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- PDB-2jku: Crystal structure of the N-terminal region of the biotin acceptor... -

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Basic information

Entry
Database: PDB / ID: 2jku
TitleCrystal structure of the N-terminal region of the biotin acceptor domain of human propionyl-CoA carboxylase
ComponentsPROPIONYL-COA CARBOXYLASE ALPHA CHAIN, MITOCHONDRIAL
KeywordsLIGASE / BIOTIN / ATP-BINDING / DISEASE MUTATION / NUCLEOTIDE-BINDING / MITOCHONDRION / PHOSPHOPROTEIN / TRANSIT PEPTIDE
Function / homology
Function and homology information


short-chain fatty acid catabolic process / branched-chain amino acid metabolic process / Propionyl-CoA catabolism / propionyl-CoA carboxylase / propionyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / biotin binding / catalytic complex / fatty acid metabolic process ...short-chain fatty acid catabolic process / branched-chain amino acid metabolic process / Propionyl-CoA catabolism / propionyl-CoA carboxylase / propionyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / biotin binding / catalytic complex / fatty acid metabolic process / mitochondrial matrix / enzyme binding / mitochondrion / ATP binding / metal ion binding / cytosol
Similarity search - Function
Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT 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. ...Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT 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 / Single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Propionyl-CoA carboxylase alpha chain, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHealy, S. / Yue, W.W. / Kochan, G. / Pilka, E.S. / Murray, J.W. / Roos, A.K. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C. / Wikstrom, M. ...Healy, S. / Yue, W.W. / Kochan, G. / Pilka, E.S. / Murray, J.W. / Roos, A.K. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C. / Wikstrom, M. / Edwards, A. / Bountra, C. / Gravel, R.A. / Oppermann, U.
CitationJournal: Biochemistry / Year: 2010
Title: Structural impact of human and Escherichia coli biotin carboxyl carrier proteins on biotin attachment.
Authors: Healy, S. / McDonald, M.K. / Wu, X. / Yue, W.W. / Kochan, G. / Oppermann, U. / Gravel, R.A.
History
DepositionAug 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Mar 4, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details ..._pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.4Dec 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROPIONYL-COA CARBOXYLASE ALPHA CHAIN, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3293
Polymers9,9401
Non-polymers3882
Water1,04558
1
A: PROPIONYL-COA CARBOXYLASE ALPHA CHAIN, MITOCHONDRIAL
hetero molecules

A: PROPIONYL-COA CARBOXYLASE ALPHA CHAIN, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6576
Polymers19,8802
Non-polymers7774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area3720 Å2
ΔGint-13 kcal/mol
Surface area4230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.107, 56.107, 58.083
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-2002-

HOH

21A-2048-

HOH

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Components

#1: Protein PROPIONYL-COA CARBOXYLASE ALPHA CHAIN, MITOCHONDRIAL / PROPANOYL-COA\:CARBON DIOXIDE LIGASE SUBUNIT ALPHA


Mass: 9940.248 Da / Num. of mol.: 1 / Fragment: BIOTIN ACCEPTOR DOMAIN, RESIDUES 633-703
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organelle: MITOCHONDRIAMitochondrion / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: P05165, propionyl-CoA carboxylase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.57 Å3/Da / Density % sol: 65.53 % / Description: NONE
Crystal growDetails: 20% PEG 3350, 0.20M NA FORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97628
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 21, 2008
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.5→48.56 Å / Num. obs: 10251 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 12.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.6
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0036refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2D5D, 3BG3

2d5d

3bg3


Resolution: 1.5→28.12 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.564 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.166 438 4.8 %RANDOM
Rwork0.148 ---
obs0.149 8711 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms242 0 23 58 323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023289
X-RAY DIFFRACTIONr_bond_other_d0.0020.02202
X-RAY DIFFRACTIONr_angle_refined_deg1.5462.12389
X-RAY DIFFRACTIONr_angle_other_deg0.8933.018469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.668541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.09526.6676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.221547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.952151
X-RAY DIFFRACTIONr_chiral_restr0.0770.250
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021294
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0239
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_it2.333188
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.8235311
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.8427101
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.2481175
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.224 33
Rwork0.191 614

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