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- PDB-4m6v: Structure of the carboxyl transferase domain from Rhizobium etli ... -

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Basic information

Entry
Database: PDB / ID: 4m6v
TitleStructure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with pyruvate and biocytin
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 / 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 / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Cyclin A; domain 1 / 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. / Aldolase-type TIM barrel / Arc Repressor Mutant, subunit A / TIM Barrel / Alpha-Beta Barrel / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biocytin / PYRUVIC ACID / Pyruvate carboxylase
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLietzan, A.D. / St.Maurice, M.
CitationJournal: Arch.Biochem.Biophys. / Year: 2014
Title: The role of biotin and oxamate in the carboxyltransferase reaction of pyruvate carboxylase.
Authors: Lietzan, A.D. / Lin, Y. / St.Maurice, M.
History
DepositionAug 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Sep 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_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

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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)283,87030
Polymers279,8544
Non-polymers4,01726
Water6,503361
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.641, 157.828, 244.953
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(-0.563578, 0.095274, -0.82055), (0.058133, -0.98629, -0.154445), (-0.824015, -0.134743, 0.550312)-20.01678, -32.89041, -13.78724
3given(-0.998661, 0.05122, -0.0072), (0.047993, 0.969525, 0.240247), (0.019286, 0.23958, -0.970685)-85.43018, -12.00077, 114.69685
4given(0.55236, -0.149221, 0.820141), (-0.121287, -0.987765, -0.098033), (0.824735, -0.045323, -0.5637)-67.23268, -43.55867, 121.45577

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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, 387 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


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


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O3
#6: Chemical
ChemComp-BYT / Biocytin / N~6~-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}-L-lysine


Mass: 372.483 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H28N4O4S
#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.: 361 / 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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 298 K / Method: batch crystallization under oil / pH: 6
Details: 11% (w/v) PEG 8000, 100 mM BisTris (pH 6.0), 345 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-D / Wavelength: 1.12706 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12706 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 128300 / Num. obs: 128103 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 25.7
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 5.2 / % possible all: 99.8

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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: 2.4→49.66 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 15.37 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22319 6448 5 %RANDOM
Rwork0.18369 ---
obs0.18568 121746 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.797 Å2
Baniso -1Baniso -2Baniso -3
1-5.58 Å20 Å20 Å2
2---1.04 Å20 Å2
3----4.54 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17838 0 206 361 18405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01918487
X-RAY DIFFRACTIONr_bond_other_d0.0010.0217207
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.97725201
X-RAY DIFFRACTIONr_angle_other_deg0.801339506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80252388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22224.204754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.923152779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.63815100
X-RAY DIFFRACTIONr_chiral_restr0.0740.22876
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02121179
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024048
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_it1.6152.9829525
X-RAY DIFFRACTIONr_mcbond_other1.6152.9829524
X-RAY DIFFRACTIONr_mcangle_it2.5634.46711895
X-RAY DIFFRACTIONr_mcangle_other2.5634.46811896
X-RAY DIFFRACTIONr_scbond_it1.6763.0638962
X-RAY DIFFRACTIONr_scbond_other1.6763.0638963
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5924.54113298
X-RAY DIFFRACTIONr_long_range_B_refined4.1323.73521110
X-RAY DIFFRACTIONr_long_range_B_other4.12723.73621104
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 463 -
Rwork0.245 8637 -
obs--97.04 %
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)
10.4976-0.0435-0.14531.39640.74021.47470.0087-0.0750.0498-0.2410.0652-0.0293-0.3519-0.0103-0.07390.1821-0.00980.00720.0413-0.03470.0801-37.5518-3.385516.1466
21.5574-0.5257-1.03812.00120.27931.9053-0.314-0.66760.11660.53810.436-0.38550.21590.5868-0.1220.19160.2068-0.08960.3998-0.16490.2158-13.2932-35.063425.6525
31.02460.4729-1.15421.2147-0.34692.9516-0.154-0.2619-0.1530.2510.0733-0.11950.2540.67470.08070.31320.23820.02830.34670.02380.1175-49.7333-12.417997.2326
41.3114-0.2725-0.64761.95620.46732.27130.1360.20920.0421-0.2436-0.10240.52440.3507-0.5099-0.03360.51740.07170.04530.29620.11480.3813-74.9426-39.603780.0667
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A471 - 1067
2X-RAY DIFFRACTION1A1101 - 1106
3X-RAY DIFFRACTION1B1101
4X-RAY DIFFRACTION1A1201 - 1343
5X-RAY DIFFRACTION1B1201
6X-RAY DIFFRACTION2B471 - 1067
7X-RAY DIFFRACTION2B1102 - 1107
8X-RAY DIFFRACTION2B1202 - 1285
9X-RAY DIFFRACTION3C471 - 1067
10X-RAY DIFFRACTION3C1101 - 1107
11X-RAY DIFFRACTION3C1201 - 1277
12X-RAY DIFFRACTION3D1201
13X-RAY DIFFRACTION4D471 - 1067
14X-RAY DIFFRACTION4D1101 - 1106
15X-RAY DIFFRACTION4D1202 - 1256

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