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- PDB-4kh0: The R state structure of E. coli ATCase with ATP and Magnesium bound -

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Basic information

Entry
Database: PDB / ID: 4kh0
TitleThe R state structure of E. coli ATCase with ATP and Magnesium bound
Components
  • Aspartate carbamoyltransferase regulatory chain
  • Aspartate carbamoyltransferase
KeywordsTRANSFERASE / pyrimidine nucleotide biosynthesis / feedback inhibition / competing pathway product activation / allostery
Function / homology
Function and homology information


Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate/ornithine carbamoyltransferase / SH3 type barrels. / Roll / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / N-(PHOSPHONACETYL)-L-ASPARTIC ACID / : / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsCockrell, G.M. / Zheng, Y. / Guo, W. / Peterson, A.W. / Kantrowitz, E.R.
CitationJournal: Biochemistry / Year: 2013
Title: New Paradigm for Allosteric Regulation of Escherichia coli Aspartate Transcarbamoylase.
Authors: Cockrell, G.M. / Zheng, Y. / Guo, W. / Peterson, A.W. / Truong, J.K. / Kantrowitz, E.R.
History
DepositionApr 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase
D: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,68014
Polymers102,9614
Non-polymers2,71810
Water8,413467
1
A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase
D: Aspartate carbamoyltransferase regulatory chain
hetero molecules

A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase
D: Aspartate carbamoyltransferase regulatory chain
hetero molecules

A: Aspartate carbamoyltransferase
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase
D: Aspartate carbamoyltransferase regulatory chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,04042
Polymers308,88412
Non-polymers8,15530
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area44160 Å2
ΔGint-207 kcal/mol
Surface area100070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.133, 121.133, 155.107
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-567-

HOH

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Aspartate carbamoyltransferase / / Aspartate transcarbamylase


Mass: 34337.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ATCC 55124 / KO11 / Gene: pyrB, EKO11_4066, KO11_22860 / Production host: Escherichia coli (E. coli) / References: UniProt: E8Y328, aspartate carbamoyltransferase
#2: Protein Aspartate carbamoyltransferase regulatory chain


Mass: 17143.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ATCC 55124 / KO11 / Gene: pyrI, EKO11_4067, KO11_22855 / Production host: Escherichia coli (E. coli) / References: UniProt: E8Y329, aspartate carbamoyltransferase

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Non-polymers , 5 types, 477 molecules

