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- PDB-3eq1: The Crystal Structure of Human Porphobilinogen Deaminase at 2.8A ... -

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Basic information

Entry
Database: PDB / ID: 3eq1
TitleThe Crystal Structure of Human Porphobilinogen Deaminase at 2.8A resolution
ComponentsPorphobilinogen deaminase
KeywordsTRANSFERASE / ALPHA AND BETA PROTEIN / Alternative splicing / Cytoplasm / Disease mutation / Heme biosynthesis / 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: 2.8 Å
AuthorsKolstoe, S.E. / Gill, R. / Mohammed, F. / Wood, S.P.
CitationJournal: Biochem.J. / Year: 2009
Title: Structure of human porphobilinogen deaminase at 2.8 A: the molecular basis of acute intermittent porphyria
Authors: Gill, R. / Kolstoe, S.E. / Mohammed, F. / Al D-Bass, A. / Mosely, J.E. / Sarwar, M. / Cooper, J.B. / Wood, S.P. / Shoolingin-Jordan, P.M.
History
DepositionSep 30, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)80,22111
Polymers78,7082
Non-polymers1,5139
Water0
1
A: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0635
Polymers39,3541
Non-polymers7094
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1596
Polymers39,3541
Non-polymers8055
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.083, 104.435, 109.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 20:55 or resseq 88:299 or resseq 312:355 )
21chain B and (resseq 20:55 or resseq 88:299 or resseq...
12chain A 400
22chain B 401

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALALAALAAA20 - 5520 - 55
121ASNASNILEILEAA88 - 29988 - 299
131ASPASPARGARGAA312 - 355312 - 355
211VALVALALAALABB20 - 5520 - 55
221ASNASNILEILEBB88 - 29988 - 299
231ASPASPARGARGBB312 - 355312 - 355
241VALVALALAALABB20 - 5520 - 55
251ASNASNILEILEBB88 - 29988 - 299
261ASPASPARGARGBB312 - 355312 - 355
112DPMDPMDPMDPMAC400
212DPMDPMDPMDPMBG401

NCS ensembles :
ID
1
2

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Components

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


Mass: 39353.945 Da / Num. of mol.: 2 / Fragment: UNP residues 19-356 / Mutation: R167Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4

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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: 3.14 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.6M ammonium sulphate, 1.2M lithium sulphate, 5% (v/v) ethylene glycol, 50mM sodium citrate, 50mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→46.8 Å / Num. obs: 25917 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 11.9
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.657 / % possible all: 96.6

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Processing

Software
NameClassification
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PDA

1pda


Resolution: 2.8→43.901 Å / FOM work R set: 0.695 / SU ML: 0.45 / σ(F): 1.35 / Phase error: 35.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.289 1711 7.72 %
Rwork0.2592 --
obs0.2615 22175 94.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.596 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso max: 1 Å2 / Biso mean: 64.176 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--35.621 Å20 Å2-0 Å2
2--60.932 Å20 Å2
3----25.311 Å2
Refinement stepCycle: LAST / Resolution: 2.8→43.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 95 0 4925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034998
X-RAY DIFFRACTIONf_angle_d0.6586768
X-RAY DIFFRACTIONf_chiral_restr0.044776
X-RAY DIFFRACTIONf_plane_restr0.002876
X-RAY DIFFRACTIONf_dihedral_angle_d14.8791860
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2241X-RAY DIFFRACTIONPOSITIONAL
12B2241X-RAY DIFFRACTIONPOSITIONAL0.019
21A30X-RAY DIFFRACTIONPOSITIONAL
22B30X-RAY DIFFRACTIONPOSITIONAL0.014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.88250.41831370.35391701X-RAY DIFFRACTION96
2.8825-2.97550.38221510.3381694X-RAY DIFFRACTION95
2.9755-3.08180.37151390.31121723X-RAY DIFFRACTION96
3.0818-3.20520.38281460.29931684X-RAY DIFFRACTION95
3.2052-3.3510.34011390.29351708X-RAY DIFFRACTION95
3.351-3.52760.31361370.27481704X-RAY DIFFRACTION94
3.5276-3.74850.27851370.2461706X-RAY DIFFRACTION95
3.7485-4.03780.271440.23931703X-RAY DIFFRACTION94
4.0378-4.44380.22731450.21471703X-RAY DIFFRACTION94
4.4438-5.0860.23111450.20371708X-RAY DIFFRACTION93
5.086-6.40460.25641410.24531707X-RAY DIFFRACTION92
6.4046-43.90680.2691500.2331723X-RAY DIFFRACTION88

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