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- PDB-6urb: Pseudomonas aeruginosa HasA mutant - H32A -

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Basic information

Entry
Database: PDB / ID: 6urb
TitlePseudomonas aeruginosa HasA mutant - H32A
ComponentsHasAp
KeywordsMETAL BINDING PROTEIN / HasA / hemophore
Function / homologyHaem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / HasAp
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.096 Å
AuthorsBrimberry, M. / Lanzilotta, W. / Wilks, A. / Dent, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RNIHXRR166642CV United States
CitationJournal: To Be Published
Title: Crystal Structure of Pseudomonas aeruginosa HasA mutant H32A
Authors: Brimberry, M. / Lanzilotta, W.
History
DepositionOct 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HasAp
B: HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0494
Polymers40,8162
Non-polymers1,2332
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-44 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.340, 51.867, 72.811
Angle α, β, γ (deg.)90.000, 130.670, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

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Components

#1: Protein HasAp / Heme acquisition protein HasA


Mass: 20408.195 Da / Num. of mol.: 2 / Mutation: H32A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: hasAp, IPC3_06435 / Production host: Escherichia coli (E. coli) / References: UniProt: O69756
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 37.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 1M Sodium Citrate, 0.1M Tris HCl pH 7.4, 0.2M Sodium Chloride

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 17648 / % possible obs: 94 % / Redundancy: 3.6 % / CC1/2: 0.995 / Net I/σ(I): 17
Reflection shellResolution: 2.09→2.17 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 17648 / CC1/2: 0.91

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ELL

3ell


Resolution: 2.096→29.891 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.33
RfactorNum. reflection% reflection
Rfree0.3022 886 5.02 %
Rwork0.233 --
obs0.2364 17647 94.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.75 Å2 / Biso mean: 49.9748 Å2 / Biso min: 10.59 Å2
Refinement stepCycle: final / Resolution: 2.096→29.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 0 86 90 2785
Biso mean--39.57 38.81 -
Num. residues----361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082823
X-RAY DIFFRACTIONf_angle_d1.1593898
X-RAY DIFFRACTIONf_chiral_restr0.053420
X-RAY DIFFRACTIONf_plane_restr0.01504
X-RAY DIFFRACTIONf_dihedral_angle_d4.8392075
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.096-2.22720.32771430.2527266690
2.2272-2.39910.30831390.2566268192
2.3991-2.64040.36891530.2759288998
2.6404-3.02210.30841540.2523288498
3.0221-3.80640.28021420.2252279394
3.8064-29.8910.28871550.2082284894

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