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- PDB-5txt: Structure of asymmetric apo/holo ALAS dimer from S. cerevisiae -

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Basic information

Entry
Database: PDB / ID: 5txt
TitleStructure of asymmetric apo/holo ALAS dimer from S. cerevisiae
Components(5-aminolevulinate synthase, mitochondrial) x 2
KeywordsTRANSFERASE / Heme biosynthesis / 5-aminolevulinic acid / Pyridoxal 5-phosphate
Function / homology
Function and homology information


positive regulation of organelle assembly / Heme biosynthesis / 5-aminolevulinate synthase / 5-aminolevulinate synthase activity / hemoglobin biosynthetic process / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion
Similarity search - Function
Tetrapyrrole biosynthesis, 5-aminolevulinic acid synthase / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-PE3 / 5-aminolevulinate synthase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBrown, B.L. / Grant, R.A. / Kardon, J.R. / Sauer, R.T. / Baker, T.A.
Funding support United States, 5items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Jane Coffin Childs Memorial Fund for Medical Research61-1529 United States
Burroughs Wellcome Fund1015092 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI-16892 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)F32DK095726 United States
CitationJournal: Structure / Year: 2018
Title: Structure of the Mitochondrial Aminolevulinic Acid Synthase, a Key Heme Biosynthetic Enzyme.
Authors: Brown, B.L. / Kardon, J.R. / Sauer, R.T. / Baker, T.A.
History
DepositionNov 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5-aminolevulinate synthase, mitochondrial
B: 5-aminolevulinate synthase, mitochondrial
D: 5-aminolevulinate synthase, mitochondrial
C: 5-aminolevulinate synthase, mitochondrial
E: 5-aminolevulinate synthase, mitochondrial
F: 5-aminolevulinate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,04414
Polymers324,5056
Non-polymers4,5398
Water5,945330
1
A: 5-aminolevulinate synthase, mitochondrial
B: 5-aminolevulinate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0735
Polymers108,1682
Non-polymers1,9043
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-52 kcal/mol
Surface area34790 Å2
MethodPISA
2
D: 5-aminolevulinate synthase, mitochondrial
C: 5-aminolevulinate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,1696
Polymers108,1682
Non-polymers2,0004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-74 kcal/mol
Surface area33860 Å2
MethodPISA
3
E: 5-aminolevulinate synthase, mitochondrial
F: 5-aminolevulinate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8033
Polymers108,1682
Non-polymers6351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-51 kcal/mol
Surface area34750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.489, 113.814, 119.344
Angle α, β, γ (deg.)116.52, 98.18, 92.56
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 5-aminolevulinate synthase, mitochondrial / 5-aminolevulinic acid synthase / Delta-ALA synthase / Delta-aminolevulinate synthase


Mass: 53970.113 Da / Num. of mol.: 3 / Fragment: UNP residues 58-548
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HEM1, CYD1, YDR232W, YD9934.16 / Production host: Escherichia coli (E. coli) / References: UniProt: P09950, 5-aminolevulinate synthase
#2: Protein 5-aminolevulinate synthase, mitochondrial / 5-aminolevulinic acid synthase / Delta-ALA synthase / Delta-aminolevulinate synthase


Mass: 54198.230 Da / Num. of mol.: 3 / Fragment: UNP residues 58-548
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HEM1, CYD1, YDR232W, YD9934.16 / Production host: Escherichia coli (E. coli) / References: UniProt: P09950, 5-aminolevulinate synthase
#3: Chemical
ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C28H58O15
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M tri-sodium citrate pH 5.5, 20% PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 80317 / % possible obs: 98.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 31.69 Å2 / Rmerge(I) obs: 0.141 / Net I/σ(I): 13.06
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 2.65 / Num. measured obs: 4012 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5-aminolevulinate synthase

Resolution: 2.7→35.003 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 24.11
RfactorNum. reflection% reflection
Rfree0.2318 1926 2.5 %
Rwork0.1862 --
obs0.1873 76970 94.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→35.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21040 0 124 330 21494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00421597
X-RAY DIFFRACTIONf_angle_d0.63629238
X-RAY DIFFRACTIONf_dihedral_angle_d14.5227896
X-RAY DIFFRACTIONf_chiral_restr0.0583297
X-RAY DIFFRACTIONf_plane_restr0.0043767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6889-2.75620.28731120.23374676X-RAY DIFFRACTION82
2.7562-2.83060.28291300.24655002X-RAY DIFFRACTION88
2.8306-2.91390.35741250.24235129X-RAY DIFFRACTION90
2.9139-3.00790.32981360.23015224X-RAY DIFFRACTION92
3.0079-3.11530.28281410.22995248X-RAY DIFFRACTION93
3.1153-3.240.25081260.21925375X-RAY DIFFRACTION94
3.24-3.38730.27611540.20965422X-RAY DIFFRACTION96
3.3873-3.56580.26471400.20365517X-RAY DIFFRACTION97
3.5658-3.78890.22731430.1935509X-RAY DIFFRACTION97
3.7889-4.08110.21461430.16055566X-RAY DIFFRACTION98
4.0811-4.4910.17081400.14495606X-RAY DIFFRACTION98
4.491-5.13910.17171400.14515583X-RAY DIFFRACTION99
5.1391-6.4680.20871490.17165580X-RAY DIFFRACTION98
6.468-35.00640.1841470.16045607X-RAY DIFFRACTION99

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