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- PDB-4o6u: 0.89A resolution structure of the hemophore HasA from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 4o6u
Title0.89A resolution structure of the hemophore HasA from Pseudomonas aeruginosa (H83A mutant)
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: 0.89 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)19,5754
Polymers18,8341
Non-polymers7413
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.378, 46.988, 100.902
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.: 2 / 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.: 235 / 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: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 1.6M ammonium sulfate, 100mM MES, 10% (v/V) dioxane, pH 6.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.89→100.902 Å / Num. all: 120441 / Num. obs: 120441 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 7.04 Å2 / Rsym value: 0.05 / Net I/σ(I): 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
0.89-0.943.70.387258355157300.38787.2
0.94-15.90.2543.194803160020.25493.1
1-1.066.10.1584.993098152560.15894.3
1.06-1.1560.1047.287882145660.10496.4
1.15-1.266.50.0819.188289136800.08198.4
1.26-1.416.40.06610.680223126170.06699.7
1.41-1.626.70.05312.475295112370.053100
1.62-1.996.30.04313.76040695360.04399.9
1.99-2.816.60.039154956874820.039100
2.81-100.9026.20.03813.52681443350.03899.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.24 Å42.6 Å
Translation1.24 Å42.6 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
PHENIXdev_730refinement
PDB_EXTRACT3.14data extraction
JDirectordata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ELL

3ell


Resolution: 0.89→32.541 Å / Occupancy max: 1 / Occupancy min: 0.34 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 9.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1338 6000 4.99 %RANDOM
Rwork0.124 ---
obs0.1245 120343 95.6 %-
all-120343 --
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.928 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso max: 38.59 Å2 / Biso mean: 8.3304 Å2 / Biso min: 3.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.6447 Å2-0 Å2-0 Å2
2---0.3785 Å20 Å2
3----0.2662 Å2
Refinement stepCycle: LAST / Resolution: 0.89→32.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 51 235 1602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151548
X-RAY DIFFRACTIONf_angle_d1.6882163
X-RAY DIFFRACTIONf_chiral_restr0.101236
X-RAY DIFFRACTIONf_plane_restr0.012285
X-RAY DIFFRACTIONf_dihedral_angle_d12.776542
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.89-0.90010.23361590.23283046320578
0.9001-0.91070.22351790.20383401358086
0.9107-0.92180.18861870.18353564375191
0.9218-0.93350.18731860.15613540372690
0.9335-0.94580.16931900.14123620381092
0.9458-0.95870.16021900.13293622381292
0.9587-0.97240.13691940.12613694388894
0.9724-0.98690.13711940.12053694388893
0.9869-1.00240.11961930.11173679387294
1.0024-1.01880.12271960.10373730392694
1.0188-1.03640.12311930.10173677387094
1.0364-1.05520.11251960.09793750394695
1.0552-1.07550.10251960.09483739393594
1.0755-1.09750.11322010.09263823402497
1.0975-1.12130.10562010.08633830403197
1.1213-1.14740.0872020.08493840404297
1.1474-1.17610.09852020.08633863406598
1.1761-1.20790.0932060.0883914412098
1.2079-1.24350.10122040.0893897410198
1.2435-1.28360.09292070.09363940414799
1.2836-1.32950.11172080.097739814189100
1.3295-1.38270.11452110.098340034214100
1.3827-1.44560.11622070.102639444151100
1.4456-1.52180.10812100.10240164226100
1.5218-1.61720.12162120.10840284240100
1.6172-1.7420.12212100.119640114221100
1.742-1.91730.13862120.127440354247100
1.9173-2.19470.13082130.127340544267100
2.1947-2.76490.15312160.148841264342100
2.7649-32.56290.17462250.161542824507100

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