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- PDB-1i8j: CRYSTAL STRUCTURE OF PORPHOBILINOGEN SYNTHASE COMPLEXED WITH THE ... -

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Basic information

Entry
Database: PDB / ID: 1i8j
TitleCRYSTAL STRUCTURE OF PORPHOBILINOGEN SYNTHASE COMPLEXED WITH THE INHIBITOR 4,7-DIOXOSEBACIC ACID
ComponentsPORPHOBILINOGEN SYNTHASE
KeywordsLYASE / HEME BIOSYNTHESIS / MAGNESIUM / 4 / 7-DIOXOSEBACIC ACID
Function / homology
Function and homology information


porphobilinogen synthase / porphobilinogen synthase activity / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / magnesium ion binding / zinc ion binding / cytosol
Similarity search - Function
Delta-aminolevulinic acid dehydratase / Delta-aminolevulinic acid dehydratase, active site / Delta-aminolevulinic acid dehydratase / Delta-aminolevulinic acid dehydratase active site. / Delta-aminolevulinic acid dehydratase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4,7-DIOXOSEBACIC ACID / Delta-aminolevulinic acid dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKervinen, J. / Jaffe, E.K. / Stauffer, F. / Neier, R. / Wlodawer, A. / Zdanov, A.
CitationJournal: Biochemistry / Year: 2001
Title: Mechanistic basis for suicide inactivation of porphobilinogen synthase by 4,7-dioxosebacic acid, an inhibitor that shows dramatic species selectivity.
Authors: Kervinen, J. / Jaffe, E.K. / Stauffer, F. / Neier, R. / Wlodawer, A. / Zdanov, A.
History
DepositionMar 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 9, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 600HETEROGEN Atoms C4 and C7 of DSB form a Schiff base to NZ of Lys246 and NZ of Lys194. The oxygens ...HETEROGEN Atoms C4 and C7 of DSB form a Schiff base to NZ of Lys246 and NZ of Lys194. The oxygens on the C4 and C7 are eliminated during this reaction.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PORPHOBILINOGEN SYNTHASE
B: PORPHOBILINOGEN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7158
Polymers71,0752
Non-polymers6406
Water5,693316
1
A: PORPHOBILINOGEN SYNTHASE
B: PORPHOBILINOGEN SYNTHASE
hetero molecules

A: PORPHOBILINOGEN SYNTHASE
B: PORPHOBILINOGEN SYNTHASE
hetero molecules

A: PORPHOBILINOGEN SYNTHASE
B: PORPHOBILINOGEN SYNTHASE
hetero molecules

A: PORPHOBILINOGEN SYNTHASE
B: PORPHOBILINOGEN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,86032
Polymers284,3018
Non-polymers2,55924
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area46270 Å2
ΔGint-379 kcal/mol
Surface area74710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.741, 128.741, 142.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein PORPHOBILINOGEN SYNTHASE / DELTA-AMINOLEVULINIC ACID DEHYDRATASE / 5-AMINOLEVULINIC ACID DEHYDRATASE


Mass: 35537.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACB2, porphobilinogen synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DSB / 4,7-DIOXOSEBACIC ACID


Mass: 230.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsATOMS C4 AND C7 OF DSB FORM A SCHIFF BASE TO NZ OF LYS246 AND NZ OF LYS194. THE OXYGENS ON THE C4 ...ATOMS C4 AND C7 OF DSB FORM A SCHIFF BASE TO NZ OF LYS246 AND NZ OF LYS194. THE OXYGENS ON THE C4 AND C7 ARE ELIMINATED DURING THIS REACTION.

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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: 4.16 Å3/Da / Density % sol: 70.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 3350, GLYCEROL, TRIS-HCL, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19 mg/mlprotein1drop
250 mMTris-HCl1drop
310 mMbeta-mercaptoethanol1drop
40.020 mM1dropZnCl2
510 mM1dropMgCl2
62.5 %PEG33501reservoir
710 %glycerol1reservoir
80.1 MTris-HCl1reservoir
90.02 %sodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 2000 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. all: 94638 / Num. obs: 94536 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 12
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 35 Å

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1b4e

1b4e


Resolution: 1.9→35 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.247 9416 RANDOM
Rwork0.1983 --
all-94638 -
obs-94242 -
Refinement stepCycle: LAST / Resolution: 1.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4906 0 32 316 5254
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.91
X-RAY DIFFRACTIONc_bond_d0.018
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 35 Å / σ(F): 0 / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS

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