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- PDB-5iqw: 1.95A resolution structure of Apo HasAp (R33A) from Pseudomonas a... -

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Basic information

Entry
Database: PDB / ID: 5iqw
Title1.95A resolution structure of Apo 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
ACETATE ION / : / Heme acquisition protein HasAp
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)19,2125
Polymers18,8151
Non-polymers3964
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Heme acquisition protein HasAp
hetero molecules

A: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,42310
Polymers37,6312
Non-polymers7938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3270 Å2
ΔGint-52 kcal/mol
Surface area14200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.781, 92.781, 95.714
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 5.47 Å3/Da / Density % sol: 77.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.0 M sodium acetate trihydrate, 0.1 M HEPES, 0.05 M Cd(SO4) hydrate

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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 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→47.86 Å / Num. obs: 31128 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 34.99 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.079 / Net I/σ(I): 21.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.95-213.21.7711100
8.94-47.8610.30.035199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.52 Å66.47 Å
Translation6.52 Å66.47 Å

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
PHASER2.5.2phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ELL

3ell


Resolution: 1.95→33.309 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 22.71
Details: The number of reflections used during refinement is greater than the number unique reflections reported for data scaling. This is due to the fact that Friedel pairs were kept separate during ...Details: The number of reflections used during refinement is greater than the number unique reflections reported for data scaling. This is due to the fact that Friedel pairs were kept separate during refinement to refine the anomalous scattering factors for the Cd2+ atoms.
RfactorNum. reflection% reflection
Rfree0.2116 2853 4.91 %
Rwork0.1852 --
obs0.1865 58073 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.3 Å2 / Biso mean: 47.7509 Å2 / Biso min: 25.14 Å2
Refinement stepCycle: final / Resolution: 1.95→33.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1284 0 7 72 1363
Biso mean--52.73 51.96 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011326
X-RAY DIFFRACTIONf_angle_d1.141813
X-RAY DIFFRACTIONf_chiral_restr0.058202
X-RAY DIFFRACTIONf_plane_restr0.007239
X-RAY DIFFRACTIONf_dihedral_angle_d9.91752
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.98360.31311330.291227832916100
1.9836-2.01970.29051150.275427882903100
2.0197-2.05860.30811290.26292755288499
2.0586-2.10060.27961320.252708284099
2.1006-2.14620.32451670.239827472914100
2.1462-2.19610.28231610.229727232884100
2.1961-2.25110.26731300.203727912921100
2.2511-2.31190.22191440.204227592903100
2.3119-2.37990.26621730.202527692942100
2.3799-2.45670.20541440.192927332877100
2.4567-2.54450.19521510.191927342885100
2.5445-2.64630.20981350.189627912926100
2.6463-2.76670.22691700.19227362906100
2.7667-2.91250.23241650.190927602925100
2.9125-3.09480.19461330.193527802913100
3.0948-3.33360.2791120.184627782890100
3.3336-3.66870.17881020.189928272929100
3.6687-4.19870.20131560.159427432899100
4.1987-5.28650.15381380.142227682906100
5.2865-33.31430.19051630.1827472910100

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