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- PDB-3ecr: Structure of human porphobilinogen deaminase -

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Basic information

Entry
Database: PDB / ID: 3ecr
TitleStructure of human porphobilinogen deaminase
ComponentsPorphobilinogen deaminase
KeywordsTRANSFERASE / human porphobilinogen deaminase / heme biosynthesis / porphobilinogen hinge / Alternative splicing / Cytoplasm / Disease mutation / Porphyrin biosynthesis
Function / homology
Function and homology information


hydroxymethylbilane synthase / hydroxymethylbilane synthase activity / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process / cytosol / cytoplasm
Similarity search - Function
Porphobilinogen deaminase, C-terminal domain / 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. / Double Stranded RNA Binding Domain ...Porphobilinogen deaminase, C-terminal domain / 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. / Double Stranded RNA Binding Domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DPM / Porphobilinogen deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.182 Å
AuthorsSong, G. / Li, Y. / Cheng, C. / Zhao, Y. / Gao, A. / Zhang, R. / Joachimiak, A. / Shaw, N. / Liu, Z.J.
CitationJournal: Faseb J. / Year: 2009
Title: Structural insight into acute intermittent porphyria.
Authors: Song, G. / Li, Y. / Cheng, C. / Zhao, Y. / Gao, A. / Zhang, R. / Joachimiak, A. / Shaw, N. / Liu, Z.J.
History
DepositionSep 1, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,1514
Polymers79,3112
Non-polymers8412
Water2,468137
1
A: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0762
Polymers39,6551
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0762
Polymers39,6551
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.610, 81.061, 109.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111A
211B

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Components

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


Mass: 39655.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMBS, PBGD, UPS / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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 Å3/Da / Density % sol: 38.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.15M ammonium citrate dibasic, 22%(w/v) PEG3350, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.5798 Å
DetectorDetector: CCD / Date: May 12, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5798 Å / Relative weight: 1
ReflectionResolution: 2.182→50 Å / Num. all: 33389 / Num. obs: 29683 / % possible obs: 88.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.2→2.24 Å / % possible all: 55.5

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Processing

Software
NameClassification
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.182→38.276 Å / SU ML: 0.37 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2714 1500 5.07 %RANDOM
Rwork0.2317 ---
obs0.2337 29562 87.57 %-
all-33389 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.48 Å2 / ksol: 0.393 e/Å3
Refinement stepCycle: LAST / Resolution: 2.182→38.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 60 137 4970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014922
X-RAY DIFFRACTIONf_angle_d1.3096671
X-RAY DIFFRACTIONf_dihedral_angle_d17.4071851
X-RAY DIFFRACTIONf_chiral_restr0.078780
X-RAY DIFFRACTIONf_plane_restr0.005858
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2168X-RAY DIFFRACTIONPOSITIONAL
12B2168X-RAY DIFFRACTIONPOSITIONAL0.085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1825-2.25290.2837600.251229X-RAY DIFFRACTION47
2.2529-2.33340.2951050.23881794X-RAY DIFFRACTION64
2.3334-2.42680.34081050.24482130X-RAY DIFFRACTION74
2.4268-2.53730.31931350.25042537X-RAY DIFFRACTION88
2.5373-2.6710.28841500.24272778X-RAY DIFFRACTION97
2.671-2.83830.31471650.24462890X-RAY DIFFRACTION100
2.8383-3.05740.28081500.24532885X-RAY DIFFRACTION100
3.0574-3.36490.3041500.23752913X-RAY DIFFRACTION100
3.3649-3.85140.28981590.24022902X-RAY DIFFRACTION99
3.8514-4.85080.21541560.20572918X-RAY DIFFRACTION99
4.8508-38.28190.23241650.21543086X-RAY DIFFRACTION100

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