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- PDB-1ohl: YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE PUTATIVE CYCLIC REACTION... -

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Basic information

Entry
Database: PDB / ID: 1ohl
TitleYEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE PUTATIVE CYCLIC REACTION INTERMEDIATE COMPLEX
ComponentsDELTA-AMINOLEVULINIC ACID DEHYDRATASE
KeywordsLYASE / DEHYDRATASE / 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 / cytosol / cytoplasm
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
BETA-MERCAPTOETHANOL / Chem-PBG / Delta-aminolevulinic acid dehydratase
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsErskine, P.T. / Coates, L. / Butler, D. / Youell, J.H. / Brindley, A.A. / Wood, S.P. / Warren, M.J. / Shoolingin-Jordan, P.M. / Cooper, J.B.
CitationJournal: Biochem.J. / Year: 2003
Title: X-Ray Structure of a Putative Reaction Intermediateof 5-Aminolaevulinic Acid Dehydratase
Authors: Erskine, P.T. / Coates, L. / Butler, D. / Youell, J.H. / Brindley, A.A. / Wood, S.P. / Warren, M.J. / Shoolingin-Jordan, P.M. / Cooper, J.B.
History
DepositionMay 27, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2003Provider: 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 / 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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1554
Polymers37,7851
Non-polymers3703
Water6,161342
1
A: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)305,23932
Polymers302,2818
Non-polymers2,95824
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)103.200, 103.200, 167.700
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-2013-

HOH

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Components

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


Mass: 37785.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CO-CRYSTALLISATION WITH SUBSTRATE AMINOLAEVULINIC 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#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


Mass: 226.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREQUIRES ZINC AS A COFACTOR FOR ACTIVITY. PART OF THE PORPHYRIN AND HEME BIOSYNTHESIS BIOSYNTHESIS. ...REQUIRES ZINC AS A COFACTOR FOR ACTIVITY. PART OF THE PORPHYRIN AND HEME BIOSYNTHESIS BIOSYNTHESIS. THE ACTIVE SUBUNIT IS A HOMO-OCTAMER WHICH BELONGS TO THE ALADH FAMILY.

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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: 2.95 Å3/Da / Density % sol: 58.37 %
Crystal growpH: 8 / Details: AS FOR PDB ENTRY 1AW5, pH 8.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 8 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 mMALA1drop
22 mg/mlenzyme1drop
32-10 %(w/v)PEG60001reservoir
4200 mMTris-HCl1reservoirpH7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.911662
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 17, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.911662 Å / Relative weight: 1
ReflectionResolution: 1.6→44.7 Å / Num. obs: 57568 / % possible obs: 96.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 28.66 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 21.7
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.5 / % possible all: 96.2
Reflection shell
*PLUS
% possible obs: 96.2 %

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Processing

Software
NameClassification
CCP4refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YLV

1ylv


Resolution: 1.6→44.7 Å / Cross valid method: FREE R-VALUE / σ(F): 0
Details: EARLY ROUNDS OF REFINEMENT PERFORMED WITH SHELX-97-2 THEN TLS TENSORS REFINED WITH RESTRAIN.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2920 5.1 %RANDOM
Rwork0.188 ---
all-57545 --
obs-57545 96.2 %-
Displacement parametersBiso mean: 40.51 Å2
Refine analyzeLuzzati d res low obs: 44.5 Å / Luzzati sigma a obs: 0.292 Å
Refinement stepCycle: LAST / Resolution: 1.6→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 21 342 3000
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.005
X-RAY DIFFRACTIONp_angle_d0.013
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.009
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.007
X-RAY DIFFRACTIONp_chiral_restr0.009
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd0.015
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_bond_d0.005
X-RAY DIFFRACTIONp_angle_d0.013
X-RAY DIFFRACTIONp_planar_d0.009
X-RAY DIFFRACTIONp_plane_restr0.007

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