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

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Basic information

Entry
Database: PDB / ID: 4mfe
TitleStructure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with 3-hydroxypyruvate
ComponentsPYRUVATE CARBOXYLASE
KeywordsLIGASE / TIM Barrel
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. / 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 / Carbamoyl-phosphate synthase subdomain signature 2. / Arc Repressor Mutant, subunit A / Aldolase-type TIM barrel / TIM Barrel / Roll / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-HYDROXYPYRUVIC ACID / BIOTIN / Pyruvate carboxylase
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsLietzan, A.D. / St.Maurice, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Insights into the carboxyltransferase reaction of pyruvate carboxylase from the structures of bound product and intermediate analogs.
Authors: Lietzan, A.D. / St.Maurice, M.
History
DepositionAug 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Sep 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 1.6Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _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)281,89625
Polymers279,8544
Non-polymers2,04321
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.254, 157.849, 243.319
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(-0.593233, 0.091875, -0.799771), (0.053551, -0.986762, -0.153077), (-0.803248, -0.133639, 0.58046)-21.73857, -32.56228, -13.97055
3given(-0.998885, 0.043903, -0.01734), (0.038777, 0.972673, 0.22892), (0.026917, 0.227992, -0.973291)-83.74801, -11.23005, 114.45314
4given(0.578133, -0.131739, 0.805237), (-0.112717, -0.990313, -0.081091), (0.808119, -0.043883, -0.587382)-64.22461, -44.27145, 121.22777

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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
Fragment: CARBOXYL TRANSFERASE DOMAIN, UNP residues 465-1067
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 , 7 types, 190 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-3PY / 3-HYDROXYPYRUVIC ACID


Mass: 104.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O4
#4: Chemical
ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O3S
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.89 Å3/Da / Density % sol: 57.45 %
Crystal growTemperature: 298 K / Method: batch crystallization under oil / pH: 6
Details: 11.3% (w/v) PEG 8000, 99 mM BisTris, 346 mM tetramethylammonium chloride, pH 6.0, BATCH CRYSTALLIZATION UNDER OIL, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2011
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 95807 / Num. obs: 91812 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 59.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 22.8
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.3 / % possible all: 93.2

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Processing

Software
NameVersionClassification
MD2diffractometer software from EMBLdata collection
PHASERphasing
REFMAC5.7.0032refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JX4

4jx4


Resolution: 2.61→49.37 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 17.624 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.45 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22463 4797 5 %RANDOM
Rwork0.17712 ---
obs0.17949 90882 95.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.213 Å2
Baniso -1Baniso -2Baniso -3
1-4.55 Å20 Å20 Å2
2---0.99 Å20 Å2
3----3.57 Å2
Refinement stepCycle: LAST / Resolution: 2.61→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17458 0 89 169 17716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01917998
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216312
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.96724535
X-RAY DIFFRACTIONr_angle_other_deg0.878337321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37352385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08724.104709
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.222152517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1041594
X-RAY DIFFRACTIONr_chiral_restr0.0880.22817
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02120920
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023979
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_it2.43.4949531
X-RAY DIFFRACTIONr_mcbond_other2.43.4949530
X-RAY DIFFRACTIONr_mcangle_it3.6135.2411904
X-RAY DIFFRACTIONr_mcangle_other3.6135.2411905
X-RAY DIFFRACTIONr_scbond_it2.9543.5858467
X-RAY DIFFRACTIONr_scbond_other2.9543.5858467
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7635.30712627
X-RAY DIFFRACTIONr_long_range_B_refined6.2728.20920628
X-RAY DIFFRACTIONr_long_range_B_other6.2728.21220629
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.605→2.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 353 -
Rwork0.238 6233 -
obs-6233 89.96 %
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)
11.0005-0.13050.00662.16450.86061.99820.0059-0.07880.0733-0.23890.0733-0.0237-0.3355-0.0499-0.07920.2377-0.03340.04750.0228-0.0120.0503-37.5506-3.227715.681
22.3304-0.5123-0.95543.25140.44752.7494-0.3143-0.7466-0.11840.80330.4219-0.59540.35850.6994-0.10760.36120.2448-0.06580.4083-0.10090.3277-13.4076-34.551824.6604
31.24070.2984-0.73822.21240.01953.1197-0.0835-0.146-0.02990.1350.1852-0.2559-0.14970.6487-0.10160.23130.10440.04370.3691-0.05880.1275-48.7512-12.691497.0487
41.5465-0.6971-1.10793.221.20773.3645-0.04760.2993-0.167-0.3601-0.22840.95010.2377-0.68390.2760.3037-0.0098-0.03240.34620.00040.576-73.7327-39.728580.5078
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A471 - 1067
2X-RAY DIFFRACTION1A1101 - 1106
3X-RAY DIFFRACTION2B471 - 1067
4X-RAY DIFFRACTION2B1101 - 1105
5X-RAY DIFFRACTION3C471 - 1067
6X-RAY DIFFRACTION3C1101 - 1105
7X-RAY DIFFRACTION3D1101
8X-RAY DIFFRACTION4D471 - 1067
9X-RAY DIFFRACTION4D1102 - 1105

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