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- PDB-1aw5: 5-AMINOLEVULINATE DEHYDRATASE FROM SACCHAROMYCES CEREVISIAE -

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Basic information

Entry
Database: PDB / ID: 1aw5
Title5-AMINOLEVULINATE DEHYDRATASE FROM SACCHAROMYCES CEREVISIAE
Components5-AMINOLEVULINATE DEHYDRATASE
KeywordsDEHYDRATASE / TETRAPYRROLE BIOSYNTHESIS / ALDOLASE / TIM-BARREL OCTAMER
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
Delta-aminolevulinic acid dehydratase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsErskine, P.T. / Cooper, J.B. / Wood, S.P.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: X-ray structure of 5-aminolaevulinate dehydratase, a hybrid aldolase.
Authors: Erskine, P.T. / Senior, N. / Awan, S. / Lambert, R. / Lewis, G. / Tickle, I.J. / Sarwar, M. / Spencer, P. / Thomas, P. / Warren, M.J. / Shoolingin-Jordan, P.M. / Wood, S.P. / Cooper, J.B.
History
DepositionOct 9, 1997Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Sep 13, 2017Group: Refinement description / Category: refine / software
Item: _refine.pdbx_ls_cross_valid_method / _refine.pdbx_method_to_determine_struct / _software.name
Revision 2.0Nov 3, 2021Group: Atomic model / Database references / Derived calculations
Category: atom_site / database_2 ...atom_site / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _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: 5-AMINOLEVULINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7513
Polymers37,6201
Non-polymers1312
Water5,531307
1
A: 5-AMINOLEVULINATE DEHYDRATASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)302,00824
Polymers300,9628
Non-polymers1,04716
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area53480 Å2
ΔGint-721 kcal/mol
Surface area79160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)102.500, 102.500, 168.300
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 5-AMINOLEVULINATE DEHYDRATASE / PORPHOBILINOGEN SYNTHASE


Mass: 37620.199 Da / Num. of mol.: 1 / Mutation: M272V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cell line: B834 / Cellular location: CYTOSOL / Gene: HEM2 / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) PLYSS / References: UniProt: P05373, porphobilinogen synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 59 %
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., pH 8.0, vapor diffusion - hanging drop
PH range: 7.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97913
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 2.3→35.6 Å / Num. obs: 459575 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 16.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 6.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
DMmodel building
MLPHAREphasing
VECSUMmodel building
RESTRAINrefinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
DMphasing
VECSUMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→6 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.27 --
obs0.198 19072 99.9 %
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2527 0 2 307 2836
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d0.023
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
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_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
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

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