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- PDB-2c15: 5-(4-Carboxy-2-oxo-butoxy)-4-oxo-pentanoic acid acid bound to Por... -

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Basic information

Entry
Database: PDB / ID: 2c15
Title5-(4-Carboxy-2-oxo-butoxy)-4-oxo-pentanoic acid acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa
ComponentsDELTA-AMINOLEVULINIC ACID DEHYDRATASE
KeywordsLYASE / ENZYME MECHANISM / METALLOENZYME / PORPHOBILINOGEN SYNTHASE / PSEUDOMONAS AERUGINOSA / MAGNESIUM / METAL-BINDING / PORPHYRIN BIOSYNTHESIS
Function / homology
Function and homology information


porphobilinogen synthase / porphobilinogen synthase activity / porphyrin-containing compound biosynthetic process / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / 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
Delta-aminolevulinic acid dehydratase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsFrere, F. / Nentwich, M. / Gacond, S. / Heinz, D.W. / Neier, R. / Frankenberg-Dinkel, N.
CitationJournal: Biochemistry / Year: 2006
Title: Probing the Active Site of Pseudomonas Aeruginosa Porphobilinogen Synthase Using Newly Developed Inhibitors.
Authors: Frere, F. / Nentwich, M. / Gacond, S. / Heinz, D.W. / Neier, R. / Frankenberg-Dinkel, N.
History
DepositionSep 11, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_validate_polymer_linkage / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_polymer_linkage / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP RECORDS THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET BELOW ... SHEET DETERMINATION METHOD: DSSP RECORDS THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
B: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6314
Polymers74,5822
Non-polymers492
Water17,457969
1
A: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
B: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
hetero molecules

A: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
B: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
hetero molecules

A: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
B: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
hetero molecules

A: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
B: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,52316
Polymers298,3298
Non-polymers1948
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-y+3/2,x-1/2,z1
crystal symmetry operation4_565y+1/2,-x+3/2,z1
crystal symmetry operation2_765-x+2,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)127.538, 127.538, 85.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-2023-

HOH

21A-2025-

HOH

31B-2023-

HOH

41B-2024-

HOH

51B-2103-

HOH

61B-2247-

HOH

71B-2467-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.81291, 0.58237, 0.00465), (0.58236, 0.81293, -0.00286), (-0.00544, 0.00038, -0.99999)
Vector: 194.20476, -62.37282, -16.38472)

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Components

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


Mass: 37291.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q59643, porphobilinogen synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 969 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsI199V EXCHANGE AS CLONING ARTEFACT

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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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROL PROTEIN SOLUTION (10 MG/ML PROTEIN, 100 MM TRIS-HCL, PH 7.5, 5 MM MGCL2, 5 MM 5-(4-CARBOXY-2-OXO-BUTOXY)-4-OXO-PENTANOIC ACID ...Details: HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROL PROTEIN SOLUTION (10 MG/ML PROTEIN, 100 MM TRIS-HCL, PH 7.5, 5 MM MGCL2, 5 MM 5-(4-CARBOXY-2-OXO-BUTOXY)-4-OXO-PENTANOIC ACID SODIUM SALT) PLUS 5 MICROL RESERVOIR SOLUTION (12.0 % (W/V) PEG-8000, 340 MM LI2SO4, 20% (V/V) GLYCEROL,)ABOVE 500 MICROL OF RESERVOIR SOLUTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9801
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 9, 2005 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.48→38.1 Å / Num. obs: 117544 / % possible obs: 96.2 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.3
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.1 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B4K

1b4k


Resolution: 1.48→90.17 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.922 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 5-(4-CARBOXY-2-OXO-BUTOXY)-4-OXO-PENTANOIC ACID IS BOUND TO K260 VIA A SCHIFF BASE.
RfactorNum. reflection% reflectionSelection details
Rfree0.171 5653 5 %RANDOM
Rwork0.148 ---
obs0.149 107399 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.48→90.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5146 0 2 969 6117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226040
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.9718279
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10723.523298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81415994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5611563
X-RAY DIFFRACTIONr_chiral_restr0.0790.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024902
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.23274
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24367
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.2790
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.2162
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.278
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5481.53849
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.86326144
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.48632408
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2324.52135
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.52 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.255 444
Rwork0.206 8001

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