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- PDB-5m7f: Human porphobilinogen deaminase in complex with DPM cofactor -

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Basic information

Entry
Database: PDB / ID: 5m7f
TitleHuman porphobilinogen deaminase in complex with DPM cofactor
ComponentsPorphobilinogen deaminase
KeywordsTRANSFERASE / Porphobilinogen deaminase / heme biosynthesis / porphyria / HMBS
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, 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: 2.78 Å
AuthorsPluta, P. / Millet, O. / Roversi, P. / Rojas, A.L. / Gu, S.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spain
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2018
Title: Structural basis of pyrrole polymerization in human porphobilinogen deaminase.
Authors: Pluta, P. / Roversi, P. / Bernardo-Seisdedos, G. / Rojas, A.L. / Cooper, J.B. / Gu, S. / Pickersgill, R.W. / Millet, O.
History
DepositionOct 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 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)81,98710
Polymers80,5702
Non-polymers1,4178
Water88349
1
A: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9945
Polymers40,2851
Non-polymers7094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9945
Polymers40,2851
Non-polymers7094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.420, 80.950, 76.220
Angle α, β, γ (deg.)90.00, 95.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 40285.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.79 Å3/Da / Density % sol: 56 % / Description: Plates
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 0.2 M sodium chloride, 2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972422 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972422 Å / Relative weight: 1
ReflectionResolution: 2.78→80.95 Å / Num. obs: 21353 / % possible obs: 98.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 39.43 Å2 / CC1/2: 0.946 / Rmerge(I) obs: 0.247 / Net I/σ(I): 3.1
Reflection shellResolution: 2.78→2.83 Å / Redundancy: 2.6 % / Rmerge(I) obs: 1.265 / Mean I/σ(I) obs: 0.9 / CC1/2: 0.477 / % possible all: 83.1

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSVERSION May 1, 2016data reduction
Aimlessversion 0.5.23data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ecr

3ecr


Resolution: 2.78→29.77 Å / Cor.coef. Fo:Fc: 0.856 / Cor.coef. Fo:Fc free: 0.848 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.986 / SU Rfree Blow DPI: 0.34
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1112 5.23 %RANDOM
Rwork0.22 ---
obs0.222 21279 98.5 %-
Displacement parametersBiso mean: 45.78 Å2
Baniso -1Baniso -2Baniso -3
1--6.3483 Å20 Å2-19.3686 Å2
2--21.049 Å20 Å2
3----14.7008 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: 1 / Resolution: 2.78→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4878 0 90 51 5019
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110067HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1618272HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2250SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes126HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1533HARMONIC5
X-RAY DIFFRACTIONt_it10067HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion16.4
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion653SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11301SEMIHARMONIC4
LS refinement shellResolution: 2.78→2.92 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.301 112 4.27 %
Rwork0.25 2509 -
all0.252 2621 -
obs--91.77 %
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)
11.43680.4354-1.10942.2999-0.05272.28950.14410.11250.14690.09890.0290.1859-0.2125-0.1479-0.17310.00670.08340.1916-0.09970.0284-0.00691.4876-0.8724.3874
21.76540.3031-1.00073.7019-0.08751.5846-0.0764-0.0929-0.2129-0.03830.0599-0.3085-0.07390.16070.0164-0.0630.00060.1441-0.05550.01930.0284-20.914214.2536-2.4437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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