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- PDB-5ov5: Bacillus megaterium porphobilinogen deaminase D82E mutant -

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Basic information

Entry
Database: PDB / ID: 5ov5
TitleBacillus megaterium porphobilinogen deaminase D82E mutant
ComponentsPorphobilinogen deaminase
KeywordsTRANSFERASE / Deaminase / mutation / domain movements / cofactor
Function / homology
Function and homology information


hydroxymethylbilane synthase / hydroxymethylbilane synthase activity / heme biosynthetic process / 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 speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsGuo, J. / Erskine, P. / Coker, A.R. / Wood, S.P. / Cooper, J.B.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Structural studies of domain movement in active-site mutants of porphobilinogen deaminase from Bacillus megaterium.
Authors: Guo, J. / Erskine, P. / Coker, A.R. / Wood, S.P. / Cooper, J.B.
History
DepositionAug 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Aug 21, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_Rrim_I_all
Revision 1.4Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8602
Polymers34,4401
Non-polymers4201
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-8 kcal/mol
Surface area13550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.160, 62.700, 91.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 34439.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: hemC / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GCA8, 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.: 1 / Source method: obtained synthetically / Formula: C20H24N2O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 1.97 Å3/Da / Density % sol: 37.46 % / Description: Clusters of thin plates with a yellow colour
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 3.7
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate pH 3.7, 25% PEG 4000
PH range: 3.5-4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.81→91.83 Å / Num. obs: 26586 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 24 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.053 / Net I/σ(I): 20.7
Reflection shellResolution: 1.81→1.86 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1907 / CC1/2: 0.766 / Rrim(I) all: 0.697 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
xia2data scaling
MOLREPphasing
Cootmodel building
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MLV

4mlv


Resolution: 1.81→43.34 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.82
RfactorNum. reflection% reflection
Rfree0.2335 1308 4.93 %
Rwork0.1937 --
obs0.1957 26528 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.81→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 30 172 2461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072329
X-RAY DIFFRACTIONf_angle_d0.9713133
X-RAY DIFFRACTIONf_dihedral_angle_d10.1441441
X-RAY DIFFRACTIONf_chiral_restr0.057352
X-RAY DIFFRACTIONf_plane_restr0.005406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8101-1.88260.26921390.25142744X-RAY DIFFRACTION100
1.8826-1.96830.29261530.23552752X-RAY DIFFRACTION100
1.9683-2.0720.25471480.22142742X-RAY DIFFRACTION100
2.072-2.20180.28211420.21312767X-RAY DIFFRACTION100
2.2018-2.37180.23111300.19812796X-RAY DIFFRACTION100
2.3718-2.61050.21281500.20522794X-RAY DIFFRACTION100
2.6105-2.98820.26131360.2022825X-RAY DIFFRACTION100
2.9882-3.76440.23691680.18482813X-RAY DIFFRACTION100
3.7644-43.35280.20281420.17332987X-RAY DIFFRACTION100

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