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- PDB-2z1b: Crystal Structure of 5-aminolevulinic acid dehydratase (ALAD) fro... -

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Basic information

Entry
Database: PDB / ID: 2z1b
TitleCrystal Structure of 5-aminolevulinic acid dehydratase (ALAD) from Mus musculs
ComponentsDelta-aminolevulinic acid dehydratase
KeywordsLYASE / Structure Genomics / conserved hypothetical protein / Porphyrin 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 / heme O biosynthetic process / heme B biosynthetic process / heme A biosynthetic process / response to aluminum ion ...Heme biosynthesis / proteasome core complex binding / response to vitamin B1 / response to platinum ion / porphobilinogen synthase / porphobilinogen synthase activity / heme O biosynthetic process / heme B biosynthetic process / heme A biosynthetic process / response to aluminum ion / negative regulation of proteasomal protein catabolic process / cellular response to lead ion / response to mercury ion / response to selenium ion / response to methylmercury / protoporphyrinogen IX biosynthetic process / response to fatty acid / response to cobalt ion / response to arsenic-containing substance / response to metal ion / response to iron ion / heme biosynthetic process / response to herbicide / response to ionizing radiation / response to zinc ion / response to vitamin E / response to amino acid / cellular response to interleukin-4 / response to cadmium ion / response to glucocorticoid / Neutrophil degranulation / response to nutrient / 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 / 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: 3.3 Å
AuthorsXie, Y. / Wang, H. / Kawazoe, M. / Kishishita, S. / Murayama, K. / Takemoto, C. / Terada, T. / Shirozu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of 5-aminolevulinic acid dehydratase (ALAD) from Mus musculs
Authors: Xie, Y. / Wang, H. / Kawazoe, M. / Kishishita, S. / Murayama, K. / Takemoto, C. / Terada, T. / Mikako, M. / Shirozu, M. / Yokoyama, S.
History
DepositionMay 8, 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 / 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: Delta-aminolevulinic acid dehydratase
B: Delta-aminolevulinic acid dehydratase
C: Delta-aminolevulinic acid dehydratase
D: Delta-aminolevulinic acid dehydratase


Theoretical massNumber of molelcules
Total (without water)144,3224
Polymers144,3224
Non-polymers00
Water1,02757
1
A: Delta-aminolevulinic acid dehydratase

A: Delta-aminolevulinic acid dehydratase


Theoretical massNumber of molelcules
Total (without water)72,1612
Polymers72,1612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area3140 Å2
ΔGint-20.3 kcal/mol
Surface area25700 Å2
MethodPISA
2
B: Delta-aminolevulinic acid dehydratase
C: Delta-aminolevulinic acid dehydratase


Theoretical massNumber of molelcules
Total (without water)72,1612
Polymers72,1612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-20.7 kcal/mol
Surface area26120 Å2
MethodPISA
3
D: Delta-aminolevulinic acid dehydratase

D: Delta-aminolevulinic acid dehydratase


Theoretical massNumber of molelcules
Total (without water)72,1612
Polymers72,1612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area3270 Å2
ΔGint-15.9 kcal/mol
Surface area26660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)240.920, 240.920, 103.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Detailsin this crystal packing, it looks like dimer in one asymmetric unit

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Components

#1: Protein
Delta-aminolevulinic acid dehydratase


Mass: 36080.500 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: cell-free protein synthesis / Gene: Alad / Plasmid: PX041202-30-MD01
References: UniProt: Q9DD05, UniProt: P10518*PLUS, porphobilinogen synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.02 Å3/Da / Density % sol: 59.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.5M Li2SO4, 0.1M HEPES-Na (pH7.5), 9.5% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97955 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2007 / Details: Mirror
RadiationMonochromator: silikon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97955 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 27448 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Rsym value: 0.108 / Net I/σ(I): 19.3
Reflection shellResolution: 3.3→3.47 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 4.01 / Num. unique all: 3839 / Rsym value: 0.641 / % 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: PDB ENTRY 2Z0I

2z0i


Resolution: 3.3→43.4 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 247047.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.353 2400 9.9 %RANDOM
Rwork0.278 ---
obs0.278 24143 88.7 %-
all-27448 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 77.4646 Å2 / ksol: 0.296522 e/Å3
Displacement parametersBiso mean: 70.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.94 Å26.72 Å20 Å2
2---4.94 Å20 Å2
3---9.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.66 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.92 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 3.3→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9166 0 0 57 9223
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.419 333 10.6 %
Rwork0.346 2817 -
obs--70.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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