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- PDB-4o6t: 1.25A resolution structure of the hemophore HasA from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 4o6t
Title1.25A resolution structure of the hemophore HasA from Pseudomonas aeruginosa (H83A mutant, pH 5.4)
ComponentsHasAp
KeywordsHeme Binding Protein / Hemophore / Y75 Loop
Function / homology
Function and homology information


Heme-binding Protein A; Chain: A; / Haem-binding HasA / Haem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / HasAp
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsLovell, S. / Kumar, R. / Battaile, K.P. / Matsumura, H. / Yao, H. / Rodriguez, J.C. / Moenne-Loccoz, P. / Rivera, M.
CitationJournal: Biochemistry / Year: 2014
Title: Replacing the Axial Ligand Tyrosine 75 or Its Hydrogen Bond Partner Histidine 83 Minimally Affects Hemin Acquisition by the Hemophore HasAp from Pseudomonas aeruginosa.
Authors: Kumar, R. / Matsumura, H. / Lovell, S. / Yao, H. / Rodriguez, J.C. / Battaile, K.P. / Moenne-Loccoz, P. / Rivera, M.
History
DepositionDec 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5133
Polymers18,8341
Non-polymers6792
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.431, 46.784, 101.807
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HasAp


Mass: 18834.465 Da / Num. of mol.: 1 / Mutation: H83A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: hasAp / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD (DE3) / References: UniProt: O69756
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.4
Details: 1.6M ammonium sulfate, 100mM MES, 10% (v/V) dioxane, pH 5.4, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→50.903 Å / Num. all: 46491 / Num. obs: 46491 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 9.57 Å2 / Rsym value: 0.092 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.25-1.326.30.80614200067070.806100
1.32-1.46.30.5931.33974863110.593100
1.4-1.496.30.4251.83756259840.425100
1.49-1.616.70.2632.83707855650.263100
1.61-1.776.60.1754.33404151200.175100
1.77-1.986.30.1176.32928046600.117100
1.98-2.286.40.0739.82665941620.073100
2.28-2.86.50.05512.62316935470.055100
2.8-3.9560.0415.51662027890.0499.9
3.95-101.8076.10.035171008016460.03599.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.46 Å42.51 Å
Translation1.46 Å42.51 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
PHENIX1.7.2_860refinement
PDB_EXTRACT3.14data extraction
JDirectordata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ELL

3ell


Resolution: 1.25→42.51 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 14.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1821 2350 5.06 %RANDOM
Rwork0.1528 ---
obs0.1543 46415 99.96 %-
all-46415 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.955 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso max: 43.51 Å2 / Biso mean: 12.3104 Å2 / Biso min: 4.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.8836 Å2-0 Å20 Å2
2---2.0979 Å20 Å2
3---1.2143 Å2
Refinement stepCycle: LAST / Resolution: 1.25→42.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 47 213 1576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111462
X-RAY DIFFRACTIONf_angle_d1.372029
X-RAY DIFFRACTIONf_chiral_restr0.088218
X-RAY DIFFRACTIONf_plane_restr0.009265
X-RAY DIFFRACTIONf_dihedral_angle_d12.821498
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.25-1.27550.3031190.257326022721
1.2755-1.30330.30121400.234825272667
1.3033-1.33360.2291510.207725542705
1.3336-1.36690.22141450.181725442689
1.3669-1.40390.23461600.16725052665
1.4039-1.44520.20091480.155225702718
1.4452-1.49180.19631290.140325842713
1.4918-1.54520.17031400.125825352675
1.5452-1.6070.16651390.123325862725
1.607-1.68020.1581290.120825762705
1.6802-1.76880.17281350.122725742709
1.7688-1.87960.13821410.130826012742
1.8796-2.02470.16671450.12825892734
2.0247-2.22850.17121290.135126132742
2.2285-2.55090.16831450.147926162761
2.5509-3.21370.1711040.16427032807
3.2137-42.53490.18311510.164527862937

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