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- PDB-4jx5: Structure of the carboxyl transferase domain from Rhizobium etli ... -

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Basic information

Entry
Database: PDB / ID: 4jx5
TitleStructure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with pyruvate
ComponentsPyruvate carboxylase
KeywordsLigase / transferase / TIM Barrel
Function / homology
Function and homology information


pyruvate carboxylase / pyruvate carboxylase activity / gluconeogenesis / ATP binding / metal ion binding / cytoplasm
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. ...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. / 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. / 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 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Homeodomain-like / Aldolase class I / Aldolase-type TIM barrel / Arc Repressor Mutant, subunit A / Carbamoyl-phosphate synthase subdomain signature 2. / TIM Barrel / Alpha-Beta Barrel / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PYRUVIC ACID / Pyruvate carboxylase
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsLietzan, A.D. / St Maurice, M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: A Substrate-induced Biotin Binding Pocket in the Carboxyltransferase Domain of Pyruvate Carboxylase.
Authors: Lietzan, A.D. / St Maurice, M.
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)280,89122
Polymers279,8544
Non-polymers1,03718
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Pyruvate carboxylase
C: Pyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,44511
Polymers139,9272
Non-polymers5199
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-16 kcal/mol
Surface area43390 Å2
MethodPISA
3
B: Pyruvate carboxylase
D: Pyruvate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,44511
Polymers139,9272
Non-polymers5199
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-15 kcal/mol
Surface area42840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.130, 157.253, 245.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.99878, 0.046387, 0.016917), (0.041068, -0.970667, 0.236894), (0.02741, -0.23591, -0.971388)40.56892, -11.69324, 7.3694
3given(-0.571904, 0.0856, -0.815842), (-0.059565, 0.987582, 0.145375), (0.818155, 0.131736, -0.559703)-51.73867, -47.71001, 38.04807
4given(-0.557652, -0.148138, -0.816749), (-0.118635, 0.988069, -0.09821), (0.821553, 0.042128, -0.568573)-37.60843, 39.77375, 52.6194

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Pyruvate carboxylase


Mass: 69963.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli (bacteria) / Strain: CFN 42 / Gene: pyc, RHE_CH04002 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)* / References: UniProt: Q2K340, pyruvate carboxylase

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Non-polymers , 6 types, 225 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 298 K / Method: batch crystallization under oil / pH: 6
Details: 11.3 (w/v) PEG 8000, 99 mM BisTris (pH 6.0), 346 mM Tetramethylammonium chloride , BATCH CRYSTALLIZATION UNDER OIL, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 31, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 107850 / Num. obs: 107658 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 24
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 4.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MD2diffractometer software from EMBLdata collection
PHASERphasing
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CT+ALLOSTERIC DOMAIN (RESI 471-1067) OF PDB ENTRY 2QF7

2qf7


Resolution: 2.55→46.88 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 19.616 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.371 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 5384 5 %RANDOM
Rwork0.1866 ---
obs0.18888 102382 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.802 Å2
Baniso -1Baniso -2Baniso -3
1-7.93 Å20 Å20 Å2
2---2.87 Å20 Å2
3----5.06 Å2
Refinement stepCycle: LAST / Resolution: 2.55→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17668 0 48 207 17923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01918144
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.96624715
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11752377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21324.188745
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.298152658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.26315100
X-RAY DIFFRACTIONr_chiral_restr0.0970.22815
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113991
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_it1.6993.0429491
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6934.55711846
X-RAY DIFFRACTIONr_scbond_it2.23.0348653
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.548→2.614 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 389 -
Rwork0.27 7135 -
obs--95.77 %
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)
10.5520.0236-0.07491.7863-0.75161.4259-0.01360.0950.04550.13420.053-0.0211-0.38140.0415-0.03940.1505-0.00580.00330.08460.01260.1061-90.1266-3.1403106.6597
20.9054-0.4045-0.85051.49460.22772.4724-0.11460.1822-0.0825-0.20150.10440.17230.1572-0.61810.01020.2849-0.21620.03270.39230.00140.1679-77.8834-12.23225.0863
31.93180.9059-1.3912.9526-0.72212.2648-0.58060.79910.1147-1.1680.74150.48350.675-0.8113-0.1610.5408-0.4025-0.1660.51220.1820.2613-114.689-34.517196.9575
41.13590.1243-0.67032.1519-0.21822.1630.0028-0.20310.00440.5872-0.0352-0.49960.47890.44820.03240.7033-0.0293-0.00860.295-0.10140.3878-52.7716-39.62542.2193
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A471 - 1067
2X-RAY DIFFRACTION2B471 - 1067
3X-RAY DIFFRACTION3C471 - 1067
4X-RAY DIFFRACTION4D470 - 1067

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