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- PDB-5hms: X-ray structure of human recombinant 5-aminolaevulinic acid dehyd... -

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Basic information

Entry
Database: PDB / ID: 5hms
TitleX-ray structure of human recombinant 5-aminolaevulinic acid dehydratase (hrALAD).
ComponentsDelta-aminolevulinic acid dehydratase
KeywordsLYASE / TIM barrel / tetrapyrrole biosynthesis / dehydratase
Function / homology
Function and homology information


proteasome core complex binding / response to vitamin B1 / response to platinum ion / porphobilinogen synthase / porphobilinogen synthase activity / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / negative regulation of proteasomal protein catabolic process / cellular response to lead ion ...proteasome core complex binding / response to vitamin B1 / response to platinum ion / porphobilinogen synthase / porphobilinogen synthase activity / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / 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 iron ion / response to herbicide / Heme biosynthesis / heme biosynthetic process / response to ionizing radiation / response to zinc ion / response to vitamin E / response to amino acid / response to cadmium ion / catalytic activity / response to glucocorticoid / cellular response to interleukin-4 / response to activity / protein homooligomerization / response to ethanol / secretory granule lumen / response to oxidative stress / ficolin-1-rich granule lumen / response to lipopolysaccharide / response to hypoxia / response to xenobiotic stimulus / Neutrophil degranulation / extracellular exosome / zinc ion binding / extracellular region / identical protein binding / nucleus / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsButler, D. / Erskine, P.T. / Cooper, J.B. / Shoolingin-Jordan, P.M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Structural studies of substrate and product complexes of 5-aminolaevulinic acid dehydratase from humans, Escherichia coli and the hyperthermophile Pyrobaculum calidifontis.
Authors: Mills-Davies, N. / Butler, D. / Norton, E. / Thompson, D. / Sarwar, M. / Guo, J. / Gill, R. / Azim, N. / Coker, A. / Wood, S.P. / Erskine, P.T. / Coates, L. / Cooper, J.B. / Rashid, N. / ...Authors: Mills-Davies, N. / Butler, D. / Norton, E. / Thompson, D. / Sarwar, M. / Guo, J. / Gill, R. / Azim, N. / Coker, A. / Wood, S.P. / Erskine, P.T. / Coates, L. / Cooper, J.B. / Rashid, N. / Akhtar, M. / Shoolingin-Jordan, P.M.
History
DepositionJan 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Mar 1, 2017Group: Database references
Revision 1.3Jan 10, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,8094
Polymers72,6782
Non-polymers1312
Water7,116395
1
A: Delta-aminolevulinic acid dehydratase
B: Delta-aminolevulinic acid dehydratase
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)291,23416
Polymers290,7118
Non-polymers5238
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area42480 Å2
ΔGint-543 kcal/mol
Surface area79540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.079, 127.079, 91.231
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Delta-aminolevulinic acid dehydratase / / ALADH / Porphobilinogen synthase / 5-aminolaevulinic acid dehydratase


Mass: 36338.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALAD / Plasmid: pT7-7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13716, porphobilinogen synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.1 M MES pH 6.2 - 6.5, 1 - 1.6 M ammonium sulphate, 10 mM dithiothreitol, 100 microM zinc chloride, 0 - 10 % dioxane.
PH range: 6.2 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→29.2 Å / Num. all: 18874 / Num. obs: 18874 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 69.1 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 11.1
Reflection shellResolution: 2.8→3 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 5.3 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+51 / Resolution: 2.8→29.2 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.887 / SU B: 16.305 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26517 973 5.1 %RANDOM
Rwork0.17229 ---
obs0.17708 17923 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.649 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---0.71 Å2-0 Å2
3---1.42 Å2
Refinement stepCycle: 1 / Resolution: 2.8→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5076 0 2 395 5473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195196
X-RAY DIFFRACTIONr_bond_other_d0.0020.024994
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9747052
X-RAY DIFFRACTIONr_angle_other_deg1.05311482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48522.613222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00815848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4731546
X-RAY DIFFRACTIONr_chiral_restr0.0860.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215870
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021180
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_it3.2074.9612630
X-RAY DIFFRACTIONr_mcbond_other3.2074.962629
X-RAY DIFFRACTIONr_mcangle_it5.3277.4343284
X-RAY DIFFRACTIONr_mcangle_other5.3277.4353285
X-RAY DIFFRACTIONr_scbond_it3.0745.2732566
X-RAY DIFFRACTIONr_scbond_other3.0735.2742567
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1637.7613769
X-RAY DIFFRACTIONr_long_range_B_refined9.12638.9215679
X-RAY DIFFRACTIONr_long_range_B_other9.08538.8015627
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 77 -
Rwork0.23 1244 -
obs--97.2 %

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