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- PDB-3tw6: Structure of Rhizobium etli pyruvate carboxylase T882A with the a... -

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Basic information

Entry
Database: PDB / ID: 3tw6
TitleStructure of Rhizobium etli pyruvate carboxylase T882A with the allosteric activator, acetyl coenzyme-A
ComponentsPyruvate carboxylase protein
KeywordsLIGASE/ACTIVATOR / BIOTIN CARBOXYLASE / LIGASE-ACTIVATOR complex
Function / homology
Function and homology information


pyruvate carboxylase / pyruvate carboxylase activity / pyruvate metabolic process / gluconeogenesis / ATP binding / metal ion binding
Similarity search - Function
pyruvate carboxylase f1077a mutant fold / pyruvate carboxylase f1077a mutant domain / Conserved carboxylase domain / Pyruvate carboxylase / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Biotin-binding site ...pyruvate carboxylase f1077a mutant fold / pyruvate carboxylase f1077a mutant domain / Conserved carboxylase domain / Pyruvate carboxylase / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Biotin-binding site / Biotin-requiring enzymes attachment site. / Rossmann fold - #20 / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Cyclin A; domain 1 / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, B domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Homeodomain-like / Aldolase class I / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Carbamoyl-phosphate synthase subdomain signature 2. / Arc Repressor Mutant, subunit A / Aldolase-type TIM barrel / TIM Barrel / Roll / Alpha-Beta Barrel / Beta Barrel / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-BTI / COENZYME A / PHOSPHONOACETIC ACID / Pyruvate carboxylase
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSt Maurice, M. / Kumar, S. / Lietzan, A.D.
CitationJournal: Biochemistry / Year: 2011
Title: Interaction between the biotin carboxyl carrier domain and the biotin carboxylase domain in pyruvate carboxylase from Rhizobium etli.
Authors: Lietzan, A.D. / Menefee, A.L. / Zeczycki, T.N. / Kumar, S. / Attwood, P.V. / Wallace, J.C. / Cleland, W.W. / St Maurice, M.
History
DepositionSep 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate carboxylase protein
B: Pyruvate carboxylase protein
C: Pyruvate carboxylase protein
D: Pyruvate carboxylase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)514,45631
Polymers510,1284
Non-polymers4,32827
Water14,286793
1
A: Pyruvate carboxylase protein
B: Pyruvate carboxylase protein
hetero molecules

A: Pyruvate carboxylase protein
B: Pyruvate carboxylase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)514,56832
Polymers510,1284
Non-polymers4,44028
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area21270 Å2
ΔGint-377 kcal/mol
Surface area154150 Å2
MethodPISA
2
C: Pyruvate carboxylase protein
D: Pyruvate carboxylase protein
hetero molecules

C: Pyruvate carboxylase protein
D: Pyruvate carboxylase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)514,34330
Polymers510,1284
Non-polymers4,21526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area20760 Å2
ΔGint-365 kcal/mol
Surface area158770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)370.445, 91.550, 261.354
Angle α, β, γ (deg.)90.00, 134.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Pyruvate carboxylase protein


Mass: 127532.008 Da / Num. of mol.: 4 / Mutation: T882A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli (bacteria) / Strain: CFN 42 / ATCC 51251 / Gene: pyc, RHE_CH04002 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2K340, pyruvate carboxylase

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Non-polymers , 8 types, 820 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#7: Chemical ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O2S
#8: Chemical ChemComp-PAE / PHOSPHONOACETIC ACID


Mass: 140.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5O5P
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 793 / 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: 3.09 Å3/Da / Density % sol: 60.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14% PEG 4000, 10% MPD, 0.45M potassium chloride, 0.1 M triethanolamine, 1 mM TCEP, 5 mM ADP, 5 mM phosphonoacetate, 1 mM acetyl-CoA, 10 mM magnesium chloride, pH 8.0, VAPOR DIFFUSION, ...Details: 14% PEG 4000, 10% MPD, 0.45M potassium chloride, 0.1 M triethanolamine, 1 mM TCEP, 5 mM ADP, 5 mM phosphonoacetate, 1 mM acetyl-CoA, 10 mM magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2009
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator, Si 111
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 243161 / Num. obs: 241087 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 3.4 / % possible all: 97

