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- PDB-1w31: YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE 5-HYDROXYLAEVULINIC ACID... -

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Basic information

Entry
Database: PDB / ID: 1w31
TitleYEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE 5-HYDROXYLAEVULINIC ACID COMPLEX
ComponentsDELTA-AMINOLEVULINIC ACID DEHYDRATASE
KeywordsLYASE / DEHYDRATASE / ALDOLASE / TIM BARREL / TETRAPYRROLE SYNTHESIS / HEME BIOSYNTHESIS / ZINC
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
5-HYDROXYLAEVULINIC ACID / Delta-aminolevulinic acid dehydratase
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsErskine, P.T. / Coates, L. / Newbold, R. / Brindley, A.A. / Stauffer, F. / Beaven, G.D.E. / Gill, R. / Wood, S.P. / Warren, M.J. / Cooper, J.B. ...Erskine, P.T. / Coates, L. / Newbold, R. / Brindley, A.A. / Stauffer, F. / Beaven, G.D.E. / Gill, R. / Wood, S.P. / Warren, M.J. / Cooper, J.B. / Shoolingin-Jordan, P.M. / Neier, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of Yeast 5-Aminolaevulinic Acid Dehydratase Complexed with the Inhibitor 5-Hydroxylaevulinic Acid
Authors: Erskine, P.T. / Coates, L. / Newbold, R. / Brindley, A.A. / Stauffer, F. / Beaven, G.D.E. / Gill, R. / Coker, A. / Wood, S.P. / Warren, M.J. / Shoolingin-Jordan, P.M. / Neier, R. / Cooper, J.B.
History
DepositionJul 11, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
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
Revision 1.5Oct 23, 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 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

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Assembly

Deposited unit
A: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9693
Polymers37,7851
Non-polymers1842
Water4,846269
1
A: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)303,75024
Polymers302,2818
Non-polymers1,46816
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)102.570, 102.570, 168.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein DELTA-AMINOLEVULINIC ACID DEHYDRATASE / 5-AMINOLAEVULINIC ACID DEHYDRATASE / ALADH


Mass: 37785.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH 5-HYDROXYLAEVULINIC 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-SHO / 5-HYDROXYLAEVULINIC ACID / 5-HYDROXYPENTANOIC ACID


Mass: 118.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O3
#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.: 269 / 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: 2.91 Å3/Da / Density % sol: 57 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: ENZYME CONCENTRATION 1 MG/ML, PH 7.0 - 8.5, BUFFER 0.2 M TRIS-HCL, PRECIPITANT PEG 6000 (<10%), 70 MICROMOLAR ZINC SULPHATE, 6 MM BETA-MERCAPTOETHANOL, HANGING DROPS AS FOR PDB ENTRY 1AW5 WITH 10 MM 5-HYDROXYLAEVULINIC ACID IN DROP.

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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 16, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.911662 Å / Relative weight: 1
ReflectionResolution: 1.9→49 Å / Num. obs: 1067852 / % possible obs: 100 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 8
Reflection shellResolution: 1.9→2 Å / Redundancy: 10 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

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

1ylv


Resolution: 1.9→44.28 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 --RANDOM
Rwork0.1895 ---
all-33934 --
obs--100 %-
Refinement stepCycle: LAST / Resolution: 1.9→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 9 269 2915
Refinement
*PLUS
Rfactor obs: 0.1895 / Rfactor Rfree: 0.2493 / Rfactor Rwork: 0.1895
Solvent computation
*PLUS
Displacement parameters
*PLUS

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