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- PDB-1w54: Stepwise introduction of a zinc binding site into Porphobilinogen... -

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Basic information

Entry
Database: PDB / ID: 1w54
TitleStepwise introduction of a zinc binding site into Porphobilinogen synthase from Pseudomonas aeruginosa (mutation D139C)
ComponentsDELTA-AMINOLEVULINIC ACID DEHYDRATASE
KeywordsSYNTHASE / EVOLUTION / METALLOENZYME / PORPHOBILINOGEN SYNTHASE / PSEUDOMONAS AERUGINOSA / PROTEIN ENGINEERING
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
FORMIC ACID / : / Delta-aminolevulinic acid dehydratase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFrere, F. / Reents, H. / Schubert, W.-D. / Heinz, D.W. / Jahn, D.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Tracking the Evolution of Porphobilinogen Synthase Metal Dependence in Vitro
Authors: Frere, F. / Reents, H. / Schubert, W.-D. / Heinz, D.W. / Jahn, D.
History
DepositionAug 5, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_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_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.pdbx_dist_value / _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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA BA" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA 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)74,45410
Polymers74,1042
Non-polymers3508
Water5,477304
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)297,81440
Polymers296,4168
Non-polymers1,39932
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)125.231, 125.232, 86.030
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: (-0.84395, 0.53629, 0.0122), (0.53631, 0.84402, -0.00172), (-0.01122, 0.00509, -0.99992)
Vector: 197.79733, -57.44056, -16.08522)

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 37051.953 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q59643, porphobilinogen synthase

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Non-polymers , 5 types, 312 molecules

#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYTIC ACTIVITY: 2 5-AMINOLEVULINATE = PORPHOBILINOGEN + 2 H(2)O. ENGINEERED MUTATION IN CHAINS ...CATALYTIC ACTIVITY: 2 5-AMINOLEVULINATE = PORPHOBILINOGEN + 2 H(2)O. ENGINEERED MUTATION IN CHAINS A AND B, ASP 139 TO CYS, ILE 199 VAL
Sequence detailsAMINO ACID EXCHANGE IN POSITION 139, ASP TURNED INTO CYS FORMIC ACID IS USED TO REPRESENT ...AMINO ACID EXCHANGE IN POSITION 139, ASP TURNED INTO CYS FORMIC ACID IS USED TO REPRESENT CARBOXYLIC GROUPS OF OTHERWISE DISORDERED MOLECULES BOUND TO THE ACTIVE SITE. THE SEQUENCE CONFLICT AT RESIDUE 199 IS DUE TO AN ACCIDENTAL POINT MUTATION IN THE GENE USED FOR THE MUTATIONAL STUDY.

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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: 2.23 Å3/Da / Density % sol: 44.38 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROL PROTEIN SOLUTION (8,7 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10 MM MGCL2, 10 ZNCL2, 10 MM DTT) PLUS 5 MICROL RESERVOIR SOLUTION ...Details: HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROL PROTEIN SOLUTION (8,7 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10 MM MGCL2, 10 ZNCL2, 10 MM DTT) PLUS 5 MICROL RESERVOIR SOLUTION (28,5 % (W/V) PEG-400, 100 MM NA-HEPES PH 7.5, 80MM MGCL2, 20MM DTT) ABOVE 500 MICROL OF RESERVOIR SOLUTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 2002 / Details: BLUE OPTIC
RadiationMonochromator: OSMIC CONFOCAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→47.1 Å / Num. obs: 35228 / % possible obs: 99.8 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 5.3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B4K

1b4k


Resolution: 2.2→87.71 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.622 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1811 5.1 %RANDOM
Rwork0.154 ---
obs0.157 33396 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--0.57 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4899 0 12 304 5215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0215082
X-RAY DIFFRACTIONr_bond_other_d0.0050.024728
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.966902
X-RAY DIFFRACTIONr_angle_other_deg1.166310897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3595644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1510.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025790
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021075
X-RAY DIFFRACTIONr_nbd_refined0.2170.21073
X-RAY DIFFRACTIONr_nbd_other0.2310.25671
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.23122
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.2140
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.55323200
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.86935135
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.19921882
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.20331767
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: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.227 130
Rwork0.151 2409

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