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- PDB-7aaj: Human porphobilinogen deaminase in complex with cofactor -

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Basic information

Entry
Database: PDB / ID: 7aaj
TitleHuman porphobilinogen deaminase in complex with cofactor
ComponentsPorphobilinogen deaminase
KeywordsTRANSFERASE / PBG-D / Hydroxymethylbilane synthase / HMBS / Porphobilinogen deaminase / heme biosynthesis / porphyria / acute intermittent porphyria
Function / homology
Function and homology information


hydroxymethylbilane synthase / hydroxymethylbilane synthase activity / heme O biosynthetic process / heme A biosynthetic process / heme B biosynthetic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process / cytoplasm / cytosol
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-DPM / Porphobilinogen deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.2Jan 31, 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

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Assembly

Deposited unit
B: Porphobilinogen deaminase
A: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1717
Polymers79,0542
Non-polymers1,1175
Water2,846158
1
B: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0403
Polymers39,5271
Non-polymers5132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1324
Polymers39,5271
Non-polymers6053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.163, 84.608, 108.913
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: 39527.141 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-DPM / 3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid / DIPYRROMETHANE COFACTOR


Mass: 420.413 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N2O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 25% polyethylene glycol 3350, 200 mM 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: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→65.08 Å / Num. obs: 69757 / % possible obs: 98.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 34.18 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.102 / Net I/σ(I): 10.24
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 7.7 % / Rmerge(I) obs: 3.763 / Mean I/σ(I) obs: 0.52 / Num. unique obs: 6877 / CC1/2: 0.54 / Rrim(I) all: 4.028

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Processing

Software
NameVersionClassification
XDSdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ECR

3ecr


Resolution: 1.8→65.08 Å / SU ML: 0.3198 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 44.5429
RfactorNum. reflection% reflection
Rfree0.2944 3510 5.06 %
Rwork0.249 --
obs0.2512 69335 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.76 Å2
Refinement stepCycle: LAST / Resolution: 1.8→65.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5000 0 78 158 5236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00695161
X-RAY DIFFRACTIONf_angle_d0.82616981
X-RAY DIFFRACTIONf_chiral_restr0.0533801
X-RAY DIFFRACTIONf_plane_restr0.0052909
X-RAY DIFFRACTIONf_dihedral_angle_d21.91821950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.67541270.66792516X-RAY DIFFRACTION96.25
1.82-1.850.64341030.6072625X-RAY DIFFRACTION97.74
1.85-1.880.60911170.56482607X-RAY DIFFRACTION98.34
1.88-1.910.53531180.53132612X-RAY DIFFRACTION98.98
1.91-1.940.49611400.49752596X-RAY DIFFRACTION98.52
1.94-1.970.49941510.48312620X-RAY DIFFRACTION98.68
1.97-2.010.47181560.4532545X-RAY DIFFRACTION99.05
2.01-2.050.51371350.42892610X-RAY DIFFRACTION98.95
2.05-2.090.46851350.39962633X-RAY DIFFRACTION98.86
2.09-2.130.39721420.36142612X-RAY DIFFRACTION98.67
2.13-2.180.35711400.34242584X-RAY DIFFRACTION98.62
2.18-2.240.35371350.31872610X-RAY DIFFRACTION98.95
2.24-2.30.35731360.29442617X-RAY DIFFRACTION98.46
2.3-2.370.31381650.28342589X-RAY DIFFRACTION99.21
2.37-2.440.30281670.25172583X-RAY DIFFRACTION98.28
2.44-2.530.32351530.24162600X-RAY DIFFRACTION98.43
2.53-2.630.28451660.24222618X-RAY DIFFRACTION99.15
2.63-2.750.30191540.23572615X-RAY DIFFRACTION99.25
2.75-2.90.31641730.23912646X-RAY DIFFRACTION99.79
2.9-3.080.2881340.23642670X-RAY DIFFRACTION99.61
3.08-3.320.3411150.22332703X-RAY DIFFRACTION99.65
3.32-3.650.29291550.21752673X-RAY DIFFRACTION99.65
3.65-4.180.21931300.19162736X-RAY DIFFRACTION99.9
4.18-5.260.19671450.17542714X-RAY DIFFRACTION99.34
5.26-65.080.20181180.18422891X-RAY DIFFRACTION99.37

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