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- PDB-5mhb: Product-Complex of E.coli 5-Amino Laevulinic Acid Dehydratase -

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Basic information

Entry
Database: PDB / ID: 5mhb
TitleProduct-Complex of E.coli 5-Amino Laevulinic Acid Dehydratase
ComponentsDelta-aminolevulinic acid dehydratase
KeywordsLYASE / Dehydratase / Tetrapyrrole Biosynthesis
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
Chem-PBG / Delta-aminolevulinic acid dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsNorton, E. / Erskine, P.T. / Shoolingin-Jordan, P.M. / Cooper, J.B.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Structural studies of substrate and product complexes of 5-aminolaevulinic acid dehydratase from humans, Escherichia coli and the hyperthermophile Pyrobaculum calidifontis.
Authors: Mills-Davies, N. / Butler, D. / Norton, E. / Thompson, D. / Sarwar, M. / Guo, J. / Gill, R. / Azim, N. / Coker, A. / Wood, S.P. / Erskine, P.T. / Coates, L. / Cooper, J.B. / Rashid, N. / ...Authors: Mills-Davies, N. / Butler, D. / Norton, E. / Thompson, D. / Sarwar, M. / Guo, J. / Gill, R. / Azim, N. / Coker, A. / Wood, S.P. / Erskine, P.T. / Coates, L. / Cooper, J.B. / Rashid, N. / Akhtar, M. / Shoolingin-Jordan, P.M.
History
DepositionNov 23, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionDec 7, 2016ID: 5IC2
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_symmetry

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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)36,3688
Polymers35,6691
Non-polymers6997
Water5,891327
1
A: Delta-aminolevulinic acid dehydratase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)290,94064
Polymers285,3508
Non-polymers5,59056
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 area54960 Å2
ΔGint-743 kcal/mol
Surface area74300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.619, 128.619, 142.815
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-800-

HOH

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Components

#1: Protein Delta-aminolevulinic acid dehydratase / / ALADH / Porphobilinogen synthase


Mass: 35668.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hemB, ncf, b0369, JW0361 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACB2, porphobilinogen synthase
#2: 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 / Porphobilinogen


Mass: 226.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 4.14 Å3/Da / Density % sol: 70.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: ALAD at 7 mg per ml mixed with equal volume of well solution: 200 mM Tris pH 8.0 - 8.4, 2 % saturated Ammonium sulphate, 200 microM zinc sulphate, 6 mM beta-mercaptoethanol and 3 mM ...Details: ALAD at 7 mg per ml mixed with equal volume of well solution: 200 mM Tris pH 8.0 - 8.4, 2 % saturated Ammonium sulphate, 200 microM zinc sulphate, 6 mM beta-mercaptoethanol and 3 mM porphobilinogen. Crystals were grown in the dark.
PH range: 8.0 - 8.4 / Temp details: Room temperature.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1411.069
SYNCHROTRONEMBL/DESY, HAMBURG X1120.834
Detector
TypeIDDetectorDate
MAR scanner 345 mm plate1IMAGE PLATENov 6, 1997
MAR scanner 300 mm plate2IMAGE PLATEJun 3, 1998
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0691
20.8341
Reflection

Entry-ID: 5MHB

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)CC1/2Rmerge(I) obsDiffraction-IDNet I/σ(I)
2.1-36.83424897.14.827.10.9940.11617.8
2.07-23.843448795.270.9980.078215.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.1-2.214.30.7251.90.692198
2.07-2.194.30.3683.20.911268.1

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Processing

Software
NameVersionClassification
MOSFLM5.8.0107data reduction
SCALAdata scaling
REFMAC5.8.0107refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1b4e

1b4e


Resolution: 2.1→95.57 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.475 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21285 1761 5.1 %RANDOM
Rwork0.15676 ---
obs0.15953 32987 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.462 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2--0.62 Å20 Å2
3----1.24 Å2
Refinement stepCycle: 1 / Resolution: 2.1→95.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 37 327 2848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0192573
X-RAY DIFFRACTIONr_bond_other_d0.0030.022489
X-RAY DIFFRACTIONr_angle_refined_deg2.5411.983463
X-RAY DIFFRACTIONr_angle_other_deg1.3463.0015726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6645326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42123.391115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63815455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4111524
X-RAY DIFFRACTIONr_chiral_restr0.1620.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022906
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02569
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9332.1141298
X-RAY DIFFRACTIONr_mcbond_other1.9332.1131297
X-RAY DIFFRACTIONr_mcangle_it2.8943.1581623
X-RAY DIFFRACTIONr_mcangle_other2.8933.1591624
X-RAY DIFFRACTIONr_scbond_it3.0052.5061275
X-RAY DIFFRACTIONr_scbond_other2.9222.5071275
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.73.6121840
X-RAY DIFFRACTIONr_long_range_B_refined7.63418.7163077
X-RAY DIFFRACTIONr_long_range_B_other7.39117.732942
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.102→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 111 -
Rwork0.218 2225 -
obs--91.36 %
Refinement TLS params.Method: refined / Origin x: -15.4608 Å / Origin y: -25.5379 Å / Origin z: 14.2922 Å
111213212223313233
T0.1868 Å2-0.1029 Å20.0495 Å2-0.0934 Å2-0.0168 Å2--0.031 Å2
L0.3228 °2-0.0187 °20.0551 °2-0.0184 °20.0043 °2--0.9253 °2
S-0.0077 Å °-0.0825 Å °0.0119 Å °-0.0103 Å °-0.0072 Å °-0.02 Å °0.2318 Å °-0.1411 Å °0.0148 Å °

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