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- PDB-4mlv: Crystal Structure of Bacillus megaterium porphobilinogen deaminase -

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Basic information

Entry
Database: PDB / ID: 4mlv
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: 1.455 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
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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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
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.320, 65.780, 97.210
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.: 325 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
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: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.455→48.6 Å / Num. all: 60772 / Num. obs: 60772 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 14.4
Reflection shellResolution: 1.455→1.53 Å / Redundancy: 6 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
MOLREPphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PDA

1pda


Resolution: 1.455→46.75 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.028 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18559 3073 5.1 %RANDOM
Rwork0.14112 ---
obs0.14331 57626 99.98 %-
all-60772 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.972 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.455→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 65 325 2643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0192366
X-RAY DIFFRACTIONr_bond_other_d0.0050.022331
X-RAY DIFFRACTIONr_angle_refined_deg2.4382.0133180
X-RAY DIFFRACTIONr_angle_other_deg2.2083.0065403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3695288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12724.608102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85415460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9851519
X-RAY DIFFRACTIONr_chiral_restr0.1580.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212613
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02469
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_it2.7961.951159
X-RAY DIFFRACTIONr_mcbond_other2.7341.9431157
X-RAY DIFFRACTIONr_mcangle_it3.3252.9191444
X-RAY DIFFRACTIONr_mcangle_other3.3312.9261445
X-RAY DIFFRACTIONr_scbond_it5.6852.5221207
X-RAY DIFFRACTIONr_scbond_other5.6892.5241205
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5893.5791736
X-RAY DIFFRACTIONr_long_range_B_refined4.9817.5972810
X-RAY DIFFRACTIONr_long_range_B_other4.80816.8822690
X-RAY DIFFRACTIONr_rigid_bond_restr8.15434697
X-RAY DIFFRACTIONr_sphericity_free25.6195114
X-RAY DIFFRACTIONr_sphericity_bonded11.81654879
LS refinement shellResolution: 1.455→1.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 249 -
Rwork0.237 4176 -
obs--99.95 %

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