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- PDB-1b4e: X-ray structure of 5-aminolevulinic acid dehydratase complexed wi... -

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Basic information

Entry
Database: PDB / ID: 1b4e
TitleX-ray structure of 5-aminolevulinic acid dehydratase complexed with the inhibitor levulinic acid
ComponentsPROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE)
KeywordsLYASE / DEHYDRATASE
Function / homology
Function and homology information


porphobilinogen synthase / porphobilinogen synthase activity / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / magnesium ion binding / zinc ion binding / 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
LAEVULINIC ACID / Delta-aminolevulinic acid dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsErskine, P.T. / Cooper, J.B. / Lewis, G. / Spencer, P. / Wood, S.P. / Shoolingin-Jordan, P.M.
CitationJournal: Biochemistry / Year: 1999
Title: X-ray structure of 5-aminolevulinic acid dehydratase from Escherichia coli complexed with the inhibitor levulinic acid at 2.0 A resolution.
Authors: Erskine, P.T. / Norton, E. / Cooper, J.B. / Lambert, R. / Coker, A. / Lewis, G. / Spencer, P. / Sarwar, M. / Wood, S.P. / Warren, M.J. / Shoolingin-Jordan, P.M.
History
DepositionDec 19, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 18, 2012Group: Derived calculations / Non-polymer description
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,41411
Polymers35,5381
Non-polymers87710
Water6,684371
1
A: PROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE)
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)291,31588
Polymers284,3018
Non-polymers7,01580
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 area59330 Å2
ΔGint-1022 kcal/mol
Surface area70080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)126.700, 126.700, 141.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE) / ALAD


Mass: 35537.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HEM2 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACB2, porphobilinogen synthase

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Non-polymers , 5 types, 381 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SHF / LAEVULINIC ACID / LEVULINIC ACID / Levulinic acid


Mass: 116.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 4 Å3/Da / Density % sol: 71 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.2
Details: 7MG/ML ENZYME AND 2 - 5 % SATURATED AMMONIUM SULPHATE AS PRECIPITANT. 0.2 M TRIS-HCL USED TO BUFFER THE PH BETWEEN 8.1 AND 8.4. 15MM LEVULINIC ACID, 40UM ZINC SULPHATE AND 4MM BETA- ...Details: 7MG/ML ENZYME AND 2 - 5 % SATURATED AMMONIUM SULPHATE AS PRECIPITANT. 0.2 M TRIS-HCL USED TO BUFFER THE PH BETWEEN 8.1 AND 8.4. 15MM LEVULINIC ACID, 40UM ZINC SULPHATE AND 4MM BETA- MERCAPTOETHANOL WERE PRESENT., pH 8.2, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
PH range low: 8.4 / PH range high: 8.1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlenzyme1drop
20.2 MTris-HCl1drop
315 mMlevulinic acid1drop
40.04 Mzinc sulfate1drop
54 mMmercaptoethanol1drop
62-5 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→8 Å / Num. obs: 33275 / % possible obs: 85.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.8
Reflection shellResolution: 2→2.1 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2.1 / % possible all: 70.8
Reflection
*PLUS
Lowest resolution: 7.7 Å
Reflection shell
*PLUS
% possible obs: 70.8 %

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Processing

Software
NameVersionClassification
ALMNmodel building
TFFC(CCP4 SUITE)model building
RESTRAINrefinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CCP4(ALMNphasing
TFFCphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: YEAST ALAD

Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 -5 %EVERY 20TH REFLECTION
Rwork0.188 ---
obs-33275 --
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 43 371 2893
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.016
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg0.032
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Lowest resolution: 7.7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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