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- PDB-1eb3: YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE 4,7-DIOXOSEBACIC ACID COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1eb3
TitleYEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE 4,7-DIOXOSEBACIC ACID COMPLEX
Components5-AMINOLAEVULINIC ACID DEHYDRATASE
KeywordsDEHYDRATASE / ALDOLASE / TIM BARREL / TETRAPYRROLE SYNTHESIS
Function / homology
Function and homology information


Heme biosynthesis / porphobilinogen synthase / porphobilinogen synthase activity / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / Neutrophil degranulation / zinc ion binding / nucleus / cytoplasm / 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
4,7-DIOXOSEBACIC ACID / Delta-aminolevulinic acid dehydratase
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsErskine, P.T. / Coates, L. / Newbold, R. / Brindley, A.A. / Stauffer, F. / Wood, S.P. / Warren, M.J. / Cooper, J.B. / Shoolingin-Jordan, P.M. / Neier, R.
CitationJournal: FEBS Lett. / Year: 2001
Title: The X-Ray Structure of Yeast 5-Aminolaevulinic Acid Dehydratase Complexed with Two Diacid Inhibitors
Authors: Erskine, P.T. / Coates, L. / Newbold, R. / Brindley, A.A. / Stauffer, F. / Wood, S.P. / Warren, M.J. / Cooper, J.B. / Shoolingin-Jordan, P.M. / Neier, R.
History
DepositionJul 18, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...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 / struct_conn
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.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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5-AMINOLAEVULINIC ACID DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8383
Polymers37,5421
Non-polymers2962
Water7,242402
1
A: 5-AMINOLAEVULINIC ACID DEHYDRATASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)302,70124
Polymers300,3368
Non-polymers2,36516
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation6_555x,-y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)104.300, 104.300, 167.200
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-2011-

HOH

21A-2099-

HOH

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Components

#1: Protein 5-AMINOLAEVULINIC ACID DEHYDRATASE / ALAD / PORPHOBILINOGEN SYNTHASE


Mass: 37541.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH 4,7-DIOXOSEBACIC ACID
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: NS1(JM109/PNS1) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P05373, porphobilinogen synthase
#2: Chemical ChemComp-DSB / 4,7-DIOXOSEBACIC ACID


Mass: 230.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14O6
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growpH: 8
Details: AS FOR PDB ENTRY 1AW5 WITH 5 MM 4,7-DIOXO-SEBACIC ACID IN DROP, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 29, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.75→36.4 Å / Num. obs: 44379 / % possible obs: 95.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 4.6
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 1.6 / % possible all: 98.5

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Processing

Software
NameClassification
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLV

1ylv


Resolution: 1.75→36.3 Å / Num. parameters: 12339 / Num. restraintsaints: 11762 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.308 2237 5 %RANDOM
obs0.239 -95.5 %-
all-44374 --
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 6
Refinement stepCycle: LAST / Resolution: 1.75→36.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 15 402 3054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.341
X-RAY DIFFRACTIONs_zero_chiral_vol0.037
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.044
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.051
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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