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- PDB-5lzl: Pyrobaculum calidifontis 5-aminolaevulinic acid dehydratase -

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Basic information

Entry
Database: PDB / ID: 5lzl
TitlePyrobaculum calidifontis 5-aminolaevulinic acid dehydratase
ComponentsDelta-aminolevulinic acid dehydratase
KeywordsLYASE / TIM-barrel / tetrapyrrole biosynthesis
Function / homology
Function and homology information


porphobilinogen synthase / porphobilinogen synthase activity / protoporphyrinogen IX biosynthetic process / metal ion binding
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 speciesPyrobaculum calidifontis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.47 Å
AuthorsAzim, N. / Erskine, P.T. / Guo, J. / 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
DepositionSep 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3Aug 8, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.4Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Delta-aminolevulinic acid dehydratase
B: Delta-aminolevulinic acid dehydratase
C: Delta-aminolevulinic acid dehydratase
D: Delta-aminolevulinic acid dehydratase
E: Delta-aminolevulinic acid dehydratase
F: Delta-aminolevulinic acid dehydratase
G: Delta-aminolevulinic acid dehydratase
H: Delta-aminolevulinic acid dehydratase
I: Delta-aminolevulinic acid dehydratase
J: Delta-aminolevulinic acid dehydratase
K: Delta-aminolevulinic acid dehydratase
L: Delta-aminolevulinic acid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)454,26136
Polymers452,69212
Non-polymers1,57024
Water63135
1
A: Delta-aminolevulinic acid dehydratase
B: Delta-aminolevulinic acid dehydratase
C: Delta-aminolevulinic acid dehydratase
D: Delta-aminolevulinic acid dehydratase
E: Delta-aminolevulinic acid dehydratase
F: Delta-aminolevulinic acid dehydratase
G: Delta-aminolevulinic acid dehydratase
H: Delta-aminolevulinic acid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,84124
Polymers301,7948
Non-polymers1,04716
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49550 Å2
ΔGint-745 kcal/mol
Surface area76910 Å2
MethodPISA
2
I: Delta-aminolevulinic acid dehydratase
J: Delta-aminolevulinic acid dehydratase
K: Delta-aminolevulinic acid dehydratase
L: Delta-aminolevulinic acid dehydratase
hetero molecules

I: Delta-aminolevulinic acid dehydratase
J: Delta-aminolevulinic acid dehydratase
K: Delta-aminolevulinic acid dehydratase
L: Delta-aminolevulinic acid dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,84124
Polymers301,7948
Non-polymers1,04716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area49970 Å2
ΔGint-749 kcal/mol
Surface area77570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.561, 205.561, 199.171
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Delta-aminolevulinic acid dehydratase


Mass: 37724.301 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum calidifontis (strain JCM 11548 / VA1) (archaea)
Gene: Pcal_1709 / Production host: Escherichia coli (E. coli) / References: UniProt: A3MWV9, porphobilinogen synthase
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.68 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein buffer was 10 mM Tris-HCl pH 8.0. Protein concentration 5 mg/ml. It was crystallised in the presence of 1 mM levulinic acid with 0.1 M HEPES pH 7.5, 10 % isopropanol and 20 % ...Details: Protein buffer was 10 mM Tris-HCl pH 8.0. Protein concentration 5 mg/ml. It was crystallised in the presence of 1 mM levulinic acid with 0.1 M HEPES pH 7.5, 10 % isopropanol and 20 % polyethylene glycol (PEG) 4000 in the well solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.04 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 3.47→178.02 Å / Num. obs: 63352 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 75.9 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 14.7
Reflection shellResolution: 3.47→3.6 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
MOSFLM5.8.0107data reduction
SCALAdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1b4e

