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- PDB-5iqx: 1.05A resolution structure of Holo HasAp (R33A) from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 5iqx
Title1.05A resolution structure of Holo HasAp (R33A) from Pseudomonas aeruginosa
ComponentsHeme acquisition protein HasAp
KeywordsHEME BINDING PROTEIN / HEMOPHORE / H32 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 / D-MALATE / Heme acquisition protein HasAp
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.05 Å
AuthorsKumar, R. / Lovell, S. / Battaile, K.P. / Yao, H. / Rivera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB0818488, MCB1158469 United States
CitationJournal: Biochemistry / Year: 2016
Title: Replacing Arginine 33 for Alanine in the Hemophore HasA from Pseudomonas aeruginosa Causes Closure of the H32 Loop in the Apo-Protein.
Authors: Kumar, R. / Qi, Y. / Matsumura, H. / Lovell, S. / Yao, H. / Battaile, K.P. / Im, W. / Moenne-Loccoz, P. / Rivera, M.
History
DepositionMar 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / diffrn_radiation_wavelength / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6587
Polymers18,8151
Non-polymers8436
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.167, 47.161, 101.374
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsMonomer according to gel filtration

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Components

#1: Protein Heme acquisition protein HasAp


Mass: 18815.418 Da / Num. of mol.: 1 / Fragment: HasAp / Mutation: R33A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: hasAp, PA3407 / Plasmid: pET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD (DE3) / References: UniProt: G3XD33
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.17 Å3/Da / Density % sol: 43.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.1 M DL-Malic Acid

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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: Oct 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.05→47.16 Å / Num. obs: 75527 / % possible obs: 97.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 8.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Net I/σ(I) obs% possible all
1.05-1.076.20.5612205435720.8593.394.4
5.75-47.165.70.04532615680.99836.499.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.02 Å50.69 Å
Translation1.02 Å50.69 Å

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
PHASER2.5.5phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ELL

3ell


Resolution: 1.05→34.527 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.09 / Phase error: 9.81
RfactorNum. reflection% reflection
Rfree0.1293 3772 5 %
Rwork0.1126 --
obs0.1134 75451 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 45.65 Å2 / Biso mean: 11.7057 Å2 / Biso min: 4.56 Å2
Refinement stepCycle: final / Resolution: 1.05→34.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1315 0 108 230 1653
Biso mean--11.27 24.09 -
Num. residues----182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081580
X-RAY DIFFRACTIONf_angle_d1.0522215
X-RAY DIFFRACTIONf_chiral_restr0.083232
X-RAY DIFFRACTIONf_plane_restr0.007288
X-RAY DIFFRACTIONf_dihedral_angle_d13.869536
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.05-1.06330.18531470.15912548269594
1.0633-1.07730.17061100.14522516262694
1.0773-1.0920.1381280.13292553268195
1.092-1.10760.15931480.12782541268996
1.1076-1.12420.12431550.12282550270595
1.1242-1.14170.1351260.10872611273797
1.1417-1.16050.13051530.10252544269796
1.1605-1.18050.12991640.10472586275096
1.1805-1.20190.09931160.10022616273297
1.2019-1.22510.10931420.12614275697
1.2251-1.25010.11181230.09792623274697
1.2501-1.27730.13741470.09652622276997
1.2773-1.3070.12231360.09732638277497
1.307-1.33970.11121390.09382635277498
1.3397-1.37590.10861270.09182674280198
1.3759-1.41640.12881310.09232654278598
1.4164-1.46210.11431430.09162652279598
1.4621-1.51430.111270.0942685281298
1.5143-1.5750.11291350.09492707284298
1.575-1.64660.10291450.09722681282699
1.6466-1.73350.11341330.10122720285399
1.7335-1.84210.11921350.10922728286399
1.8421-1.98430.12391620.10627312893100
1.9843-2.18390.10411410.10627402881100
2.1839-2.49990.11541580.116427702928100
2.4999-3.14920.14921420.132728212963100
3.1492-34.54580.16121590.13032919307899

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