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- PDB-5hnr: The X-ray structure of octameric human native 5-aminolaevulinic a... -

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Basic information

Entry
Database: PDB / ID: 5hnr
TitleThe X-ray structure of octameric human native 5-aminolaevulinic acid dehydratase.
ComponentsDelta-aminolevulinic acid dehydratase
KeywordsLYASE / Tetrapyrrole biosynthesis enzyme / TIM barrel / substrate complex.
Function / homology
Function and homology information


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 ...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 iron ion / Heme biosynthesis / heme biosynthetic process / response to herbicide / response to ionizing radiation / response to zinc ion / catalytic activity / response to vitamin E / response to amino acid / cellular response to interleukin-4 / response to cadmium ion / response to glucocorticoid / response to activity / protein homooligomerization / secretory granule lumen / response to ethanol / ficolin-1-rich granule lumen / response to oxidative stress / 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-AMINO VALERIC ACID / Delta-aminolevulinic acid dehydratase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsMills-Davies, N.L. / Thompson, D. / Shoolingin-Jordan, P.M. / Erskine, P.T. / Cooper, J.B.
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 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)73,0536
Polymers72,6782
Non-polymers3764
Water2,162120
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)292,21424
Polymers290,7118
Non-polymers1,50316
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area43980 Å2
ΔGint-503 kcal/mol
Surface area78500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.530, 125.530, 200.910
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 / ALADH / Porphobilinogen synthase


Mass: 36338.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: Blood / References: UniProt: P13716, porphobilinogen synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DAV / DELTA-AMINO VALERIC ACID


Mass: 118.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 10 mg/ml protein concentration in 10 milliM Tris pH 7.4, 10 milliM diothiothreitol and 100 microM zinc chloride. 5 microlitres of this were mixed with an equal volume of 0.1 M MES pH range 6. ...Details: 10 mg/ml protein concentration in 10 milliM Tris pH 7.4, 10 milliM diothiothreitol and 100 microM zinc chloride. 5 microlitres of this were mixed with an equal volume of 0.1 M MES pH range 6.2 - 6.5, 1.0 - 1.6 M ammonium sulphate and 0 - 10 % dioxane.
PH range: 6.2 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.87 Å
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.8→54.2 Å / Num. all: 18652 / Num. obs: 18652 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 6
Reflection shellResolution: 2.8→3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 2.9 / % possible all: 76.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1aw5

1aw5


Resolution: 2.83→44.38 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.906 / SU B: 13.612 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23785 872 4.7 %RANDOM
Rwork0.1653 ---
obs0.1687 17779 95.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å2-0 Å2
2---1.04 Å20 Å2
3---2.08 Å2
Refinement stepCycle: 1 / Resolution: 2.83→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4825 0 19 120 4964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194956
X-RAY DIFFRACTIONr_bond_other_d0.0030.024793
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.9796717
X-RAY DIFFRACTIONr_angle_other_deg1.2243.00111007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2535618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.96122.464207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07115809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9861544
X-RAY DIFFRACTIONr_chiral_restr0.0850.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215523
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021113
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_it4.1635.7072491
X-RAY DIFFRACTIONr_mcbond_other4.1595.7062490
X-RAY DIFFRACTIONr_mcangle_it6.6748.5323102
X-RAY DIFFRACTIONr_mcangle_other6.6748.5343103
X-RAY DIFFRACTIONr_scbond_it4.5876.2122465
X-RAY DIFFRACTIONr_scbond_other4.5886.2142462
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1829.1233610
X-RAY DIFFRACTIONr_long_range_B_refined11.04944.6665357
X-RAY DIFFRACTIONr_long_range_B_other11.03244.6695356
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.833→2.906 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.72 5 -
Rwork0.272 795 -
obs--56.78 %

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