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- PDB-3bg9: Crystal Structure of Human Pyruvate Carboxylase (missing the biot... -

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Basic information

Entry
Database: PDB / ID: 3bg9
TitleCrystal Structure of Human Pyruvate Carboxylase (missing the biotin carboxylase domain at the N-terminus) F1077A Mutant
ComponentsPyruvate carboxylase, mitochondrial
KeywordsLIGASE / TIM barrel / ATP-binding / Biotin / Disease mutation / Gluconeogenesis / Lipid synthesis / Manganese / Mitochondrion / Multifunctional enzyme / Nucleotide-binding / Phosphoprotein / Transit peptide
Function / homology
Function and homology information


pyruvate carboxylase / pyruvate carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / viral RNA genome packaging / NADP metabolic process / Pyruvate metabolism / positive regulation by host of viral process / Gluconeogenesis / NADH metabolic process ...pyruvate carboxylase / pyruvate carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / viral RNA genome packaging / NADP metabolic process / Pyruvate metabolism / positive regulation by host of viral process / Gluconeogenesis / NADH metabolic process / pyruvate metabolic process / biotin binding / viral release from host cell / gluconeogenesis / lipid metabolic process / mitochondrial matrix / negative regulation of gene expression / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol / 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. / 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 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 / 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
: / Pyruvate carboxylase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsXiang, S. / Tong, L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction.
Authors: Xiang, S. / Tong, L.
History
DepositionNov 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)315,1018
Polymers314,8814
Non-polymers2204
Water00
1
A: Pyruvate carboxylase, mitochondrial
B: Pyruvate carboxylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,5504
Polymers157,4402
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
MethodPISA
2
C: Pyruvate carboxylase, mitochondrial
D: Pyruvate carboxylase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,5504
Polymers157,4402
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.540, 107.540, 524.470
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Pyruvate carboxylase, mitochondrial / Pyruvic carboxylase / PCB


Mass: 78720.219 Da / Num. of mol.: 4 / Fragment: CT+PT+BCCP Domain / Mutation: F1077A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PC / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: P11498, pyruvate carboxylase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn

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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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200 mM ammonium tartrate, 15% (w/v) PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twinType: hemihedral / Operator: -h,-k,l / Fraction: 0.366
ReflectionResolution: 3→30 Å / Num. all: 63377 / Num. obs: 63285 / % possible obs: 88.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 16.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 3.2 / Num. unique all: 6348 / Rsym value: 0.419 / % possible all: 90.9

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30 Å / σ(F): 5108 / Stereochemistry target values: Engh & Huber
Details: The crystal is twinned, and twinned refinement was carried out by CNS. The twin operator = -h,-k,l; and twin fraction = 0.369
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2799 3.9 %RANDOM
Rwork0.189 ---
all0.189 71992 --
obs0.189 58177 80.8 %-
Solvent computationBsol: 17.785 Å2
Displacement parametersBiso mean: 47.426 Å2
Baniso -1Baniso -2Baniso -3
1--5.169 Å2-13.72 Å20 Å2
2---5.169 Å20 Å2
3---10.337 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18512 0 4 0 18516
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0095981.5
X-RAY DIFFRACTIONc_angle_deg1.436932
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param

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