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- PDB-2z0i: Crystal Structure of 5-aminolevulinic acid dehydratase (ALAD) fro... -

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Basic information

Entry
Database: PDB / ID: 2z0i
TitleCrystal Structure of 5-aminolevulinic acid dehydratase (ALAD) from Mus musculus
ComponentsDelta-aminolevulinic acid dehydratase
KeywordsLYASE / DEHYDRATASE / TETRAPYRROLE BIOSYNTHESIS / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Heme biosynthesis / proteasome core complex binding / response to vitamin B1 / response to platinum ion / porphobilinogen synthase / porphobilinogen synthase activity / negative regulation of proteasomal protein catabolic process / cellular response to lead ion / response to mercury ion / response to aluminum ion ...Heme biosynthesis / proteasome core complex binding / response to vitamin B1 / response to platinum ion / porphobilinogen synthase / porphobilinogen synthase activity / negative regulation of proteasomal protein catabolic process / cellular response to lead ion / response to mercury ion / response to aluminum ion / response to selenium ion / protoporphyrinogen IX biosynthetic process / response to fatty acid / response to cobalt ion / response to methylmercury / response to arsenic-containing substance / response to metal ion / response to iron ion / response to herbicide / heme biosynthetic process / response to ionizing radiation / response to zinc ion / response to vitamin E / response to amino acid / response to cadmium ion / response to glucocorticoid / Neutrophil degranulation / cellular response to interleukin-4 / response to nutrient / response to organic substance / response to activity / protein homooligomerization / response to ethanol / response to oxidative stress / response to lipopolysaccharide / response to hypoxia / response to xenobiotic stimulus / extracellular space / zinc ion binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
Delta-aminolevulinic acid dehydratase / Delta-aminolevulinic acid dehydratase, active site / Delta-aminolevulinic acid dehydratase / Delta-aminolevulinic acid dehydratase active site. / Delta-aminolevulinic acid dehydratase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Delta-aminolevulinic acid dehydratase / Delta-aminolevulinic acid dehydratase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWang, H. / Xie, Y. / Kawazoe, M. / Kishishita, S. / Murayama, K. / Takemoto, C. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of 5-aminolevulinic acid dehydratase (ALAD) from Mus musculus
Authors: Wang, H. / Xie, Y. / Kawazoe, M. / Kishishita, S. / Murayama, K. / Takemoto, C. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 15, 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

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Assembly

Deposited unit
A: Delta-aminolevulinic acid dehydratase
B: Delta-aminolevulinic acid dehydratase


Theoretical massNumber of molelcules
Total (without water)73,0992
Polymers73,0992
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-30 kcal/mol
Surface area22200 Å2
MethodPISA
2
A: Delta-aminolevulinic acid dehydratase
B: Delta-aminolevulinic acid dehydratase

A: Delta-aminolevulinic acid dehydratase
B: Delta-aminolevulinic acid dehydratase

A: Delta-aminolevulinic acid dehydratase
B: Delta-aminolevulinic acid dehydratase

A: Delta-aminolevulinic acid dehydratase
B: Delta-aminolevulinic acid dehydratase


Theoretical massNumber of molelcules
Total (without water)292,3968
Polymers292,3968
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area32170 Å2
ΔGint-204 kcal/mol
Surface area74290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.510, 121.510, 196.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Delta-aminolevulinic acid dehydratase / / MS0399


Mass: 36549.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PX041202-30 / Production host: Cell-free protein synthesis
References: UniProt: Q9DD05, UniProt: P10518*PLUS, porphobilinogen synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: TRIS, PEG 400, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 12792 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Rsym value: 0.176 / Net I/σ(I): 14.2
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 1254 / Rsym value: 0.64 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+51 / Resolution: 3.2→42.68 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 25267.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 623 5.2 %RANDOM
Rwork0.233 ---
obs0.233 12063 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.1807 Å2 / ksol: 0.371122 e/Å3
Displacement parametersBiso mean: 47.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.6 Å20 Å20 Å2
2---6.6 Å20 Å2
3---13.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 3.2→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4299 0 0 48 4347
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.7
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.65
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 98 5.3 %
Rwork0.28 1754 -
obs--91.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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