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

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Basic information

Entry
Database: PDB / ID: 4mfd
TitleStructure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with oxalate
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 / Cyclin A; domain 1 / Rudiment single hybrid motif / 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
OXALATE ION / 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: 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)280,89022
Polymers279,8544
Non-polymers1,03718
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.657, 157.368, 244.827
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(-0.999051, 0.039113, 0.019151), (0.033605, 0.972072, -0.232264), (-0.027701, -0.2314, -0.972464)80.71976, 69.03878, 597.84326
3given(-0.560163, 0.089435, 0.82354), (0.05871, -0.987369, 0.147161), (0.826299, 0.130784, 0.547837)-181.30305, -3.27092, 96.95734
4given(0.548512, -0.136787, -0.824878), (-0.109839, -0.989766, 0.091092), (-0.828897, 0.040639, -0.557923)269.18262, 21.01823, 503.08987

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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 , 6 types, 208 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#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.: 190 / 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: 2.95 Å3/Da / Density % sol: 58.28 %
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: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 108391 / Num. obs: 108188 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 21.1
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 4.4 / % possible all: 99.3

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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: 2.55→48.26 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 20.046 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23951 5409 5 %RANDOM
Rwork0.19283 ---
obs0.1952 102898 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.346 Å2
Baniso -1Baniso -2Baniso -3
1-8.57 Å20 Å20 Å2
2---4.64 Å20 Å2
3----3.93 Å2
Refinement stepCycle: LAST / Resolution: 2.55→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17794 0 48 190 18032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01918280
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216802
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.96724855
X-RAY DIFFRACTIONr_angle_other_deg0.869338538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61752390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24724.11747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.028152727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.43515105
X-RAY DIFFRACTIONr_chiral_restr0.0860.22818
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02121095
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024022
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_it1.6582.6299551
X-RAY DIFFRACTIONr_mcbond_other1.6582.6299550
X-RAY DIFFRACTIONr_mcangle_it2.6173.94211932
X-RAY DIFFRACTIONr_mcangle_other2.6173.94211933
X-RAY DIFFRACTIONr_scbond_it2.3412.7158729
X-RAY DIFFRACTIONr_scbond_other2.3162.7068709
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.634412896
X-RAY DIFFRACTIONr_long_range_B_refined5.7421.24220928
X-RAY DIFFRACTIONr_long_range_B_other5.73821.23120923
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.547→2.613 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 395 -
Rwork0.262 7074 -
obs-7074 93.93 %
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)
10.6421-0.09140.00282.5817-0.81611.37810.0004-0.0686-0.04210.16520.05950.03050.32690.0641-0.05990.14310.0118-0.02750.16640.00290.152937.683.2465260.7041
20.91410.4780.63651.98850.17992.2609-0.0915-0.09340.1037-0.04130.10160.2113-0.2002-0.5381-0.01010.32280.1732-0.02170.41930.01520.225750.306812.2466342.3853
32.0683-1.0751.18684.1543-0.21381.7961-0.6768-0.7283-0.23861.75860.84220.7288-0.7129-0.6441-0.16540.99590.51680.34110.49090.26280.402713.468334.8117270.0933
41.1811-0.11020.69752.5001-0.34912.22040.07170.1942-0.0006-0.9002-0.079-0.6432-0.39560.46260.00730.98290.02480.1710.3466-0.07480.475675.314439.6249325.4341
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A471 - 1067
2X-RAY DIFFRACTION1A1101 - 1105
3X-RAY DIFFRACTION2B471 - 1067
4X-RAY DIFFRACTION2B1101 - 1105
5X-RAY DIFFRACTION3C471 - 1067
6X-RAY DIFFRACTION3C1101 - 1104
7X-RAY DIFFRACTION4D471 - 1067
8X-RAY DIFFRACTION4D1101 - 1104

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