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- PDB-5qra: PanDDA analysis group deposition -- Crystal Structure of human AL... -

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Basic information

Entry
Database: PDB / ID: 5qra
TitlePanDDA analysis group deposition -- Crystal Structure of human ALAS2A in complex with Z1101755952
Components5-aminolevulinate synthase, erythroid-specific, mitochondrial
KeywordsTRANSFERASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


5-aminolevulinate synthase / 5-aminolevulinate synthase activity / hemoglobin biosynthetic process / intracellular oxygen homeostasis / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process / erythrocyte development / erythrocyte differentiation / pyridoxal phosphate binding ...5-aminolevulinate synthase / 5-aminolevulinate synthase activity / hemoglobin biosynthetic process / intracellular oxygen homeostasis / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process / erythrocyte development / erythrocyte differentiation / pyridoxal phosphate binding / intracellular iron ion homeostasis / mitochondrial inner membrane / response to hypoxia / mitochondrial matrix / mitochondrion
Similarity search - Function
5-aminolevulinate synthase presequence / 5-aminolevulinate synthase presequence / 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-NVM / PYRIDOXAL-5'-PHOSPHATE / 5-aminolevulinate synthase, erythroid-specific, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.72 Å
AuthorsBezerra, G.A. / Foster, W. / Bailey, H. / Shrestha, L. / Krojer, T. / Talon, R. / Brandao-Neto, J. / Douangamath, A. / Nicola, B.B. / von Delft, F. ...Bezerra, G.A. / Foster, W. / Bailey, H. / Shrestha, L. / Krojer, T. / Talon, R. / Brandao-Neto, J. / Douangamath, A. / Nicola, B.B. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Brennan, P.E. / Yue, W.W.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Bezerra, G.A. / Foster, W. / Bailey, H. / Shrestha, L. / Krojer, T. / Talon, R. / Brandao-Neto, J. / Douangamath, A. / Nicola, B.B. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / ...Authors: Bezerra, G.A. / Foster, W. / Bailey, H. / Shrestha, L. / Krojer, T. / Talon, R. / Brandao-Neto, J. / Douangamath, A. / Nicola, B.B. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Brennan, P.E. / Yue, W.W.
History
DepositionMay 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: 5-aminolevulinate synthase, erythroid-specific, mitochondrial
A: 5-aminolevulinate synthase, erythroid-specific, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2185
Polymers104,5012
Non-polymers7173
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-65 kcal/mol
Surface area27700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.849, 108.395, 75.745
Angle α, β, γ (deg.)90.000, 109.010, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-380-

HIS

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Components

#1: Protein 5-aminolevulinate synthase, erythroid-specific, mitochondrial / ALAS-E / 5-aminolevulinic acid synthase 2 / Delta-ALA synthase 2 / Delta-aminolevulinate synthase 2


Mass: 52250.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALAS2, ALASE, ASB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P22557, 5-aminolevulinate synthase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-NVM / [(4R)-4-methyl-2,3,4,5-tetrahydro-1H-azepin-1-yl](1,3-thiazol-4-yl)methanone


Mass: 222.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N2OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 47.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.2 M magnesium chloride, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.726→60.381 Å / Num. obs: 67094 / % possible obs: 93.8 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rpim(I) all: 0.057 / Rrim(I) all: 0.106 / Net I/σ(I): 9.3 / Num. measured all: 226333
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.726-1.9483.11028233560.5660.4850.8771.661.8
5.397-60.3813.31120933550.9990.0190.0362899.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimlessdata scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6hrh

6hrh


Resolution: 1.72→60.45 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.627 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3244 4.8 %RANDOM
Rwork0.2055 ---
obs0.2071 63853 66.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.09 Å2 / Biso mean: 23.837 Å2 / Biso min: 7.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å2-0 Å20.01 Å2
2---0 Å2-0 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 1.72→60.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6605 0 47 252 6904
Biso mean--31.82 26.03 -
Num. residues----857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137606
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176513
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.6359966
X-RAY DIFFRACTIONr_angle_other_deg1.3351.56815076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7815929
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.80121.312381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.103151134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7851544
X-RAY DIFFRACTIONr_chiral_restr0.0720.2908
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028485
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021693
X-RAY DIFFRACTIONr_mcbond_it1.6762.4543725
X-RAY DIFFRACTIONr_mcbond_other1.6772.4543720
X-RAY DIFFRACTIONr_mcangle_it2.5853.6634579
LS refinement shellResolution: 1.724→1.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 10 -
Rwork0.309 130 -
all-140 -
obs--1.87 %

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