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- PDB-6kj9: E. coli ATCase catalytic subunit mutant - G128/130A -

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Basic information

Entry
Database: PDB / ID: 6kj9
TitleE. coli ATCase catalytic subunit mutant - G128/130A
ComponentsAspartate carbamoyltransferase catalytic subunit
KeywordsTRANSFERASE / aspartate transcarbamoylase catalytic subunit / de novo pyrimidine biosynthesis
Function / homology
Function and homology information


aspartate carbamoyltransferase complex / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / glutamine metabolic process / amino acid binding / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Aspartate carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold ...Aspartate carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aspartate carbamoyltransferase catalytic subunit
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLei, Z. / Zheng, J. / Jia, Z.C.
Funding support China, Canada, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21773014 China
Natural Sciences and Engineering Research Council (Canada)RGPIN-2018-04427 Canada
CitationJournal: Febs J. / Year: 2020
Title: New regulatory mechanism-based inhibitors of aspartate transcarbamoylase for potential anticancer drug development.
Authors: Lei, Z. / Wang, B. / Lu, Z. / Wang, N. / Tan, H. / Zheng, J. / Jia, Z.
History
DepositionJul 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate carbamoyltransferase catalytic subunit
B: Aspartate carbamoyltransferase catalytic subunit
C: Aspartate carbamoyltransferase catalytic subunit
D: Aspartate carbamoyltransferase catalytic subunit
E: Aspartate carbamoyltransferase catalytic subunit
F: Aspartate carbamoyltransferase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)206,1916
Polymers206,1916
Non-polymers00
Water10,503583
1
A: Aspartate carbamoyltransferase catalytic subunit
B: Aspartate carbamoyltransferase catalytic subunit
E: Aspartate carbamoyltransferase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)103,0953
Polymers103,0953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-26 kcal/mol
Surface area34290 Å2
MethodPISA
2
C: Aspartate carbamoyltransferase catalytic subunit
D: Aspartate carbamoyltransferase catalytic subunit
F: Aspartate carbamoyltransferase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)103,0953
Polymers103,0953
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-26 kcal/mol
Surface area33250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.758, 96.729, 121.694
Angle α, β, γ (deg.)90.000, 94.161, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Aspartate carbamoyltransferase catalytic subunit / Aspartate transcarbamylase / ATCase


Mass: 34365.156 Da / Num. of mol.: 6 / Mutation: G128A, G130A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: pyrB, b4245, JW4204 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M NH4Ac, 0.1M Tris pH 8.5, 20% PEG3350, and 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 65582 / % possible obs: 100 % / Redundancy: 4.1 % / CC1/2: 0.994 / Net I/σ(I): 18.7
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 3280 / CC1/2: 0.784

