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- PDB-4mlq: Crystal structure of Bacillus megaterium porphobilinogen deaminase -

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Basic information

Entry
Database: PDB / ID: 4mlq
TitleCrystal structure of Bacillus megaterium porphobilinogen deaminase
ComponentsPorphobilinogen deaminase
KeywordsTRANSFERASE / tetrapyrrole biosynthesis / porphobilinogen deaminase / dipyrromethane cofactor / three-domain fold / domains 1 and 2 resemble the fold of type II periplasmic binding proteins / pyrrole polymerisation
Function / homology
Function and homology information


hydroxymethylbilane synthase / hydroxymethylbilane synthase activity / protoporphyrinogen IX 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-29P / ACETIC ACID / Chem-DPM / Porphobilinogen deaminase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAzim, N. / Deery, E. / Warren, M.J. / Erskine, P. / Cooper, J.B. / Coker, A. / Wood, S.P. / Akhtar, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution.
Authors: Azim, N. / Deery, E. / Warren, M.J. / Wolfenden, B.A. / Erskine, P. / Cooper, J.B. / Coker, A. / Wood, S.P. / Akhtar, M.
History
DepositionSep 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Porphobilinogen deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4304
Polymers34,5131
Non-polymers9173
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.010, 65.120, 96.780
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 / Pre-uroporphyrinogen synthase


Mass: 34512.770 Da / Num. of mol.: 1 / Fragment: porphobilinogen deaminase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: hemC / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / 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: Chemical ChemComp-29P / 3-[(5S)-5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-2-oxo-2,5-dihydro-1H-pyrrol-3-yl]propanoic acid / Dipyrromethanone


Mass: 436.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N2O9
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium cacodylate, 0.2M magnesium acetate, 25-30% PEG 8K, pH 6.5 - 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
PH range: 6.5 - 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.072 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 3, 2013
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.6→31.33 Å / Num. all: 42866 / Num. obs: 42866 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.493 / Mean I/σ(I) obs: 0.9 / % possible all: 88.7

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→31.33 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.939 / SU ML: 0.086 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24215 2176 5.1 %RANDOM
Rwork0.16061 ---
obs0.16462 40552 95.05 %-
all-42728 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.019 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0 Å20 Å2
2--0.47 Å2-0 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2245 0 65 249 2559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192350
X-RAY DIFFRACTIONr_bond_other_d0.0040.022325
X-RAY DIFFRACTIONr_angle_refined_deg2.1422.0133160
X-RAY DIFFRACTIONr_angle_other_deg1.5263.0065378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.185287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53924.5100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.115453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.71519
X-RAY DIFFRACTIONr_chiral_restr0.1210.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212598
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02468
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.8392.3551155
X-RAY DIFFRACTIONr_mcbond_other5.8282.3491153
X-RAY DIFFRACTIONr_mcangle_it6.9473.5511439
X-RAY DIFFRACTIONr_mcangle_other6.9683.5541440
X-RAY DIFFRACTIONr_scbond_it7.8742.9661195
X-RAY DIFFRACTIONr_scbond_other7.8712.9681193
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.6484.2461721
X-RAY DIFFRACTIONr_long_range_B_refined8.56320.5062738
X-RAY DIFFRACTIONr_long_range_B_other8.5620.5042738
X-RAY DIFFRACTIONr_rigid_bond_restr5.22434675
X-RAY DIFFRACTIONr_sphericity_free39.0635105
X-RAY DIFFRACTIONr_sphericity_bonded19.97654790
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 150 -
Rwork0.38 2615 -
obs--84.53 %

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