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

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Basic information

Entry
Database: PDB / ID: 4kgz
TitleThe R state structure of E. coli ATCase with UTP 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
N-(PHOSPHONACETYL)-L-ASPARTIC ACID / URIDINE 5'-TRIPHOSPHATE / : / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 / Item: _software.classification / _software.name

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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)105,58814
Polymers102,9614
Non-polymers2,62610
Water6,107339
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)316,76342
Polymers308,88412
Non-polymers7,87930
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 area39500 Å2
ΔGint-196 kcal/mol
Surface area99510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.378, 121.378, 155.135
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
11C-586-

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, 349 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-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*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.: 339 / 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: 3.2 Å3/Da / Density % sol: 61.61 %
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: Jan 31, 2012
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: 2.4→50 Å / Num. all: 52389 / Num. obs: 52389 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 24.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.4921.20.6831100
2.49-2.5921.50.4881100
2.59-2.721.80.3711100
2.7-2.85220.2681100
2.85-3.0222.20.1951100
3.02-3.2622.20.1391100
3.26-3.5822.20.1051100
3.58-4.123.60.1161100
4.1-5.1732.30.1311100
5.17-5031.20.07199.9

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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: PDB entry 1D09
Resolution: 2.4→49.779 Å / Occupancy max: 1 / Occupancy min: 0.64 / SU ML: 0.24 / σ(F): 0 / Phase error: 21.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2025 2671 5.1 %
Rwork0.1646 --
obs0.1665 52382 99.98 %
all-52382 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.8684 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7074 0 152 339 7565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017370
X-RAY DIFFRACTIONf_angle_d1.06810036
X-RAY DIFFRACTIONf_dihedral_angle_d14.522769
X-RAY DIFFRACTIONf_chiral_restr0.0711153
X-RAY DIFFRACTIONf_plane_restr0.0051281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.44090.31691250.23092592X-RAY DIFFRACTION100
2.4409-2.48780.28231470.20962564X-RAY DIFFRACTION100
2.4878-2.53860.22831310.19152582X-RAY DIFFRACTION100
2.5386-2.59380.27281640.18942562X-RAY DIFFRACTION100
2.5938-2.65410.26831310.1892597X-RAY DIFFRACTION100
2.6541-2.72050.23381620.18022573X-RAY DIFFRACTION100
2.7205-2.7940.23321330.17712584X-RAY DIFFRACTION100
2.794-2.87620.26591350.18372606X-RAY DIFFRACTION100
2.8762-2.96910.25421430.18942599X-RAY DIFFRACTION100
2.9691-3.07520.26181510.1822593X-RAY DIFFRACTION100
3.0752-3.19830.21441240.17882601X-RAY DIFFRACTION100
3.1983-3.34380.22511240.18412636X-RAY DIFFRACTION100
3.3438-3.520.21761370.17492607X-RAY DIFFRACTION100
3.52-3.74050.21031270.15942633X-RAY DIFFRACTION100
3.7405-4.02920.18181270.15212633X-RAY DIFFRACTION100
4.0292-4.43450.16951450.13932632X-RAY DIFFRACTION100
4.4345-5.07560.15831500.13532644X-RAY DIFFRACTION100
5.0756-6.39260.23451680.17252675X-RAY DIFFRACTION100
6.3926-49.78970.15231470.15642798X-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)
10.2805-0.0799-0.24460.26720.11980.1920.12420.25470.2094-0.34860.04960.1962-0.0356-0.09420.41840.29510.0278-0.13630.38360.14670.257141.275237.82371.0381
20.3433-0.0101-0.11040.21060.03310.15610.0953-0.01050.0679-0.09570.04660.1495-0.0162-0.025700.20080.03390.01330.23110.06210.247649.103542.927912.18
30.16050.1351-0.0260.16940.04620.34250.0003-0.0535-0.3288-0.0270.13160.3314-0.0063-0.09120.2560.183-0.0605-0.1310.35530.13360.498230.412826.748710.4609
40.0468-0.01220.0040.4181-0.05570.0352-0.0384-0.0305-0.0829-0.02020.22940.72120.0901-0.15080.05410.09360.0054-0.04390.43490.24430.660626.266430.554516.9728
