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- PDB-5qr1: PanDDA analysis group deposition -- Crystal Structure of human AL... -

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Basic information

Entry
Database: PDB / ID: 5qr1
TitlePanDDA analysis group deposition -- Crystal Structure of human ALAS2A in complex with Z396380540
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-HR5 / 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: 1.44 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)105,2035
Polymers104,5012
Non-polymers7023
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-66 kcal/mol
Surface area27730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.757, 108.412, 75.740
Angle α, β, γ (deg.)90.000, 109.110, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-380-

HIS

21A-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-HR5 / ~{N}-(cyclobutylmethyl)-1,5-dimethyl-pyrazole-4-carboxamide


Mass: 207.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N3O / 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: 2.33 Å3/Da / Density % sol: 47.31 %
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 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.442→80.088 Å / Num. obs: 110686 / % possible obs: 95.1 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rpim(I) all: 0.027 / Rrim(I) all: 0.05 / Net I/σ(I): 14 / Num. measured all: 372666
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.442-1.62631653355350.7520.3390.6061.870.2
4.56-80.0883.41906655340.9990.0120.02246.299.5

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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: 1.44→80.09 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.793 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 5394 4.9 %RANDOM
Rwork0.2099 ---
obs0.211 105299 63.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.22 Å2 / Biso mean: 20.417 Å2 / Biso min: 8.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å20.01 Å2
2---0.02 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 1.44→80.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6605 0 47 252 6904
Biso mean--24.65 24.61 -
Num. residues----857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137603
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176515
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.6349962
X-RAY DIFFRACTIONr_angle_other_deg1.4271.56815072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7475926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.54821.372379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.051151134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.21544
X-RAY DIFFRACTIONr_chiral_restr0.0850.2906
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028461
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021687
X-RAY DIFFRACTIONr_mcbond_it1.7172.0473722
X-RAY DIFFRACTIONr_mcbond_other1.7172.0463717
X-RAY DIFFRACTIONr_mcangle_it2.4963.0564570
LS refinement shellResolution: 1.438→1.475 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 8 -
Rwork0.33 243 -
all-251 -
obs--1.96 %

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