#3: Chemical ChemComp-PAL / N-(PHOSPHONACETYL)-L-ASPARTIC ACID


Mass: 255.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10NO8P
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 5.9
Details: 50 mM maleic acid, 1 mM PALA, 3 mM sodium azide, pH 5.9, Microdialysis, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2011
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 62983 / Num. obs: 62983 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 24.1 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.25-2.33220.7411100
2.33-2.4222.40.5371100
2.42-2.5322.40.3611100
2.53-2.6722.40.261100
2.67-2.8322.40.1841100
2.83-3.0522.40.1241100
3.05-3.3622.30.0831100
3.36-3.8522.20.0581100
3.85-4.8530.40.0961100
4.85-5031.30.0591100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D09
Resolution: 2.25→49.688 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.23 / σ(F): 0 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2077 3195 5.07 %
Rwork0.1682 --
obs0.1702 62973 99.98 %
all-62973 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.1575 Å2
Refinement stepCycle: LAST / Resolution: 2.25→49.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7199 0 160 467 7826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017511
X-RAY DIFFRACTIONf_angle_d1.13610229
X-RAY DIFFRACTIONf_dihedral_angle_d15.8572810
X-RAY DIFFRACTIONf_chiral_restr0.0721174
X-RAY DIFFRACTIONf_plane_restr0.0041306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.2830.30581240.23062585X-RAY DIFFRACTION100
2.283-2.31870.27751510.22512513X-RAY DIFFRACTION100
2.3187-2.35670.30351360.2132594X-RAY DIFFRACTION100
2.3567-2.39730.28191320.20552572X-RAY DIFFRACTION100
2.3973-2.44090.24691360.19852555X-RAY DIFFRACTION100
2.4409-2.48790.22861350.17982574X-RAY DIFFRACTION100
2.4879-2.53870.26121480.17742559X-RAY DIFFRACTION100
2.5387-2.59390.2381430.1862586X-RAY DIFFRACTION100
2.5939-2.65420.24521340.17932566X-RAY DIFFRACTION100
2.6542-2.72060.2141360.18042588X-RAY DIFFRACTION100
2.7206-2.79410.25621430.17552570X-RAY DIFFRACTION100
2.7941-2.87630.22551350.18742593X-RAY DIFFRACTION100
2.8763-2.96920.26171400.19592610X-RAY DIFFRACTION100
2.9692-3.07530.26451440.1932553X-RAY DIFFRACTION100
3.0753-3.19840.26511410.19572586X-RAY DIFFRACTION100
3.1984-3.34390.23181390.1922624X-RAY DIFFRACTION100
3.3439-3.52020.21061290.17412599X-RAY DIFFRACTION100
3.5202-3.74060.19521210.1592616X-RAY DIFFRACTION100
3.7406-4.02930.19511660.15192601X-RAY DIFFRACTION100
4.0293-4.43460.16321340.14222620X-RAY DIFFRACTION100
4.4346-5.07570.16421370.13622649X-RAY DIFFRACTION100
5.0757-6.39280.20521550.17182670X-RAY DIFFRACTION100
6.3928-49.70.15411360.15422795X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.01880.00280.024-0.0010.00310.02720.0240.17010.023-0.23330.07740.15870.0117-0.04760.20590.25380.0037-0.16850.3460.1760.211541.140337.64641.0247
20.2230.0674-0.00420.0753-0.01320.25040.1270.08350.0406-0.12130.08140.21440.0069-0.11310.57630.07570.0628-0.05290.06970.13960.116648.941742.773212.1488
30.01330.0210.00540.03850.0020.01310.03510.0117-0.0861-0.04610.03850.10050.0647-0.02250.07240.1368-0.0481-0.21770.22370.13860.412730.371926.499810.4376
40.00560.00540.00790.00550.00850.0129-0.0012-0.0021-0.0076-0.03980.02430.09280.0227-0.0280.0070.1032-0.0146-0.09020.23390.16210.409325.76930.338213.6174
50.0024-0.00250.00440.04590.02820.0405-0.0135-0.003-0.0082-0.02-0.0490.0937-0.0037-0.0591-0.02110.16210.01450.00020.36840.23450.643322.098431.470921.5471
60.0671-0.03320.03640.0461-0.05310.07150.0249-0.0469-0.0952-0.00130.05350.12860.04460.04120.02390.1067-0.0291-0.01590.2740.15810.407231.743923.299221.3869
70.0050.0132-0.01230.0335-0.03450.03870.0427-0.0715-0.11270.0884-0.0120.0924-0.08030.03830.01160.2771-0.1011-0.02160.33330.18780.574131.961817.520524.3134