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.43 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 11.953 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23531 12133 5 %RANDOM
Rwork0.1894 ---
obs0.1917 228949 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.238 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-0.21 Å2
2--0.88 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31746 0 215 793 32754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01932652
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0261.9744553
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.26454305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55623.8951312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.188154788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.91115201
X-RAY DIFFRACTIONr_chiral_restr0.1290.25122
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02124960
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 804 -
Rwork0.216 15139 -
obs--91.32 %
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)
10.7072-0.0242-0.2221.2127-0.3611.28740.0221-0.194-0.28240.1439-0.0499-0.24660.17560.27370.02780.0834-0.0161-0.07980.41420.11060.230696.6627-3.0789-36.7346
20.44780.0355-0.01950.8331-0.14410.86610.06910.15470.085-0.1771-0.0912-0.1441-0.08030.15540.02210.07820.05380.05920.45120.09310.1184108.69527.5053-146.4489
30.37270.1518-0.19971.4733-0.19240.849-0.0825-0.1024-0.1480.0786-0.04290.13750.2844-0.23140.12540.1722-0.08780.03770.3858-0.04830.1295-58.1853-24.39443.4938
40.70420.07820.20660.9726-0.02321.14090.0315-0.17240.10880.2564-0.1301-0.1356-0.28730.27690.09860.2536-0.1302-0.08470.38210.04160.071351.70029.112316.6559
51.69390.0471.29090.51330.5043.87810.0925-0.08340.0242-0.0030.0066-0.07650.1230.575-0.09910.01770.0064-0.01060.2591-0.02890.139580.083310.7807-77.4104
61.6227-1.0486-0.2810.72780.15481.52620.04750.3088-0.062-0.0176-0.1170.0904-0.02020.30.06950.00460.01330.01990.27960.06330.140474.822428.0973-125.5418
73.492-0.434-1.00531.44521.40841.5342-0.1653-0.6095-0.13780.1250.10130.02530.11670.07090.0640.17120.06290.00630.33750.01790.0156-15.8161-11.1967-12.4833
81.0875-0.10370.89241.4932-0.58831.7559-0.0321-0.166-0.0143-0.0331-0.0082-0.07070.00550.21480.04030.1444-0.0317-0.01030.25110.01120.024231.66566.3742-17.3899
90.25960.11630.08320.7338-0.13460.63690.0094-0.0559-0.0662-0.109-0.0034-0.10260.13310.0184-0.0060.11580.00710.0250.04310.01320.092147.07310.4004-89.2673
100.2918-0.13080.00620.7136-0.10250.63380.01450.05370.07740.0662-0.0209-0.1337-0.12140.00670.00640.1002-0.0132-0.00930.03930.02250.110845.052738.545-107.1093
110.8192-0.0426-0.08210.72730.09690.33820.0081-0.0316-0.15440.1059-0.0086-0.08030.0696-0.02680.00060.1225-0.0215-0.00830.03790.00150.118-4.0097-22.1695-45.1042
120.66880.090.05230.7221-0.13750.2705-0.0034-0.0170.140.1309-0.03210.0797-0.05230.03480.03560.1207-0.01980.02790.0431-0.01550.091413.355815.9305-47.4464
131.94871.47350.0615.91421.09622.97490.09790.0720.50990.2-0.02040.03-0.45350.5175-0.07750.1538-0.13930.07090.48340.08580.2893102.547447.8537-130.6345
145.0062-0.77361.23435.47840.76331.7755-0.275-0.93830.51870.5888-0.32770.3457-0.6547-0.62780.60270.76130.1219-0.12560.5255-0.2420.264133.654328.704310.1557
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 465
2X-RAY DIFFRACTION2B1 - 465
3X-RAY DIFFRACTION3C1 - 465
4X-RAY DIFFRACTION4D1 - 465
5X-RAY DIFFRACTION5A472 - 489
6X-RAY DIFFRACTION5A1004 - 1065
7X-RAY DIFFRACTION6B472 - 489
8X-RAY DIFFRACTION6B1004 - 1065
9X-RAY DIFFRACTION7C472 - 489
10X-RAY DIFFRACTION7C1004 - 1065
11X-RAY DIFFRACTION8D472 - 489
12X-RAY DIFFRACTION8D1004 - 1065
13X-RAY DIFFRACTION9A518 - 1000
14X-RAY DIFFRACTION10B518 - 1000
15X-RAY DIFFRACTION11C518 - 1000
16X-RAY DIFFRACTION12D518 - 1000
17X-RAY DIFFRACTION13B1088 - 1149
18X-RAY DIFFRACTION14D1088 - 1147

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