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- PDB-7aak: Human porphobilinogen deaminase R173W mutant crystallized in the ... -

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Basic information

Entry
Database: PDB / ID: 7aak
TitleHuman porphobilinogen deaminase R173W mutant crystallized in the ES2 intermediate state
ComponentsPorphobilinogen deaminase
KeywordsTRANSFERASE / PBG-D / Hydroxymethylbilane synthase / HMBS / Porphobilinogen deaminase / heme biosynthesis / porphyria / acute intermittent porphyria / ES2 / reaction intermediate
Function / homology
Function and homology information


hydroxymethylbilane synthase / hydroxymethylbilane synthase activity / heme O biosynthetic process / heme B biosynthetic process / heme A biosynthetic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process / cytosol / cytoplasm
Similarity search - Function
Porphobilinogen deaminase / Porphobilinogen deaminase, N-terminal / Porphobilinogen deaminase, C-terminal / Porphobilinogen deaminase, dipyrromethane cofactor binding site / Porphobilinogen deaminase, C-terminal domain superfamily / Porphobilinogen deaminase, dipyromethane cofactor binding domain / Porphobilinogen deaminase, C-terminal domain / Porphobilinogen deaminase cofactor-binding site.
Similarity search - Domain/homology
Chem-7J8 / Porphobilinogen deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKallio, J.P. / Bustad, H.J. / Martinez, A.
Citation
Journal: Iscience / Year: 2021
Title: Characterization of porphobilinogen deaminase mutants reveals that arginine-173 is crucial for polypyrrole elongation mechanism.
Authors: Bustad, H.J. / Kallio, J.P. / Laitaoja, M. / Toska, K. / Kursula, I. / Martinez, A. / Janis, J.
#1: Journal: Iscience / Year: 2021
Title: Structural characterization of hydroxymethylbilane synthase mutants associated with acute intermittent porphyria reveals that Arg173 is crucial for the elongation mechanism
Authors: Bustad, H.J. / Kallio, J.P. / Laitaoja, M. / Toska, K. / Kursula, I. / Martinez, A. / Janis, J.
History
DepositionSep 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 1, 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
A: Porphobilinogen deaminase
B: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1588
Polymers79,1122
Non-polymers2,0466
Water9,098505
1
A: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5794
Polymers39,5561
Non-polymers1,0233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5794
Polymers39,5561
Non-polymers1,0233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.241, 86.127, 107.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Porphobilinogen deaminase / PBG-D / Hydroxymethylbilane synthase / HMBS / Pre-uroporphyrinogen synthase


Mass: 39556.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: -amino acids 1-2 (GS) in the sample sequence derive from expression tag and biological sequence starts from 3 -Ligand is covalently bound to Cys261
Source: (gene. exp.) Homo sapiens (human) / Gene: HMBS, PBGD, UPS / Production host: Escherichia coli (E. coli) / References: UniProt: P08397, hydroxymethylbilane synthase
#2: Chemical ChemComp-7J8 / 3-[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-3-(3-hydroxy-3-oxopropyl)-5-methyl-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-1~{H}-pyrrol-3-yl]propanoic acid


Mass: 838.810 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H46N4O16 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1 / Details: polyethylene glycol 3350, ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.7→59.1 Å / Num. obs: 83105 / % possible obs: 99.47 % / Redundancy: 6.6 % / Biso Wilson estimate: 25.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.074 / Net I/σ(I): 15.48
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.56 / Mean I/σ(I) obs: 1.62 / Num. unique obs: 8199 / CC1/2: 0.73 / Rrim(I) all: 1.69

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASER1.17.1_3660phasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292107576

Resolution: 1.7→59.1 Å / SU ML: 0.2318 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5378
RfactorNum. reflection% reflection
Rfree0.2128 4022 4.85 %
Rwork0.1827 --
obs0.1841 82992 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.82 Å2
Refinement stepCycle: LAST / Resolution: 1.7→59.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5169 0 144 505 5818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00665515
X-RAY DIFFRACTIONf_angle_d0.88087486
X-RAY DIFFRACTIONf_chiral_restr0.0578842
X-RAY DIFFRACTIONf_plane_restr0.0053979
X-RAY DIFFRACTIONf_dihedral_angle_d23.98962126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.35911370.35822712X-RAY DIFFRACTION99.55
1.72-1.740.35451430.33992645X-RAY DIFFRACTION99.01
1.74-1.760.34141330.33242699X-RAY DIFFRACTION99.06
1.76-1.790.39451340.3332645X-RAY DIFFRACTION98.97
1.79-1.810.30951430.30212684X-RAY DIFFRACTION98.74
1.81-1.840.29361280.26422727X-RAY DIFFRACTION99.72
1.84-1.860.30491450.25582641X-RAY DIFFRACTION98.9
1.86-1.890.31651390.242659X-RAY DIFFRACTION98.52
1.89-1.920.26531620.2312698X-RAY DIFFRACTION99.44
1.92-1.960.26531300.2192706X-RAY DIFFRACTION99.61
1.96-1.990.26551230.21572710X-RAY DIFFRACTION99.65
1.99-2.030.28231400.2112714X-RAY DIFFRACTION99.72
2.03-2.070.22711430.20672712X-RAY DIFFRACTION99.69
2.07-2.120.23551440.20352691X-RAY DIFFRACTION99.72
2.12-2.170.22111420.19282708X-RAY DIFFRACTION99.62
2.17-2.220.24461280.1812715X-RAY DIFFRACTION99.61
2.22-2.280.19981380.17682720X-RAY DIFFRACTION99.41
2.28-2.350.19531220.1892743X-RAY DIFFRACTION99.83
2.35-2.420.22381370.18832713X-RAY DIFFRACTION99.79
2.42-2.510.1971470.18052696X-RAY DIFFRACTION99.23
2.51-2.610.19981640.1772725X-RAY DIFFRACTION99.55
2.61-2.730.19131210.17362729X-RAY DIFFRACTION99.65
2.73-2.870.20581360.1772756X-RAY DIFFRACTION99.76
2.87-3.050.22751420.17162750X-RAY DIFFRACTION99.9
3.05-3.290.19731520.17052754X-RAY DIFFRACTION99.83
3.29-3.620.19061270.16362780X-RAY DIFFRACTION99.73
3.62-4.140.17491550.14572767X-RAY DIFFRACTION99.62
4.15-5.220.15871310.14022807X-RAY DIFFRACTION99.09
5.22-59.10.2071360.17862964X-RAY DIFFRACTION99.58
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)
12.40510832740.3328756048710.130581913210.300422794051-0.04996307168341.4289087975-0.0102639599694-0.0350706664724-0.07688385732530.009643499354610.00564009391778-0.009839156800830.1075559632940.008367085850620.0008324925170240.1792292238170.01649444985920.009331095703520.0803160010454-0.007821160288390.15566187695994.256839581135.73426848825.61894203764
21.739219956190.110371751098-0.3932551833440.593088140682-0.06433620618272.28246442427-0.0376135739854-0.106308885009-0.1298979370215.54159433005E-5-0.0686530727322-0.1210385395320.2161330573130.3071718749650.08964923499310.1810361925850.03678329524390.02891831578340.1677235291280.05483993686090.21022512620793.865926530575.924175499618.2783016857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 17 through 361)
2X-RAY DIFFRACTION2(chain 'B' and resid 18 through 358)

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