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- PDB-3obk: Crystal structure of delta-aminolevulinic acid dehydratase (porph... -

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Basic information

Entry
Database: PDB / ID: 3obk
TitleCrystal structure of delta-aminolevulinic acid dehydratase (porphobilinogen synthase) from toxoplasma gondii ME49 in complex with the reaction product porphobilinogen
ComponentsDelta-aminolevulinic acid dehydratase
KeywordsLYASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / DEHYDRATASE
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Chem-PBG / :
Function and homology information
Biological speciesToxoplasma gondii ME49 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structure of Toxoplasma gondii Porphobilinogen Synthase: INSIGHTS ON OCTAMERIC STRUCTURE AND PORPHOBILINOGEN FORMATION.
Authors: Jaffe, E.K. / Shanmugam, D. / Gardberg, A. / Dieterich, S. / Sankaran, B. / Stewart, L.J. / Myler, P.J. / Roos, D.S.
History
DepositionAug 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
B: Delta-aminolevulinic acid dehydratase
C: Delta-aminolevulinic acid dehydratase
D: Delta-aminolevulinic acid dehydratase
E: Delta-aminolevulinic acid dehydratase
F: Delta-aminolevulinic acid dehydratase
G: Delta-aminolevulinic acid dehydratase
H: Delta-aminolevulinic acid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,08859
Polymers316,3378
Non-polymers3,75151
Water10,557586
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57070 Å2
ΔGint-120 kcal/mol
Surface area80390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.110, 187.170, 95.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 356
2114B1 - 356
3114C1 - 356
4114D1 - 356
5114E1 - 356
6114F1 - 356
7114G1 - 356
8114H1 - 356

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Delta-aminolevulinic acid dehydratase /


Mass: 39542.141 Da / Num. of mol.: 8 / Fragment: residues 303-658
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii ME49 (eukaryote) / Gene: TGME49_053900 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B6KNM2, porphobilinogen synthase

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Non-polymers , 5 types, 637 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PBG / 3-[5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROL-3-YL]PROPANOIC ACID / 2-AMINOMETHYLPYRROL-3-ACETIC ACID 4-PROPIONIC ACID / PORPHOBILINOGEN / 5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROLE-3-PROPANOIC ACID / Porphobilinogen


Mass: 226.229 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N2O4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 586 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 90% PACT SCREEN CONDITION E4 + 10% ADDIT SCREEN D7: 0.18 M KSCN, 18% PEG 3350, 3% W/V DIAMINOOCTANE, 5 MM AMINOLEVULINIC ACID, TOGOA.17087.A.Y2 AT 6.3 MG/ML, VAPOR DIFFUSION, SITTING DROP, ...Details: 90% PACT SCREEN CONDITION E4 + 10% ADDIT SCREEN D7: 0.18 M KSCN, 18% PEG 3350, 3% W/V DIAMINOOCTANE, 5 MM AMINOLEVULINIC ACID, TOGOA.17087.A.Y2 AT 6.3 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, pH 7.00, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→49.93 Å / Num. all: 110745 / Num. obs: 109171 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.04 % / Biso Wilson estimate: 31.45 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 11.8
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.3 / % possible all: 90.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B4K