1b4e


Resolution: 3.47→178.02 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.897 / SU B: 72.087 / SU ML: 0.499 / Cross valid method: THROUGHOUT / ESU R Free: 0.641 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25002 3154 5 %RANDOM
Rwork0.14762 ---
obs0.1528 60159 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.638 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å2-0.51 Å20 Å2
2---1.02 Å20 Å2
3---3.31 Å2
Refinement stepCycle: 1 / Resolution: 3.47→178.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31680 0 24 35 31739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01932424
X-RAY DIFFRACTIONr_bond_other_d0.0020.0231284
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.96643935
X-RAY DIFFRACTIONr_angle_other_deg1.161371844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.46354020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62222.8461476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.877155364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.07815288
X-RAY DIFFRACTIONr_chiral_restr0.110.24776
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02136408
X-RAY DIFFRACTIONr_gen_planes_other0.0020.027380
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_it2.9666.77116116
X-RAY DIFFRACTIONr_mcbond_other2.9666.77116115
X-RAY DIFFRACTIONr_mcangle_it5.04510.15320124
X-RAY DIFFRACTIONr_mcangle_other5.04510.15320125
X-RAY DIFFRACTIONr_scbond_it2.5717.06816308
X-RAY DIFFRACTIONr_scbond_other2.5717.06816309
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.50210.50123812
X-RAY DIFFRACTIONr_long_range_B_refined7.73554.36136269
X-RAY DIFFRACTIONr_long_range_B_other7.73554.36236270
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.468→3.558 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 256 -
Rwork0.196 4379 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.77560.0052-0.3410.11710.02040.17090.153-0.14250.04680.0198-0.1011-0.0313-0.09730.1133-0.05190.1607-0.29070.01750.5921-0.02190.0668-52.199790.4375-24.7031
20.12590.0598-0.06290.347-0.33370.65080.11910.04250.0247-0.1462-0.00580.0659-0.01260.0453-0.11330.3090.05040.01180.52520.0410.0249-90.299179.9835-68.1103
30.44150.0743-0.22210.1938-0.07160.49790.12080.0765-0.0758-0.0097-0.0564-0.00790.07860.1247-0.06430.18520.06050.03820.4571-0.0720.1315-61.726357.2828-47.8918
40.35690.2215-0.02950.1816-0.06620.54840.21990.06270.17780.05330.04060.0684-0.14050.0391-0.26050.4166-0.04680.29590.14170.0410.312-80.8128113.2817-44.6374
50.43960.1201-0.33070.0934-0.00480.55980.0372-0.14470.0366-0.0024-0.05780.05820.16610.15180.02060.25310.0123-0.04450.45320.05840.0669-73.820655.0783-18.5205
60.4569-0.0271-0.07130.02950.00650.59210.28780.07570.11320.03070.02720.0325-0.2294-0.1274-0.3150.3230.1470.23560.28990.11640.2398-108.200399.7106-35.8438
70.3972-0.1646-0.20640.2342-0.19850.60450.1387-0.16810.07340.01470.01050.0405-0.14570.1523-0.14920.3127-0.26940.10990.4318-0.1430.0663-78.388495.0822-6.9628
80.5750.167-0.26720.1106-0.14390.44580.10240.12070.0122-0.00150.02650.00660.0793-0.1045-0.1290.2726-0.0796-0.08560.43550.01230.0689-103.704659.9872-46.9925
90.31430.19120.07920.2341-0.07370.3941-0.05920.082-0.05730.1108-0.0544-0.1231-0.196-0.05820.11360.4114-0.0766-0.01350.26980.05810.1199-28.22780.777432.9614
100.17450.0631-0.19850.42520.28350.5829-0.05610.117-0.1258-0.1706-0.047-0.0776-0.1239-0.10660.10320.24580.00420.08660.5303-0.07480.1004-31.063854.02071.1112
110.1758-0.1048-0.13670.3454-0.00180.2061-0.02240.0528-0.04240.2594-0.0934-0.1112-0.04030.1150.11580.2777-0.1018-0.19460.36090.20020.2389-1.992954.716752.3911
120.0460.07390.11790.24560.18240.38210.05140.043-0.04280.0294-0.1161-0.10890.22010.13630.06460.17040.15420.13660.30770.05290.438-4.921327.917720.4685
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 402
2X-RAY DIFFRACTION2B1 - 402
3X-RAY DIFFRACTION3C1 - 402
4X-RAY DIFFRACTION4D1 - 402
5X-RAY DIFFRACTION5E1 - 402
6X-RAY DIFFRACTION6F1 - 402
7X-RAY DIFFRACTION7G1 - 402
8X-RAY DIFFRACTION8H1 - 402
9X-RAY DIFFRACTION9I1 - 402
10X-RAY DIFFRACTION10J1 - 402
11X-RAY DIFFRACTION11K1 - 402
12X-RAY DIFFRACTION12L1 - 402

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