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- PDB-4es6: Crystal structure of HemD (PA5259) from Pseudomonas aeruginosa (P... -

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Basic information

Entry
Database: PDB / ID: 4es6
TitleCrystal structure of HemD (PA5259) from Pseudomonas aeruginosa (PAO1) at 2.22 A resolution
ComponentsUroporphyrinogen-III synthase
KeywordsLYASE / HEME-biosynthesis / Uroporphyrinogen-III synthase / cytoplasmic
Function / homology
Function and homology information


uroporphyrinogen-III synthase / uroporphyrinogen-III synthase activity / uroporphyrinogen III biosynthetic process / protoporphyrinogen IX biosynthetic process
Similarity search - Function
Rossmann fold - #10090 / Tetrapyrrole biosynthesis, uroporphyrinogen III synthase / Tetrapyrrole biosynthesis, uroporphyrinogen III synthase superfamily / Uroporphyrinogen-III synthase / Uroporphyrinogen-III synthase HemD / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uroporphyrinogen-III synthase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.22 Å
AuthorsSchnell, R. / Schneider, G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: The AEROPATH project targeting Pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery.
Authors: Moynie, L. / Schnell, R. / McMahon, S.A. / Sandalova, T. / Boulkerou, W.A. / Schmidberger, J.W. / Alphey, M. / Cukier, C. / Duthie, F. / Kopec, J. / Liu, H. / Jacewicz, A. / Hunter, W.N. / ...Authors: Moynie, L. / Schnell, R. / McMahon, S.A. / Sandalova, T. / Boulkerou, W.A. / Schmidberger, J.W. / Alphey, M. / Cukier, C. / Duthie, F. / Kopec, J. / Liu, H. / Jacewicz, A. / Hunter, W.N. / Naismith, J.H. / Schneider, G.
History
DepositionApr 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uroporphyrinogen-III synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6593
Polymers27,5881
Non-polymers712
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.070, 132.070, 42.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Uroporphyrinogen-III synthase / UROS / Hydroxymethylbilane hydrolyase [cyclizing] / Uroporphyrinogen-III cosynthase


Mass: 27588.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: hemD, PA5259 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P48246, uroporphyrinogen-III synthase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.35 Å3/Da / Density % sol: 63.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 0.1M Na-Cacodylate pH 6.7, 0.87M Na-Citrate , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2009 / Details: mirrors
RadiationMonochromator: SI (311) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.22→66.04 Å / Num. all: 18993 / Num. obs: 18993 / % possible obs: 99 % / Observed criterion σ(F): 3.1 / Observed criterion σ(I): 3.1 / Redundancy: 6.3 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 12
Reflection shellResolution: 2.22→2.34 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2611 / Rsym value: 0.539 / % possible all: 95.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.22→41.76 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.775 / SU ML: 0.143 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 3.1 / σ(I): 3.1 / ESU R: 0.217 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25183 940 5 %RANDOM
Rwork0.21234 ---
obs0.21428 17976 98.75 %-
all-17976 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.413 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.73 Å2
Refine analyzeLuzzati coordinate error free: 0.191 Å
Refinement stepCycle: LAST / Resolution: 2.22→41.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 2 98 2005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221953
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.9992664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5625250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86722.52987
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39815311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4681524
X-RAY DIFFRACTIONr_chiral_restr0.0710.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221517
X-RAY DIFFRACTIONr_mcbond_it0.6251.51248
X-RAY DIFFRACTIONr_mcangle_it1.20121991
X-RAY DIFFRACTIONr_scbond_it1.7523705
X-RAY DIFFRACTIONr_scangle_it3.0684.5672
LS refinement shellResolution: 2.22→2.278 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 64 -
Rwork0.381 1246 -
obs-1246 93.71 %

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