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZA1

1za1


Resolution: 2.5→48.36 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2283 2005 3.08 %
Rwork0.1916 --
obs0.1928 65143 99.21 %
Refinement stepCycle: LAST / Resolution: 2.5→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13605 0 0 583 14188
LS refinement shellResolution: 2.5→2.56 Å
RfactorNum. reflection% reflection
Rfree0.3183 134 -
Rwork0.2587 4152 -
obs--92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.2153-0.01130.10720.4385-0.15660.2482-0.0876-0.35240.27320.24250.338-0.7833-0.07680.3361-0.01530.4557-0.0084-0.14470.5119-0.09480.47846.91112.6197107.3117
20.18-0.31180.10610.0660.07640.4861-0.0060.13460.10170.18390.1454-0.3269-0.1484-0.18890.0010.41360.0029-0.03960.2735-0.03740.356435.44286.769697.2791
30.31490.02140.02840.5226-0.5370.3654-0.3206-0.55610.099-0.12080.17370.0331-0.0254-0.0287-0.00020.45270.019-0.07030.3834-0.00520.320930.68941.339595.8413
40.8074-0.43050.40051.2433-0.62330.5294-0.0392-0.10580.08680.02050.1175-0.34410.022-0.19580.07050.3436-0.0205-0.09830.3685-0.01180.33439.7156-5.989103.7658
50.3031-0.3913-0.0510.2550.08210.2188-0.3156-0.4065-0.1530.27280.325-0.30130.18180.3545-0.02640.55180.1181-0.17440.5727-0.00090.448642.5126-16.4064119.3567
60.1823-0.19420.310.2387-0.28050.5105-0.6139-0.334-0.54091.10190.54780.0983-0.5041-0.18940.48490.63010.2911-0.18730.75620.16020.14435.9437-14.5163127.4817
70.1734-0.03750.07660.11620.0640.1386-0.58550.2291-0.13310.32330.2450.76770.0814-0.375-0.00980.6574-0.00760.13810.51360.02860.463123.6908-24.7006117.3484
81.1964-0.2402-0.20790.252-0.02450.0857-0.6631-0.2811-0.77770.59220.43620.099-0.3513-0.369-0.34570.65280.3058-0.06370.630.13110.196424.3724-6.9814124.1388
90.4634-0.35350.21570.401-0.36850.1581-0.4272-0.86960.53760.20760.2289-0.2153-0.69910.121-0.11270.5284-0.0118-0.13060.4146-0.11540.451938.26455.8803107.591
100.9561-0.51690.24710.2132-0.34190.8953-0.0168-0.00710.1215-0.2088-0.0318-0.1004-0.1735-0.1679-0.00230.4232-0.01630.0390.2243-0.01140.39630.793615.512773.9641
111.26920.1395-0.6520.8209-0.42110.43910.01550.03040.0464-0.1103-0.0017-0.0334-0.1171-0.072-00.29820.0197-0.00740.2807-0.00410.253620.86877.728477.9069
120.96230.1193-0.35490.9179-0.45141.8138-0.110.1013-0.0124-0.10440.0954-0.02640.1209000.2869-0.00730.09180.21080.00080.390739.6093-0.14957.8936
130.1112-0.25850.00490.21970.00020.06220.2777-0.0921-0.11730.0817-0.2638-0.07990.24-0.25670.00930.4882-0.07620.12830.2239-0.04090.365135.5296-16.218963.0589
140.50870.4323-0.33090.3539-0.04751.315-0.0274-0.1767-0.12790.1839-0.0425-0.10010.12170.206-0.00060.33650.02850.04420.24130.05070.40643.6222-0.135371.5469
152.01990.2683-0.80570.5548-0.57221.496-0.0456-0.15540.00110.1437-0.0748-0.02920.01980.09890.00020.27060.01070.02510.28240.00920.23844.354-38.374105.8921
160.65710.3179-0.31211.9559-0.50221.38910.0594-0.01730.08310.30330.10840.1417-0.059-0.13820.00680.3132-0.00860.07080.34580.00120.2603-9.9776-52.0697118.8308
170.48770.08560.15770.6236-0.51710.4643-0.19890.22070.1643-0.30530.2255-0.178-0.19730.1925-0.00090.2364-0.02410.01830.21960.0230.317419.3479-25.315276.8426
180.50950.39040.36930.58980.58020.44080.0222-0.1818-0.0199-0.1305-0.03080.0532-0.0708-0.06670.00020.21540.01680.00820.2224-0.00060.28768.8739-37.034885.1196
191.08230.15560.30340.21410.31140.87-0.13920.1626-0.0956-0.12970.0632-0.0898-0.10170.063400.23990.0003-0.00630.21930.01090.295821.9653-36.445580.1459
200.5-0.719-0.01950.68180.36260.801-0.16240.251-0.2546-0.20310.3484-0.3957-0.18170.55640.15820.2051-0.09140.02310.3713-0.0170.447241.6618-30.822485.8658
