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- PDB-2woq: Porphobilinogen Synthase (HemB) in Complex with 5-acetamido-4- ox... -

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Basic information

Entry
Database: PDB / ID: 2woq
TitlePorphobilinogen Synthase (HemB) in Complex with 5-acetamido-4- oxohexanoic acid (Alaremycin 2)
ComponentsDELTA-AMINOLEVULINIC ACID DEHYDRATASE
KeywordsLYASE/ANTIBIOTIC / LYASE-ANTIBIOTIC COMPLEX / LYASE ANTIBIOTIC COMPLEX / METAL-BINDING / HEME BIOSYNTHESIS / PORPHYRIN BIOSYNTHESIS / PORPOBILINOGEN SYNTHASE / HEMB / LYASE / INHIBITOR
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
ALAREMYCIN 2 / Delta-aminolevulinic acid dehydratase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHeinemann, I.U. / Schulz, C. / Schubert, W.-D. / Heinz, D.W. / Wang, Y.-G. / Kobayashi, Y. / Awa, Y. / Wachi, M. / Jahn, D. / Jahn, M.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2010
Title: Structure of the heme biosynthetic Pseudomonas aeruginosa porphobilinogen synthase in complex with the antibiotic alaremycin.
Authors: Heinemann, I.U. / Schulz, C. / Schubert, W.D. / Heinz, D.W. / Wang, Y.G. / Kobayashi, Y. / Awa, Y. / Wachi, M. / Jahn, D. / Jahn, M.
History
DepositionJul 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry / struct_biol / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_symmetry / _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 / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,43312
Polymers37,0781
Non-polymers2,35511
Water3,171176
1
A: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)315,46396
Polymers296,6238
Non-polymers18,84088
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area51970 Å2
ΔGint-172.61 kcal/mol
Surface area70990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.444, 84.444, 158.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-1338-

EPE

21A-2156-

HOH

31A-2176-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 37077.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 PLUS / References: UniProt: Q59643, porphobilinogen synthase

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Non-polymers , 5 types, 187 molecules

#2: Chemical ChemComp-AYC / ALAREMYCIN 2 / (5R)-5-ACETAMIDO-4-OXO-HEXANOIC ACID


Mass: 187.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13NO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsTHE HETGROUP AYC (ALAREMYCIN 2) DIFFERS FROM ALAREMYCIN, AN ANTIBIOTIC ISOLATED FROM STREPTOMYCES ...THE HETGROUP AYC (ALAREMYCIN 2) DIFFERS FROM ALAREMYCIN, AN ANTIBIOTIC ISOLATED FROM STREPTOMYCES SP. ATCC: A012304, BY THE REDUCTION/HYDROGENATION OF THE C5 C=C DOUBLE BOND ADJACENT TO THE CENTRAL KETONE GROUP. THIS RESULTS IN A NON-PLANAR SP3-HYBRIDIZED C5 AND AN ADJACENT METHYL GROUP. ALAREMYCIN AND ITS PURIFICATION ARE DESCRIBED IN HTTP://WWW.JSTAGE.JST.GO.JP/ARTICLE/BBB/69/9/69_1721/ THE BOND BETWEEN ATOM NZ OF LYS A260 AND AYC A1333 IS A DOUBLE SCHIFF BASE BOND.

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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: 2.14 Å3/Da / Density % sol: 42.58 % / Description: NONE
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 100 MM HEPES PH 7.5, 200 MM MGCL2, 30 % PEG400 TEMPERATURE = 17 C PROTEIN CONCENTRATION = 20 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.95373
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 19, 2006 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.75→25.3 Å / Num. obs: 29316 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 13.7 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 46
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 5.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GZG

1gzg


Resolution: 1.75→25.31 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.847 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17966 1488 5.1 %RANDOM
Rwork0.1456 ---
obs0.14736 27822 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.053 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→25.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 97 176 2804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222848
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.9983867
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1745374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.36623.285137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79815478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1321531
X-RAY DIFFRACTIONr_chiral_restr0.1240.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212161
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5621.51715
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.37822772
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.72531133
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9214.51071
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 103 -
Rwork0.235 2006 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.98940.9109-1.11932.0523-0.75632.8123-0.03070.0422-0.07540.0095-0.024-0.00880.01610.01640.05460.0680.0045-0.02180.034-0.01540.0451-20.75891.7783-20.1697
20.6218-0.0926-0.63340.3550.26191.15790.07710.06790.0707-0.0193-0.04760.0952-0.1044-0.2262-0.02950.04460.0266-0.00280.1145-0.01810.0738-36.604317.962813.8051
31.2595-0.7158-1.16543.26261.06741.773-0.0340.1867-0.1965-0.1218-0.1850.5115-0.0279-0.3640.2190.01250.0111-0.00820.1039-0.03730.1002-39.499811.577116.2279
41.38510.41430.14351.57810.62881.25420.0026-0.12360.01450.0967-0.09730.1987-0.0129-0.20090.09470.04810.01790.02640.0869-0.01170.0616-32.770216.212428.8235
51.9287-0.2049-0.20920.7407-0.02111.0744-0.0308-0.08120.18780.0110.0201-0.0751-0.15940.02020.01070.08980.01170.0080.0745-0.02890.0609-18.396521.881230.6489
60.76260.3188-0.25311.0611-0.31651.35480.0007-0.0230.03710.0627-0.00170.0698-0.0612-0.04980.0010.05190.00870.0070.0557-0.01690.0527-19.446313.222522.5112
74.64770.4121-0.81780.24910.21140.52420.15880.0710.4577-0.08590.0406-0.0364-0.16830.058-0.19940.1264-0.01570.0210.0325-0.010.1081-21.3230.790718.1478
80.606-0.0633-0.02980.2692-0.22620.6781-0.00920.04920.0159-0.03950-0.0113-0.0260.02280.00930.05470.00140.00290.0558-0.00460.0358-12.385113.926811.2865
91.2236-0.79540.42452.0139-1.11841.75380.02330.09870.0521-0.0210.00260.0373-0.0692-0.1602-0.02590.05010.00140.010.0993-0.0050.0568-26.099318.31843.9982
101.3269-0.6477-0.56760.67430.32711.73330.00460.1162-0.0691-0.0264-0.02280.0903-0.0168-0.13360.01820.0362-0.003-0.0040.06-0.00860.0337-27.000512.71242.6271
1117.0296-3.91180.196513.07573.891814.09630.371.2057-0.9731-0.8242-0.15370.6577-0.2807-0.3481-0.21630.05470.0294-0.04910.2005-0.00240.1811-38.594812.18863.2024
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 28
2X-RAY DIFFRACTION2A29 - 67
3X-RAY DIFFRACTION3A68 - 87
4X-RAY DIFFRACTION4A88 - 130
5X-RAY DIFFRACTION5A131 - 167
6X-RAY DIFFRACTION6A168 - 215
7X-RAY DIFFRACTION7A216 - 229
8X-RAY DIFFRACTION8A230 - 274
9X-RAY DIFFRACTION9A275 - 303
10X-RAY DIFFRACTION10A304 - 326
11X-RAY DIFFRACTION11A327 - 333

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