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Basic information

Entry
Database: PDB / ID: 1gzg
TitleComplex of a Mg2-dependent porphobilinogen synthase from Pseudomonas aeruginosa (mutant D139N) with 5-fluorolevulinic acid
ComponentsDELTA-AMINOLEVULINIC ACID DEHYDRATASE
KeywordsLYASE / HEME BIOSYNTHESIS / 5-FLUOROLEVULINIC 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
: / 5-FLUOROLEVULINIC ACID / Delta-aminolevulinic acid dehydratase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsFrere, F. / Schubert, W.-D. / Stauffer, F. / Frankenberg, N. / Neier, R. / Jahn, D. / Heinz, D.W.
CitationJournal: J. Mol. Biol. / Year: 2002
Title: Structure of porphobilinogen synthase from Pseudomonas aeruginosa in complex with 5-fluorolevulinic acid suggests a double Schiff base mechanism.
Authors: Frere, F. / Schubert, W.D. / Stauffer, F. / Frankenberg, N. / Neier, R. / Jahn, D. / Heinz, D.W.
History
DepositionMay 21, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 21, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / entity / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site.type_symbol / _citation.journal_abbrev / _citation.page_last / _citation.title / _citation_author.name / _entity.pdbx_number_of_molecules / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_site.pdbx_num_residues
Revision 2.1May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Dec 13, 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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_ptnr1_label_alt_id / _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.ptnr1_symmetry / _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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 2.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
B: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,02714
Polymers74,1262
Non-polymers90112
Water12,088671
1
A: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
B: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
hetero molecules

A: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
B: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
hetero molecules

A: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
B: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
hetero molecules

A: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
B: DELTA-AMINOLEVULINIC ACID DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,10956
Polymers296,5038
Non-polymers3,60548
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-y+3/2,x-1/2,z1
crystal symmetry operation4_565y+1/2,-x+3/2,z1
crystal symmetry operation2_765-x+2,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)127.131, 127.131, 86.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-2007-

HOH

21B-2086-

HOH

31B-2285-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DELTA-AMINOLEVULINIC ACID DEHYDRATASE / PORPHOBILINOGEN SYNTHASE / ALAD / ALADH


Mass: 37062.914 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SCHIFF BASE LINKS BETWEEN ATOMS NZ OF LYS205 AND LYS260 AND ATOMS C5 OF 5-FLUOROLEVULINIC ACID
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q59643, porphobilinogen synthase

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Non-polymers , 6 types, 683 molecules

#2: Chemical
ChemComp-LAF / 5-FLUOROLEVULINIC ACID


Mass: 134.106 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H7FO3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsMUTANT D139N, THE CRYSTALLIZED PROTEIN CONTAINS VAL AT THE POSITION 199.

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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 growMethod: vapor diffusion, sitting drop / pH: 9
Details: PROTEIN SOLUTION: 12 MG/ML PBGS MUTANT D139N IN 50 MM K-HEPES, 10 MM MGCL2. CRYSTALLIZATION SOLUTION: 0.99 ML PROTEIN SOLUTION = 0.01 ML 2MM 5F-LA IN 50 MM K-HEPES, 10 MM MGCL2. RESERVOIR ...Details: PROTEIN SOLUTION: 12 MG/ML PBGS MUTANT D139N IN 50 MM K-HEPES, 10 MM MGCL2. CRYSTALLIZATION SOLUTION: 0.99 ML PROTEIN SOLUTION = 0.01 ML 2MM 5F-LA IN 50 MM K-HEPES, 10 MM MGCL2. RESERVOIR SOLUTION: 1 M NA/K-TARTRATE, 0.2M LI2SO4, 0.1 M CHES PH = 9,5. SITTING DROP: 0.003 ML CRYSTALLISATION SOLUTION + 0.003 ML RESERVOIR SOLUTION
Crystal grow
*PLUS
pH: 7.5 / Method: sparse matrix screening
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMpotassium-HEPES11pH7.5
210 mM11MgCl2
312 mg/mlprotein11
42 mM5F-LA11
530 %(v/v)glycerol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 2001 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.66→20 Å / Num. obs: 82775 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 11
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 4.1 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.66 Å / Lowest resolution: 20 Å / Num. measured all: 433947
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 4.9 % / Mean I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
REFMAC5.0.32refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B4K

1b4k


Resolution: 1.66→91.29 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.31 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: LAST TWO C-TERMINAL RESIDUES WERE NOT SEEN IN THE DENSITY MAP
RfactorNum. reflection% reflectionSelection details
Rfree0.198 4131 5 %RANDOM
Rwork0.175 ---
obs-78644 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 20.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.66→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5050 0 57 671 5778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215557
X-RAY DIFFRACTIONr_bond_other_d0.0010.025034
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.9717719
X-RAY DIFFRACTIONr_angle_other_deg0.805311642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5843783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14215946
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1510.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026437
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021163
X-RAY DIFFRACTIONr_nbd_refined0.3320.31488
X-RAY DIFFRACTIONr_nbd_other0.2170.35452
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.5597
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3810.510
X-RAY DIFFRACTIONr_metal_ion_refined0.2320.510
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3610.334
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.3123
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.552
X-RAY DIFFRACTIONr_symmetry_hbond_other0.020.52
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5811.53466
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05725733
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.67332091
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8294.51977
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.66→1.7 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.241 295
Rwork0.214 5780
Software
*PLUS
Name: REFMAC / Version: '5.0.32 18/01/2001' / Classification: refinement
Refinement
*PLUS
Lowest resolution: 91.3 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.9

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