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- PDB-6hrh: Structure of human erythroid-specific 5'-aminolevulinate synthase... -

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Basic information

Entry
Database: PDB / ID: 6hrh
TitleStructure of human erythroid-specific 5'-aminolevulinate synthase, ALAS2
Components5-aminolevulinate synthase, erythroid-specific, mitochondrial
KeywordsOXIDOREDUCTASE / 5-aminolevulinate synthase / erythroid-specific / Mitochondrial / Structural Genomics / Structural Genomics Consortium / SGC
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
PYRIDOXAL-5'-PHOSPHATE / 5-aminolevulinate synthase, erythroid-specific, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsBailey, H.J. / Shrestha, L. / Rembeza, E. / Newman, J. / Kupinska, K. / Diaz-saez, L. / Kennedy, E. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. ...Bailey, H.J. / Shrestha, L. / Rembeza, E. / Newman, J. / Kupinska, K. / Diaz-saez, L. / Kennedy, E. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Structure of human erythroid-specific 5'-aminolevulinate synthase, ALAS2
Authors: Bailey, H.J. / Shrestha, L. / Rembeza, E. / Newman, J. / Kupinska, K. / Diaz-saez, L. / Kennedy, E. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W.
History
DepositionSep 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
B: 5-aminolevulinate synthase, erythroid-specific, mitochondrial
A: 5-aminolevulinate synthase, erythroid-specific, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9954
Polymers104,5012
Non-polymers4942
Water4,468248
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10920 Å2
ΔGint-64 kcal/mol
Surface area27970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.771, 107.703, 75.713
Angle α, β, γ (deg.)90.000, 109.050, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 137 through 145 or (resid 146...
21(chain D and (resid 137 through 146 or (resid 147...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain B and (resid 137 through 145 or (resid 146...B137 - 145
121(chain B and (resid 137 through 145 or (resid 146...B146 - 147
131(chain B and (resid 137 through 145 or (resid 146...B137 - 578
141(chain B and (resid 137 through 145 or (resid 146...B137 - 578
151(chain B and (resid 137 through 145 or (resid 146...B137 - 578
161(chain B and (resid 137 through 145 or (resid 146...B137 - 578
211(chain D and (resid 137 through 146 or (resid 147...D137 - 146
221(chain D and (resid 137 through 146 or (resid 147...D147
231(chain D and (resid 137 through 146 or (resid 147...D1 - 2
241(chain D and (resid 137 through 146 or (resid 147...D1 - 2
251(chain D and (resid 137 through 146 or (resid 147...D1 - 2
261(chain D and (resid 137 through 146 or (resid 147...D1 - 2

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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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: 46.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M bis-tris pH 6.7, 25% PEG3350, 0.3M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→71.53 Å / Num. obs: 40141 / % possible obs: 94.8 % / Redundancy: 2.3 % / Biso Wilson estimate: 43.16 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.088 / Net I/σ(I): 5.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.3-2.362.30.70510.551195
10.29-71.532.30.03119.50.995193.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bwn

