094	0.106467552592	0.214528644301	0.972830059311	0.0946212937047	0.641222792516	-40.0926355167	-7.90680408779	-108.576378182
11	1.7794711191	0.279504139056	0.424365150695	2.43877205727	-0.634104644537	2.85139421694	-0.16908340207	0.435478028553	0.144108137286	-0.0931560086425	0.131150616014	-0.370822066633	0.132394775308	0.494984983716	0.0253007813279	0.415019071588	0.162600836566	0.133463421065	0.651408268426	0.0282876031977	0.542390921296	-38.6449928787	-10.3756682657	-92.3126130304

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 147 )	A	A	1 - 147	1 - 147
2	2	chain 'A' and (resid 148 through 273 )	A	A	148 - 273	148 - 273
3	3	chain 'A' and (resid 274 through 543 )	A	A	274 - 543	274 - 535
4	4	chain 'B' and (resid 1 through 48 )	B	E	1 - 48	1 - 48
5	5	chain 'B' and (resid 49 through 105 )	B	E	49 - 105	49 - 105
6	6	chain 'B' and (resid 106 through 164 )	B	E	106 - 164	106 - 164
7	7	chain 'B' and (resid 165 through 273 )	B	E	165 - 273	165 - 273
8	8	chain 'B' and (resid 274 through 452 )	B	E	274 - 452	274 - 445
9	9	chain 'B' and (resid 453 through 482 )	B	E	453 - 482	446 - 475
10	10	chain 'B' and (resid 483 through 508 )	B	E	483 - 508	476 - 501
11	11	chain 'B' and (resid 509 through 543 )	B	E	509 - 543	502 - 536

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