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- PDB-5qr2: PanDDA analysis group deposition -- Crystal Structure of human AL... -

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Basic information

Entry
Database: PDB / ID: 5qr2
TitlePanDDA analysis group deposition -- Crystal Structure of human ALAS2A in complex with Z1348371854
Components5-aminolevulinate synthase, erythroid-specific, mitochondrialAminolevulinic acid synthase
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 / erythrocyte development / heme biosynthetic process / erythrocyte differentiation / pyridoxal phosphate binding ...5-aminolevulinate synthase / 5-aminolevulinate synthase activity / hemoglobin biosynthetic process / intracellular oxygen homeostasis / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / erythrocyte development / heme biosynthetic process / erythrocyte differentiation / pyridoxal phosphate binding / mitochondrial inner membrane / intracellular iron ion homeostasis / 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
5-(1,4-oxazepan-4-yl)pyridine-2-carbonitrile / 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: 1.66 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)105,1995
Polymers104,5012
Non-polymers6983
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10940 Å2
ΔGint-63 kcal/mol
Surface area27820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.522, 108.137, 75.521
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

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Components

#1: Protein 5-aminolevulinate synthase, erythroid-specific, mitochondrial / Aminolevulinic acid synthase / 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 / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-NTG / 5-(1,4-oxazepan-4-yl)pyridine-2-carbonitrile


Mass: 203.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.32 Å3/Da / Density % sol: 46.92 %
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: 1.662→79.91 Å / Num. obs: 70623 / % possible obs: 91.1 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rpim(I) all: 0.05 / Rrim(I) all: 0.093 / Net I/σ(I): 9.6 / Num. measured all: 242960
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Num. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.662-1.8461202635310.6210.4590.8561.573.7
5.29-79.911198135300.9990.0190.03628.899.3

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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: 1.66→79.91 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.097 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 3449 4.9 %RANDOM
Rwork0.2052 ---
obs0.2065 67174 63.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.56 Å2 / Biso mean: 20.945 Å2 / Biso min: 5.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.01 Å2
2--0.02 Å20 Å2
3----0.17 Å2
Refinement stepCycle: final / Resolution: 1.66→79.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6605 0 47 248 6900
Biso mean--37.5 23.84 -
Num. residues----857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137379
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176423
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.6339751
X-RAY DIFFRACTIONr_angle_other_deg1.3731.56814855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5885905
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.45421.386368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.834151116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8111544
X-RAY DIFFRACTIONr_chiral_restr0.0760.2894
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028242
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021650
X-RAY DIFFRACTIONr_mcbond_it1.5722.1013629
X-RAY DIFFRACTIONr_mcbond_other1.5722.1013628
X-RAY DIFFRACTIONr_mcangle_it2.4173.1354483
LS refinement shellResolution: 1.662→1.705 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 11 -
Rwork0.286 211 -
all-222 -
obs--2.7 %

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