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- PDB-1ulz: Crystal structure of the biotin carboxylase subunit of pyruvate c... -

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Basic information

Entry
Database: PDB / ID: 1ulz
TitleCrystal structure of the biotin carboxylase subunit of pyruvate carboxylase
Componentspyruvate carboxylase n-terminal domain
KeywordsLIGASE / Biotin Carboxylase / Pyruvate Carboxylase / Aquifex aeolicus
Function / homology
Function and homology information


ligase activity / ATP binding / metal ion binding
Similarity search - Function
Acetyl-CoA carboxylase, biotin carboxylase / 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 / Rossmann fold - #20 / Carbamoyl-phosphate synthase subdomain signature 1. ...Acetyl-CoA carboxylase, biotin carboxylase / 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 / Rossmann fold - #20 / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Rudiment single hybrid motif / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Carbamoyl-phosphate synthase subdomain signature 2. / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acetyl-CoA carboxylase subunit A
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKondo, S. / Nakajima, Y. / Sugio, S. / Yong-Biao, J. / Sueda, S. / Kondo, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the biotin carboxylase subunit of pyruvate carboxylase from Aquifex aeolicus at 2.2 A resolution.
Authors: Kondo, S. / Nakajima, Y. / Sugio, S. / Yong-Biao, J. / Sueda, S. / Kondo, H.
History
DepositionSep 18, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pyruvate carboxylase n-terminal domain


Theoretical massNumber of molelcules
Total (without water)50,7161
Polymers50,7161
Non-polymers00
Water4,954275
1
A: pyruvate carboxylase n-terminal domain

A: pyruvate carboxylase n-terminal domain


Theoretical massNumber of molelcules
Total (without water)101,4322
Polymers101,4322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)92.418, 122.145, 59.011
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer generated by crystallographic symmetry operation: -x, -y, z.

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Components

#1: Protein pyruvate carboxylase n-terminal domain / Biotin Carboxylase / Subunit of Pyruvate Carboxylase


Mass: 50716.105 Da / Num. of mol.: 1 / Fragment: residues 1-451 / Mutation: F2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / References: UniProt: O67483, pyruvate carboxylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 3.1 Å3/Da / Density % sol: 60.07 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.836 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.836 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 39589 / % possible obs: 99.9 % / Rsym value: 0.068 / Net I/σ(I): 37.6
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 7.17 / Rsym value: 0.304 / % possible all: 99.8

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNXrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.236 1732 RANDOM
Rwork0.199 --
all0.201 34583 -
obs0.201 34583 -
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3565 0 0 275 3840
LS refinement shellResolution: 2.2→2.3 Å
RfactorNum. reflection
Rfree0.242 205
Rwork0.202 -
obs-4214

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