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- PDB-1pda: STRUCTURE OF PORPHOBILINOGEN DEAMINASE REVEALS A FLEXIBLE MULTIDO... -

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Basic information

Entry
Database: PDB / ID: 1pda
TitleSTRUCTURE OF PORPHOBILINOGEN DEAMINASE REVEALS A FLEXIBLE MULTIDOMAIN POLYMERASE WITH A SINGLE CATALYTIC SITE
ComponentsPORPHOBILINOGEN DEAMINASE
KeywordsTRANSFERASE / PORPHYRIN
Function / homology
Function and homology information


tetrapyrrole biosynthetic process / hydroxymethylbilane synthase / hydroxymethylbilane synthase activity / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / cytoplasm / cytosol
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
ACETIC ACID / Chem-DPM / Porphobilinogen deaminase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.76 Å
AuthorsLouie, G.V. / Brownlie, P.D. / Lambert, R. / Cooper, J.B. / Blundell, T.L. / Wood, S.P. / Warren, M.J. / Woodcock, S.C. / Jordan, P.M.
CitationJournal: Nature / Year: 1992
Title: Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site.
Authors: Louie, G.V. / Brownlie, P.D. / Lambert, R. / Cooper, J.B. / Blundell, T.L. / Wood, S.P. / Warren, M.J. / Woodcock, S.C. / Jordan, P.M.
History
DepositionNov 17, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2013Group: Non-polymer description
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification

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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)34,3723
Polymers33,8921
Non-polymers4802
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.000, 75.900, 50.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: THE SIDE CHAINS OF ARG 44, LYS 59, AND LEU 61 HAVE POOR ELECTRON DENSITY, AND THE ATOMIC MODEL INCLUDES ONLY THE CB ATOMS FOR THESE SIDE CHAINS.

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Components

#1: Protein PORPHOBILINOGEN DEAMINASE


Mass: 33891.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P06983, 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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: 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

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: batch method / PH range low: 5.5 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMsodium acetate11
21 %(w/v)sodium chloride11
39 %(w/v)PEG600011

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. all: 180969 / Num. obs: 33726 / Rmerge(I) obs: 0.107

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.188 / Rfactor obs: 0.188 / Highest resolution: 1.76 Å
Refinement stepCycle: LAST / Highest resolution: 1.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 34 249 2527
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.871.5
X-RAY DIFFRACTIONx_mcangle_it2.611.8
X-RAY DIFFRACTIONx_scbond_it3.532
X-RAY DIFFRACTIONx_scangle_it5.32.5
Refinement
*PLUS
Highest resolution: 1.9 Å / Rfactor obs: 0.184 / Lowest resolution: 10 Å / Num. reflection obs: 24379 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.020.032
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_planar_d0.050.065
X-RAY DIFFRACTIONx_plane_restr0.020.021
X-RAY DIFFRACTIONx_chiral_restr0.150.195
X-RAY DIFFRACTIONx_angle_deg3.4

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