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- PDB-1b4k: High resolution crystal structure of a MG2-dependent 5-aminolevul... -

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Basic information

Entry
Database: PDB / ID: 1b4k
TitleHigh resolution crystal structure of a MG2-dependent 5-aminolevulinic acid dehydratase
ComponentsPROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE)
KeywordsLYASE / HEME BIOSYNTHESIS / MAGNESIUM / LEVULINIC ACID
Function / homology
Function and homology information


porphobilinogen synthase / porphobilinogen synthase activity / porphyrin-containing compound biosynthetic process / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / 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 speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsFrankenberg, N. / Jahn, D. / Heinz, D.W.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: High resolution crystal structure of a Mg2+-dependent porphobilinogen synthase.
Authors: Frankenberg, N. / Erskine, P.T. / Cooper, J.B. / Shoolingin-Jordan, P.M. / Jahn, D. / Heinz, D.W.
History
DepositionDec 22, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 13, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jan 18, 2012Group: Derived calculations / Non-polymer description
Revision 1.4Aug 9, 2023Group: 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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_asym_id / _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_asym_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_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,6057
Polymers74,1562
Non-polymers4495
Water10,305572
1
A: PROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE)
B: PROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE)
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)298,41828
Polymers296,6238
Non-polymers1,79520
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_645-y+3/2,x-1/2,z1
crystal symmetry operation4_565y+1/2,-x+3/2,z1
Buried area47930 Å2
ΔGint-226 kcal/mol
Surface area77720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.240, 128.240, 86.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.812422, 0.582386, -0.02822), (0.582564, 0.812782, 0.002297), (0.024275, -0.014573, -0.999599)
Vector: 195.5399, -62.8235, -14.1395)

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Components

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


Mass: 37077.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SCHIFF BASE LINK BETWEEN ATOM NZ OF LYS260 AND ATOM C4 OF LEVULINIC ACID
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Cellular location: CYTOPLASM / Gene: HEMB / Plasmid: PGEX-6P-1 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): HEMB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q59643, porphobilinogen synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SHF / LAEVULINIC ACID / LEVULINIC ACID


Mass: 116.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsCARBONYL OXYGEN OF LEVULINIC ACID MISSING CARBONYL OXYGEN OF LEVULINIC ACID MISSING BECAUSE OF SCHIFF

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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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Details: drop contained equal volume of protein and reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMHEPES1drop
310 mM1dropMgCl2
41.2 Mammonium sulfate1reservoir
512 %(v/v)glycerol1reservoir
63 %(v/v)isopropanol1reservoir
70.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 16, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8345 Å / Relative weight: 1
ReflectionResolution: 1.67→51.3 Å / Num. obs: 81840 / % possible obs: 98.2 % / Redundancy: 8.8 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.054 / Net I/σ(I): 9
Reflection shellResolution: 1.67→1.76 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.269 / % possible all: 94.1
Reflection
*PLUS
Num. measured all: 719706 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 94.1 % / Rmerge(I) obs: 0.269

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AW5

1aw5


Resolution: 1.67→51.3 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.18
RfactorNum. reflection% reflectionSelection details
Rfree0.208 3988 5 %RANDOM
Rwork0.178 ---
obs-75401 98.2 %-
Displacement parametersBiso mean: 19.4 Å2
Refinement stepCycle: LAST / Resolution: 1.67→51.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5007 0 25 572 5604
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0820.05
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_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 81840
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.3

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