210.46160.1579-0.07020.49830.07720.7799-0.0649-0.2141-0.02880.07190.0614-0.15190.0554-0.0819-0.03690.20580.0186-0.03870.19430.05470.282427.0017-30.503995.0628
220.35260.160.1540.5418-0.25450.4266-0.3923-0.32310.10060.44090.67530.2109-0.6152-0.27640.01950.72930.38180.12310.66820.0440.40397.244921.9887104.7077
230.642-0.3854-0.1040.8515-0.37720.8259-0.1933-0.0809-0.11040.13920.2310.0145-0.3708-0.29050.00680.4170.1386-0.00080.52540.04120.300117.03678.0758101.8504
240.9029-0.6405-0.33090.48220.56080.8175-0.1965-0.5313-0.04840.28850.54490.344-0.0742-0.37260.1610.48290.14860.11630.79970.33460.491-9.840816.442894.3738
25-0.0237-0.3628-0.04281.1542-0.30290.2928-0.2344-0.2006-0.30830.19520.49080.4221-0.1223-0.0861-0.01440.41040.14860.03820.51260.13250.43730.882917.520585.9015
260.74270.52590.19140.8824-0.12911.58250.0772-0.1277-0.00620.0473-0.03390.11010.0082-0.0808-0.00010.24130.0123-0.01530.34640.03980.2907-11.2287-48.885584.4729
270.3380.5951-0.39761.07960.04851.0168-0.0695-0.0311-0.0478-0.30040.1993-0.0030.0511-0.18540.0080.3193-0.0321-0.0890.2777-0.00820.2992-12.5157-60.694160.8624
280.4507-0.0872-0.39050.25590.05640.224-0.03850.0422-0.233-0.41750.13580.02910.16870.09070.00050.4015-0.0077-0.01720.3563-0.05560.32470.7658-62.589258.2128
290.57041.10810.11761.07070.38910.33690.0765-0.06850.0516-0.14670.1963-0.1787-0.13870.05150.00210.25420.0294-0.02480.3211-0.0050.2813-4.4054-47.17568.9064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 32 )A2 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 52 )A33 - 52
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 87 )A53 - 87
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 166 )A88 - 166
5X-RAY DIFFRACTION5chain 'A' and (resid 167 through 204 )A167 - 204
6X-RAY DIFFRACTION6chain 'A' and (resid 205 through 227 )A205 - 227
7X-RAY DIFFRACTION7chain 'A' and (resid 228 through 247 )A228 - 247
8X-RAY DIFFRACTION8chain 'A' and (resid 248 through 284 )A248 - 284
9X-RAY DIFFRACTION9chain 'A' and (resid 285 through 309 )A285 - 309
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 52 )B1 - 52
11X-RAY DIFFRACTION11chain 'B' and (resid 53 through 134 )B53 - 134
12X-RAY DIFFRACTION12chain 'B' and (resid 135 through 223 )B135 - 223
13X-RAY DIFFRACTION13chain 'B' and (resid 224 through 242 )B224 - 242
14X-RAY DIFFRACTION14chain 'B' and (resid 243 through 310 )B243 - 310
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 134 )C1 - 134
16X-RAY DIFFRACTION16chain 'C' and (resid 135 through 309 )C135 - 309
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 32 )D1 - 32
18X-RAY DIFFRACTION18chain 'D' and (resid 33 through 87 )D33 - 87
19X-RAY DIFFRACTION19chain 'D' and (resid 88 through 166 )D88 - 166
20X-RAY DIFFRACTION20chain 'D' and (resid 167 through 227 )D167 - 227
21X-RAY DIFFRACTION21chain 'D' and (resid 228 through 310 )D228 - 310
22X-RAY DIFFRACTION22chain 'E' and (resid 1 through 32 )E1 - 32
23X-RAY DIFFRACTION23chain 'E' and (resid 33 through 126 )E33 - 126
24X-RAY DIFFRACTION24chain 'E' and (resid 127 through 223 )E127 - 223
25X-RAY DIFFRACTION25chain 'E' and (resid 224 through 310 )E224 - 310
26X-RAY DIFFRACTION26chain 'F' and (resid 2 through 134 )F2 - 134
27X-RAY DIFFRACTION27chain 'F' and (resid 135 through 221 )F135 - 221
28X-RAY DIFFRACTION28chain 'F' and (resid 222 through 265 )F222 - 265
29X-RAY DIFFRACTION29chain 'F' and (resid 266 through 309 )F266 - 309

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