2bwn


Resolution: 2.3→71.53 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.88
RfactorNum. reflection% reflection
Rfree0.2338 1995 5.01 %
Rwork0.2132 --
obs0.2142 39817 93.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.48 Å2 / Biso mean: 55.1635 Å2 / Biso min: 21.36 Å2
Refinement stepCycle: final / Resolution: 2.3→71.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6605 0 32 248 6885
Biso mean--61.06 46.89 -
Num. residues----857
Refine LS restraints NCSNumber: 2564 / Rms: 8.946 / Type: TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2975-2.3550.33121480.34542512266089
2.355-2.41870.31241370.32162667280493
2.4187-2.48980.35991570.30772627278491
2.4898-2.57020.28561310.30422709284094
2.5702-2.66210.34891270.29022728285595
2.6621-2.76870.28291400.27192752289295
2.7687-2.89470.31851290.27572735286494
2.8947-3.04730.33211470.26272691283893
3.0473-3.23820.25851470.23172701284895
3.2382-3.48820.26221560.21672770292696
3.4882-3.83920.18721330.19972748288195
3.8392-4.39470.19561660.16232716288294
4.3947-5.53660.19161590.15822726288594
5.5366-71.60120.16451180.17632740285892
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.72090.02270.02771.0533-0.6433.87140.12560.1701-0.0616-0.0483-0.0903-0.11870.33750.52150.06190.36480.0311-0.00780.54510.02420.567648.574-36.125513.2048
22.4083-1.4261-0.77272.49390.35642.57860.17040.11550.4705-0.0694-0.1524-0.4497-0.4980.1696-0.06170.4473-0.0632-0.02040.36730.06670.438636.4804-13.92290.9011
31.56530.75460.12821.25460.56122.9105-0.20030.5460.4593-0.2606-0.07710.5805-0.7452-0.3043-0.02430.46810.0922-0.06160.42350.05020.443717.7617-17.55351.9205
41.3192-0.0854-0.30271.27750.11482.3370.00970.3213-0.2367-0.07380.03140.20860.1033-0.3209-0.0070.3527-0.0095-0.07150.4699-0.03650.406419.3965-34.38360.1214
53.6494-2.0907-1.35265.41023.04858.70990.15160.6832-0.034-1.0487-0.30860.1062-0.2485-0.12740.15290.4397-0.02610.01560.40680.06390.319831.3863-19.7972-13.5936
61.5616-1.28490.07395.2113-1.30762.81390.24990.5255-0.2766-0.7429-0.4387-0.58320.20750.61010.20920.46630.11360.11830.5641-0.00540.493346.4174-35.1269-10.3887
71.6678-0.91550.39254.6287-0.85942.34940.26730.4004-0.0651-0.9861-0.5501-0.76460.18390.60740.23570.51940.11840.11740.63870.06440.431745.7244-32.4321-12.6195
87.1340.26590.99966.92591.25367.6839-0.17080.1214-0.6616-0.2101-0.3864-0.35941.2054-0.43480.7020.46750.0293-0.06690.373-0.00540.496935.2475-46.5122-1.3888
91.34540.42280.72052.74291.19562.6350.04510.111-0.1050.3254-0.08010.3755-0.1269-0.70080.0660.28480.08640.01470.59780.01710.41929.9946-22.798612.1665
101.3894-0.5081-0.17312.5411-0.75832.0692-0.0229-0.07010.0360.3475-0.0433-0.2016-0.19040.02150.0850.3762-0.0286-0.10580.3376-0.0140.316635.3538-23.275719.9484
111.3739-0.3294-0.20071.9721-0.37742.3004-0.1212-0.23320.17820.7461-0.0012-0.3174-0.44170.22820.10010.5228-0.012-0.14630.4202-0.01620.363239.0441-22.164927.0396
122.29471.7795-0.14234.1927-0.04561.9117-0.0197-0.27270.25140.73910.16250.5041-0.5855-0.4047-0.12320.75930.22070.10350.63620.01010.448517.0138-9.610231.5139
134.7617-2.5453-1.33235.82813.11036.8938-0.34920.1963-0.27251.26430.11510.56090.6868-0.62040.28050.7127-0.01820.11310.65020.12520.540916.8488-27.836633.8072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 137 through 176 )B137 - 176
2X-RAY DIFFRACTION2chain 'B' and (resid 177 through 233 )B177 - 233
3X-RAY DIFFRACTION3chain 'B' and (resid 234 through 257 )B234 - 257
4X-RAY DIFFRACTION4chain 'B' and (resid 258 through 424 )B258 - 424
5X-RAY DIFFRACTION5chain 'B' and (resid 425 through 463 )B425 - 463
6X-RAY DIFFRACTION6chain 'B' and (resid 464 through 505 )B464 - 505
7X-RAY DIFFRACTION7chain 'B' and (resid 506 through 543 )B506 - 543
8X-RAY DIFFRACTION8chain 'B' and (resid 544 through 578 )B544 - 578
9X-RAY DIFFRACTION9chain 'D' and (resid 137 through 176 )D137 - 176
10X-RAY DIFFRACTION10chain 'D' and (resid 177 through 315 )D177 - 315
11X-RAY DIFFRACTION11chain 'D' and (resid 316 through 463 )D316 - 463
12X-RAY DIFFRACTION12chain 'D' and (resid 464 through 543 )D464 - 543
13X-RAY DIFFRACTION13chain 'D' and (resid 544 through 578 )D544 - 578

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