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- PDB-1l6y: Crystal Structure of Porphobilinogen Synthase Complexed with the ... -

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Basic information

Entry
Database: PDB / ID: 1l6y
TitleCrystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4-Oxosebacic Acid
ComponentsPORPHOBILINOGEN SYNTHASE
KeywordsLYASE / DEHYDRATASE
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-OXODECANEDIOIC ACID / Delta-aminolevulinic acid dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJaffe, E.K. / Kervinen, J. / Martins, J. / Stauffer, F. / Neier, R. / Wlodawer, A. / Zdanov, A.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Species-Specific Inhibition of Porphobilinogen Synthase by 4-Oxosebacic Acid
Authors: Jaffe, E.K. / Kervinen, J. / Martins, J. / Stauffer, F. / Neier, R. / Wlodawer, A. / Zdanov, A.
#1: Journal: 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, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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_ref_seq_dif / 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.conn_type_id / _struct_conn.details / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN Atom C4 of 4OX forms a Schiff base to NZ of Lys246. The oxygen on the C4 is eliminated ...HETEROGEN Atom C4 of 4OX forms a Schiff base to NZ of Lys246. The oxygen on the C4 is eliminated during this reaction.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,30013
Polymers71,2272
Non-polymers1,07211
Water7,764431
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)289,19952
Polymers284,9108
Non-polymers4,28944
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 area49550 Å2
ΔGint-384 kcal/mol
Surface area76180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)129.0, 129.0, 142.8
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsThe biological assembly is an octamer.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PORPHOBILINOGEN SYNTHASE / Delta-aminolevulinic acid dehydratase / 5-AMINOLEVULINIC ACID DEHYDRATASE


Mass: 35613.727 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

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Non-polymers , 5 types, 442 molecules

#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-4OX / 4-OXODECANEDIOIC ACID / 4-OXOSEBACIC ACID


Mass: 216.231 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O5
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 4.17 Å3/Da / Density % sol: 70.5 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, 10% GLYCEROL, 0.1M TRIS-HCL, PH 8.5, 0.02% SODIUM AZIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
19 mg/mlprotein1drop
250 mMTris-HCl1droppH8.0
310 mMbeta-mercaptoethanol1drop
40.020 mM1dropZnCl2
510 mM1dropMgCl2
61-6 %PEG33501reservoir
710 %glycerol1reservoir
80.1 MTris-HCl1reservoirpH8.5
90.02 %sodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.28 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 18, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 92900 / Num. obs: 92714 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.9→2.03 Å / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 40 Å / Rmerge(I) obs: 0.056

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L6S

1l6s


Resolution: 1.9→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 7736 -RANDOM
Rwork0.206 ---
all-92714 --
obs-92714 99.8 %-
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4926 0 62 431 5419
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg2
Refinement
*PLUS
Lowest resolution: 40 Å / Rfactor obs: 0.206 / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS

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