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

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Basic information

Entry
Database: PDB / ID: 4loc
TitleStructure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with oxamate and biotin
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 / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Rudiment single hybrid motif / Single hybrid motif / Cyclin A; domain 1 / 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 / Roll / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BIOTIN / OXAMIC ACID / Pyruvate carboxylase
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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
DepositionJul 12, 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 1.5Dec 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)281,83625
Polymers279,8544
Non-polymers1,98321
Water9,638535
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.870, 157.123, 244.714
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(-0.564017, 0.088647, -0.820991), (0.053733, -0.988174, -0.143613), (-0.824013, -0.125115, 0.552584)-18.5188, -32.4971, -12.51746
3given(0.547226, -0.135887, 0.82588), (-0.108134, -0.989941, -0.091232), (0.82997, -0.039382, -0.556416)-66.67191, -42.66513, 120.78899
4given(-0.999362, 0.033957, -0.011038), (0.030543, 0.973107, 0.228321), (0.018495, 0.227838, -0.973523)-83.94727, -11.84477, 114.33305

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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, 556 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 / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-BTN / BIOTIN / Biotin


Mass: 244.311 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O3S
#6: Chemical
ChemComp-OXM / OXAMIC ACID / Oxamic acid


Mass: 89.050 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3NO3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 535 / 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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 298 K / Method: batch crystallization under oil / pH: 6
Details: 14% (w/v) PEG 8000, 110 mM MOPS (pH 6.0), 165 mM Tetramethylammonium chloride, 2% (v/v) glycerol, 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: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2011
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. all: 148360 / Num. obs: 145868 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 20.6
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 3.4 / % possible all: 94.7

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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: 2.26→43.75 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.969 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21628 7444 5 %RANDOM
Rwork0.17635 ---
obs0.17837 140726 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.934 Å2
Baniso -1Baniso -2Baniso -3
1-4.52 Å20 Å20 Å2
2---1.78 Å20 Å2
3----2.74 Å2
Refinement stepCycle: LAST / Resolution: 2.26→43.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17888 0 111 535 18534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01918448
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217195
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.97325081
X-RAY DIFFRACTIONr_angle_other_deg0.896339456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35952382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42824.045754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.782152817
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.81315108
X-RAY DIFFRACTIONr_chiral_restr0.10.22855
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02121129
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024071
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_it1.6562.3399519
X-RAY DIFFRACTIONr_mcbond_other1.6552.3389518
X-RAY DIFFRACTIONr_mcangle_it2.4623.50111886
X-RAY DIFFRACTIONr_mcangle_other2.4623.50111887
X-RAY DIFFRACTIONr_scbond_it2.2412.478929
X-RAY DIFFRACTIONr_scbond_other2.2412.478930
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9313.64113190
X-RAY DIFFRACTIONr_long_range_B_refined5.79419.24221633
X-RAY DIFFRACTIONr_long_range_B_other5.79419.24321634
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.263→2.322 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 522 -
Rwork0.227 9461 -
obs-9461 90.61 %
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)
10.554-0.01410.01811.35010.39891.1651-0.0197-0.10430.04690.02670.0520.0312-0.1287-0.0681-0.03230.07810.01790.0130.0296-0.0070.0419-36.4373-3.150615.6937
21.6446-0.7695-0.96512.54890.56721.8789-0.4101-0.59150.03680.89370.5082-0.27020.43610.5572-0.09810.40520.2897-0.09530.3095-0.07760.129-11.8728-33.978625.4968
31.02280.054-0.5942.00720.17611.9194-0.01830.19730.0786-0.5485-0.00690.39120.3181-0.33870.02520.43-0.0049-0.07040.16360.05530.2239-74.6198-39.261480.068
40.83360.5066-0.41071.349-0.20731.8886-0.0466-0.0444-0.0622-0.00290.0474-0.16410.05550.4049-0.00080.11630.09770.02860.2031-0.0150.103-49.2183-12.185497.403
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A471 - 1067
2X-RAY DIFFRACTION1A1101 - 1105
3X-RAY DIFFRACTION1B1101
4X-RAY DIFFRACTION2B471 - 1067
5X-RAY DIFFRACTION2B1102 - 1105
6X-RAY DIFFRACTION3C471 - 1067
7X-RAY DIFFRACTION3C1101 - 1106
8X-RAY DIFFRACTION4D471 - 1067
9X-RAY DIFFRACTION4D1101 - 1105

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