50.28480.16710.13330.09330.09880.1585-0.087-0.2118-0.290.0476-0.21250.17990.078-0.2967-0.37080.1346-0.03040.14170.55660.35380.997220.642829.111419.6901
60.20380.178-0.39960.2078-0.4080.83770.061-0.2608-0.26920.1593-0.04250.5773-0.0880.2260.10920.16680.03640.00220.35890.14070.561734.004125.638321.5574
70.1750.1456-0.02120.5301-0.27490.1702-0.0873-0.4459-0.53480.36940.12980.408-0.1472-0.23020.0320.3007-0.11870.03030.47230.25820.75331.964917.765224.3782
80.1450.04790.00320.0390.05340.15430.0797-0.0452-0.4506-0.03830.08760.36150.31190.00950.06060.3391-0.0606-0.10840.27380.16750.711938.004715.808316.2035
90.31310.1182-0.07080.48940.01760.01690.11330.2762-0.2309-0.3367-0.00870.2-0.02810.02250.0026-0.07320.0071-0.43210.26060.00620.178941.722331.8745-0.015
100.1811-0.1370.07570.1249-0.03140.058-0.10670.0337-0.1214-0.0066-0.17960.1345-0.0877-0.0962-0.09330.34470.32860.00920.4866-0.04110.629418.33481.696526.6599
110.1023-0.00320.08230.1209-0.1090.22690.01910.11520.08870.0491-0.22880.2287-0.1418-0.164-0.05370.58240.25190.00830.5436-0.17580.512620.365273.100632.2954
120.219-0.1189-0.03810.2375-0.22730.3871-0.09220.14510.0548-0.2091-0.1297-0.00520.0075-0.3868-0.05550.52610.3085-0.06860.6761-0.15990.561518.352771.156922.5923
130.1128-0.0418-0.19030.16280.04890.3622-0.1271-0.08850.1863-0.2588-0.25170.15990.1387-0.1904-0.03540.30510.1598-0.04850.5157-0.09670.684324.759761.028222.3535
140.0210.01840.00990.11140.04120.0616-0.0774-0.33320.12580.1123-0.1094-0.00110.265-0.2876-0.00240.14740.02310.05790.5089-0.02580.478329.103250.895824.3171
150.0780.0660.01890.06630.00840.02520.1871-0.36910.32080.33140.00290.1631-0.3442-0.22330.00590.49770.00960.07270.4931-0.10780.336359.707461.082279.2995
160.0829-0.04450.01540.08020.02170.01420.0628-0.0302-0.19920.07610.0258-0.11110.1577-0.1214-0.00010.38510.00680.02350.3794-0.0090.193560.657843.745973.7064
170.1409-0.21890.09440.3236-0.14340.1285-0.0389-0.0660.2685-0.02790.00480.065-0.2805-0.079900.4082-0.0230.02950.373-0.01280.240958.506955.340966.8453
180.03680.0231-0.01780.0073-0.00610.0050.21220.08860.63140.0054-0.0263-0.0278-0.34910.0645-00.5725-0.06750.03750.4193-0.00070.475268.42769.419566.003
190.01560.02-0.0080.0477-0.0360.0243-0.18610.13450.484-0.51120.21420.0942-0.46490.17280.00020.7375-0.02680.06370.49880.12180.607569.469373.06457.9289
200.02170.0143-0.03020.0094-0.01620.03770.17540.14620.2566-0.16170.0328-0.1422-0.06630.03780.00010.5779-0.05690.08720.4849-0.00630.416973.433161.254958.2726
210.3285-0.3608-0.00950.7710.1990.11830.08870.26550.5141-0.34740.1412-0.51250.1649-0.0296-0.01060.6305-0.14750.16960.7807-0.03340.533580.657562.117655.1648
220.0911-0.05840.13980.0752-0.04860.1770.0094-0.11180.08630.13810.0031-0.2051-0.13370.0481-0.00010.4283-0.01180.05620.3831-0.05710.358373.394454.648771.77
230.13720.01490.0940.17460.11690.15-0.2807-0.1473-0.030.77860.09150.01040.17810.0354-0.00090.8250.25670.00130.5666-0.06540.421726.296778.679247.2052
241.61520.2209-0.96570.5497-0.2320.6053-0.20090.1018-0.00870.0045-0.3604-0.1834-0.6181-0.0041-0.52110.85140.1139-0.28920.39280.01430.368542.380670.862955.1242
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 195 )
5X-RAY DIFFRACTION5chain 'A' and (resid 196 through 219 )
6X-RAY DIFFRACTION6chain 'A' and (resid 220 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 89 )
13X-RAY DIFFRACTION13chain 'B' and (resid 90 through 114 )
14X-RAY DIFFRACTION14chain 'B' and (resid 115 through 153 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 32 )
16X-RAY DIFFRACTION16chain 'C' and (resid 33 through 79 )
17X-RAY DIFFRACTION17chain 'C' and (resid 80 through 166 )
18X-RAY DIFFRACTION18chain 'C' and (resid 167 through 187 )
19X-RAY DIFFRACTION19chain 'C' and (resid 188 through 218 )
20X-RAY DIFFRACTION20chain 'C' and (resid 219 through 236 )
21X-RAY DIFFRACTION21chain 'C' and (resid 237 through 261 )
22X-RAY DIFFRACTION22chain 'C' and (resid 262 through 310 )
23X-RAY DIFFRACTION23chain 'D' and (resid 11 through 87 )
24X-RAY DIFFRACTION24chain 'D' and (resid 88 through 153 )

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