80.02320.01570.01880.01150.010.0180.0165-0.0092-0.0698-0.00910.00110.0350.030.0004-0.00540.1357-0.0235-0.13640.14070.13720.460338.089715.677116.125
90.06860.0027-0.03070.06340.01590.01980.0230.0964-0.0643-0.06350.00030.0277-0.02020.00740.08790.2176-0.0407-0.21140.23170.03360.241741.609631.6618-0.0091
100.0522-0.01940.02690.0071-0.01010.01370.020.01760.0225-0.0018-0.0023-0.0083-0.0204-0.010.00220.31880.2331-0.01560.4008-0.02350.42218.625581.685826.5883
110.01190.0072-0.01320.02420.02020.0578-0.02970.0095-0.0323-0.0068-0.05080.01420.0377-0.0248-0.04610.40580.2777-0.00510.4406-0.08230.339720.079172.613632.344
120.0011-0.0012-0.00020.00120.00040.00020.0045-0.0067-0.0138-0.01560.0168-0.00080.0104-0.0308-00.47150.2717-0.02320.5717-0.1380.459218.323465.581723.3722
130.03340.0156-0.01680.0068-0.00730.0079-0.02870.0646-0.0628-0.0364-0.0437-0.0397-0.0332-0.0567-0.00880.43160.2666-0.0760.4876-0.060.557617.747671.690419.6819
140.0520.0160.01780.00960.00450.0097-0.0309-0.10330.01760.0179-0.02660.00190.0189-0.0174-0.05520.05810.03280.03880.31320.04230.455629.976250.740724.7625
150.00070.00160.00230.00850.00820.00630.07410.00550.09560.06250.06950.0337-0.0283-0.0564-0.00010.42810.0350.04380.327-0.07570.258159.518260.975279.2552
160.0069-0.00110.0040.00680.00010.00170.0226-0.0203-0.0238-0.00350.01050.01720.0174-0.0112-00.30420.03350.02970.3360.02410.098959.793845.04976.9549
170.0439-0.0204-0.01820.05050.01020.05350.0476-0.02320.1488-0.05970.01830.0292-0.2536-0.050300.2722-0.01040.03780.2317-0.00170.153659.00552.28267.8078
180.00370.0048-0.00050.0085-0.00340.00150.02430.04150.1616-0.06140.0386-0.0259-0.07060.03290.00010.5842-0.0330.0450.2870.03230.317668.309968.860162.6296
190.00320.001-0.00140.0087-0.00280.0019-0.0410.02130.0167-0.0516-0.0192-0.0126-0.07620.0649-0.00020.79130.00110.12110.47570.10070.676171.306574.308660.123
200.0170.0042-0.00830.02880.01370.02330.06770.04460.196-0.08340.0561-0.1799-0.0160.04630.00020.4771-0.11030.10860.4205-0.01580.326676.807860.877156.0503
210.0244-0.01220.00840.0517-0.01190.0052-0.0239-0.05850.08230.0077-0.0011-0.1744-0.0796-0.0208-0.00530.3534-0.03720.05240.3285-0.06480.217473.148354.543571.8563
220.0682-0.0473-0.02430.11190.05510.1518-0.1021-0.0698-0.01030.0956-0.09370.04240.0090.0117-0.02020.55890.2942-0.02590.5051-0.00750.315724.141578.213645.1188
230.1025-0.0086-0.01320.1779-0.09690.0536-0.0484-0.07040.01110.079-0.1197-0.0979-0.1832-0.0314-0.08590.62110.1794-0.16210.3610.02240.33239.173972.343254.8819
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 134 )
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 166 )
4X-RAY DIFFRACTION4chain 'A' and (resid 167 through 187 )
5X-RAY DIFFRACTION5chain 'A' and (resid 188 through 215 )
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 236 )
7X-RAY DIFFRACTION7chain 'A' and (resid 237 through 261 )
8X-RAY DIFFRACTION8chain 'A' and (resid 262 through 284 )
9X-RAY DIFFRACTION9chain 'A' and (resid 285 through 310 )
10X-RAY DIFFRACTION10chain 'B' and (resid 10 through 19 )
11X-RAY DIFFRACTION11chain 'B' and (resid 20 through 67 )
12X-RAY DIFFRACTION12chain 'B' and (resid 68 through 84 )
13X-RAY DIFFRACTION13chain 'B' and (resid 85 through 104 )
14X-RAY DIFFRACTION14chain 'B' and (resid 105 through 153 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 32 )
16X-RAY DIFFRACTION16chain 'C' and (resid 33 through 53 )
17X-RAY DIFFRACTION17chain 'C' and (resid 54 through 166 )
18X-RAY DIFFRACTION18chain 'C' and (resid 167 through 195 )
19X-RAY DIFFRACTION19chain 'C' and (resid 196 through 221 )
20X-RAY DIFFRACTION20chain 'C' and (resid 222 through 261 )
21X-RAY DIFFRACTION21chain 'C' and (resid 262 through 310 )
22X-RAY DIFFRACTION22chain 'D' and (resid 10 through 67 )
23X-RAY DIFFRACTION23chain 'D' and (resid 68 through 153 )

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