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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

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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

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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