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- PDB-4o6q: 0.95A resolution structure of the hemophore HasA from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 4o6q
Title0.95A resolution structure of the hemophore HasA from Pseudomonas aeruginosa (Y75A 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
FORMIC ACID / PROTOPORPHYRIN IX CONTAINING FE / HasAp
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.95 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)19,4723
Polymers18,8091
Non-polymers6632
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.437, 46.729, 101.037
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: 18809.438 Da / Num. of mol.: 1 / Mutation: Y75A
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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#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.: 322 / 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: 43.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 1.6M ammonium sulfate, 100mM Hepes, 200mM NaCl, pH 7.5, 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 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.95→50.519 Å / Num. all: 97317 / Num. obs: 97317 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Biso Wilson estimate: 8.57 Å2 / Rsym value: 0.055 / Net I/σ(I): 18.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
0.95-15.60.6011.367153119400.60180
1-1.065.60.3642.170408125180.36488.7
1.06-1.145.20.2193.464613124150.21993.8
1.14-1.238.30.1564.799882120510.15697.2
1.23-1.3411.80.1225.9133208112740.12298.6
1.34-1.512.40.0937.5128449103460.09399.2
1.5-1.73130.0699.511973592070.06999.8
1.73-2.1212.20.052119565278180.05299.7
2.12-3130.04512.68028461670.045100
3-34.43711.90.04212.24246435810.04299.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.32 Å42.41 Å
Translation1.32 Å42.41 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.14data extraction
JDirectordata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ELL

3ell


Resolution: 0.95→34.304 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 12.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.146 4861 5 %RANDOM
Rwork0.135 ---
obs0.1355 97223 93.93 %-
all-97223 --
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.551 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso max: 70.97 Å2 / Biso mean: 12.0884 Å2 / Biso min: 5.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.3928 Å20 Å2-0 Å2
2--0.6742 Å20 Å2
3----0.2814 Å2
Refinement stepCycle: LAST / Resolution: 0.95→34.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 46 322 1679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121454
X-RAY DIFFRACTIONf_angle_d1.4562020
X-RAY DIFFRACTIONf_chiral_restr0.091219
X-RAY DIFFRACTIONf_plane_restr0.01264
X-RAY DIFFRACTIONf_dihedral_angle_d12.588492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.95-0.9840.24353880.23277691807979
0.984-1.02340.20934500.19638071852184
1.0234-1.06990.18324220.16318821924390
1.0699-1.12630.1514960.13519104960094
1.1263-1.19690.13574900.12099420991096
1.1969-1.28930.13365480.113695701011898
1.2893-1.41910.11925040.106997241022899
1.4191-1.62440.12134700.107598181028899
1.6244-2.04660.13265470.1231987810425100
2.0466-34.32630.15475460.14761026510811100

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