1b4k


Resolution: 2.5→49.93 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.905 / SU B: 17.723 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.232 5439 5 %RANDOM
Rwork0.177 ---
all0.18 110745 --
obs0.18 108861 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.16 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å20 Å2
2---1.25 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21476 0 228 586 22290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02222086
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215087
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.99329857
X-RAY DIFFRACTIONr_angle_other_deg0.928336850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10752810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.50624.17916
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.417153755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.26615143
X-RAY DIFFRACTIONr_chiral_restr0.080.23280
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02124670
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024229
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_it0.5031.514075
X-RAY DIFFRACTIONr_mcbond_other0.1231.55633
X-RAY DIFFRACTIONr_mcangle_it0.974222496
X-RAY DIFFRACTIONr_scbond_it1.67838011
X-RAY DIFFRACTIONr_scangle_it2.8164.57360
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 4385 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.280.5
Bmedium positional0.270.5
Cmedium positional0.280.5
Dmedium positional0.220.5
Emedium positional0.210.5
Fmedium positional0.230.5
Gmedium positional0.250.5
Hmedium positional0.260.5
Amedium thermal0.572
Bmedium thermal0.482
Cmedium thermal0.552
Dmedium thermal0.482
Emedium thermal0.452
Fmedium thermal0.442
Gmedium thermal0.452
Hmedium thermal0.442
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 361 -
Rwork0.273 6927 -
obs--90.08 %
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)
10.6787-0.173-0.14950.50370.08240.61760.033-0.04940.0546-0.0113-0.0056-0.0714-0.09270.0106-0.02740.0623-0.01780.01320.01010.00460.1002-35.493-29.09336.125
20.20310.1597-0.20790.38130.0850.49720.02950.00340.0125-0.0151-0.00590.0109-0.0414-0.0412-0.02370.1070.00750.02640.04250.0080.0889-42.385-32.3133.08
30.49660.01760.24790.3926-0.02250.48960.04020.03060.0332-0.1289-0.01880.1454-0.0414-0.1696-0.02130.14720.0244-0.01210.10890.01340.0961-62.912-42.27620.861
40.4393-0.02370.05110.94250.18350.92720.030.0525-0.0153-0.0798-0.05770.0754-0.0572-0.0730.02770.11650.00350.01730.05340.00990.0906-56.214-39.78924.703
51.4290.05240.01830.4927-0.04540.42740.031-0.03130.08270.0845-0.01160.1016-0.1105-0.0562-0.01940.12360.01750.0320.0304-0.01460.0656-67.736-27.05360.231
60.8854-0.0693-0.1480.8149-0.2950.55840.0066-0.01520.02110.16030.0436-0.0107-0.117-0.0154-0.05020.16070.00270.03440.038-0.0070.071-61.218-30.05663.978
71.06880.08520.24360.4412-0.05810.51060.055-0.160.02770.2294-0.0565-0.1095-0.11530.12810.00150.2049-0.0393-0.03330.0924-0.00210.0881-40.835-39.03376.989
80.31870.1555-0.12940.5653-0.3010.6690.028-0.02920.03640.1841-0.024-0.0825-0.12750.0924-0.00390.1983-0.0199-0.00410.0745-0.01090.0838-47.547-36.80673.095
91.12210.02530.10850.6493-0.14430.4252-0.00340.0778-0.0694-0.1255-0.0201-0.160.1730.08860.02340.17160.02690.05510.0244-0.01660.1256-34.23-70.26526.198
100.66560.0027-0.07941.0143-0.38670.46750.0060.014-0.0388-0.1424-0.0509-0.07580.1219-0.00160.0450.17390.0210.02970.0328-0.01060.098-41.926-72.50328.574
110.73180.05640.06270.6474-0.12070.6987-0.02660.0485-0.1032-0.11450.03170.13880.2607-0.12-0.00510.1992-0.0628-0.00320.0474-0.01840.1196-65.012-81.79935.907
120.2540.3259-0.11880.5338-0.15280.8019-0.02380.0419-0.032-0.08380.03070.03540.2066-0.029-0.00690.1943-0.0182-0.01080.0441-0.0220.1147-57.399-79.0634.012
131.160.02650.11790.7166-0.01760.7612-0.0027-0.0936-0.00960.1592-0.0446-0.15790.12350.14980.04720.18460.0421-0.0090.05320.03280.1045-39.409-80.06367.26
140.55340.09890.01350.93970.47610.288-0.021-0.06860.00690.14070.0203-0.07910.07920.06360.00070.20330.0178-0.00250.06580.02850.1056-46.926-76.97868.442
151.16070.07750.02870.9039-0.04270.5323-0.0003-0.0837-0.06160.18430.02950.20390.0796-0.0857-0.02920.1859-0.00950.07220.04060.03750.1185-69.993-66.75875.25
160.36510.1216-0.11061.47020.15350.6002-0.04150.0007-0.03670.1906-0.01960.13240.10810.020.06110.1792-0.00950.04160.05580.00910.1026-62.391-69.37273.185
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 213
2X-RAY DIFFRACTION2A214 - 356
3X-RAY DIFFRACTION3B1 - 213
4X-RAY DIFFRACTION4B214 - 356
5X-RAY DIFFRACTION5C1 - 213
6X-RAY DIFFRACTION6C214 - 356
7X-RAY DIFFRACTION7D1 - 213
8X-RAY DIFFRACTION8D214 - 356
9X-RAY DIFFRACTION9E1 - 213
10X-RAY DIFFRACTION10E214 - 356
11X-RAY DIFFRACTION11F1 - 213
12X-RAY DIFFRACTION12F214 - 356
13X-RAY DIFFRACTION13G1 - 213
14X-RAY DIFFRACTION14G214 - 356
15X-RAY DIFFRACTION15H1 - 213
16X-RAY DIFFRACTION16H214 - 356

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