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- PDB-5ov4: Bacillus megaterium porphobilinogen deaminase D82A mutant -

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Basic information

Entry
Database: PDB / ID: 5ov4
TitleBacillus megaterium porphobilinogen deaminase D82A mutant
ComponentsPorphobilinogen deaminase
KeywordsTRANSFERASE / Deaminase / mutation / domain movements / cofactor
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
Porphobilinogen deaminase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.692 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 1.0Oct 11, 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 1.3Jan 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

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Assembly

Deposited unit
A: Porphobilinogen deaminase


Theoretical massNumber of molelcules
Total (without water)34,3821
Polymers34,3821
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.092, 62.487, 91.391
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: 34381.684 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.95 Å3/Da / Density % sol: 36.86 %
Description: Clusters formed by thin plates with a dark 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: 2.69→29.564 Å / Num. obs: 8221 / % possible obs: 99.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 51.8 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.151 / Net I/σ(I): 11.8
Reflection shellResolution: 2.69→2.76 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 579 / CC1/2: 0.797 / Rrim(I) all: 0.585 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
REFMAC5.8.0158refinement
xia2data scaling
MOLREPphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MLV

4mlv


Resolution: 2.692→29.564 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 22.28
RfactorNum. reflection% reflection
Rfree0.2391 394 4.81 %
Rwork0.2094 --
obs0.2108 8186 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.692→29.564 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2245 0 0 47 2292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022280
X-RAY DIFFRACTIONf_angle_d0.4793067
X-RAY DIFFRACTIONf_dihedral_angle_d14.2541420
X-RAY DIFFRACTIONf_chiral_restr0.042351
X-RAY DIFFRACTIONf_plane_restr0.002397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6921-3.08120.28631390.24922525X-RAY DIFFRACTION99
3.0812-3.88070.22811190.21452576X-RAY DIFFRACTION100
3.8807-29.56540.22651360.19142691X-RAY DIFFRACTION99

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