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- PDB-5xa4: Crystal Structure of HasAp with Fe-5,15-Diazaporphyrin -

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Basic information

Entry
Database: PDB / ID: 5xa4
TitleCrystal Structure of HasAp with Fe-5,15-Diazaporphyrin
ComponentsHeme acquisition protein HasAp
KeywordsTRANSPORT PROTEIN / HEME ACQUISITION PROTEIN
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
10,20-Diphenyl-5,15-diaza-porphyrin containing FE / Heme acquisition protein HasAp
Similarity search - Component
Biological speciesPseudomonas aeruginosa str. PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsShoji, O. / Uehara, H. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Structures of the Heme Acquisition Protein HasA with Iron(III)-5,15-Diphenylporphyrin and Derivatives Thereof as an Artificial Prosthetic Group
Authors: Uehara, H. / Shisaka, Y. / Nishimura, T. / Sugimoto, H. / Shiro, Y. / Miyake, Y. / Shinokubo, H. / Watanabe, Y. / Shoji, O.
History
DepositionMar 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Heme acquisition protein HasAp
B: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8404
Polymers37,8032
Non-polymers1,0372
Water8,665481
1
A: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4202
Polymers18,9021
Non-polymers5181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4202
Polymers18,9021
Non-polymers5181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)154.002, 154.002, 36.626
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Heme acquisition protein HasAp


Mass: 18901.535 Da / Num. of mol.: 2 / Fragment: Residues 1-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa str. PAO1 (bacteria)
Strain: PAO1 / Gene: hasAp, PA3407 / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[PREP4] / References: UniProt: G3XD33
#2: Chemical ChemComp-83L / 10,20-Diphenyl-5,15-diaza-porphyrin containing FE


Mass: 518.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H18FeN6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 3.32 Å3/Da / Density % sol: 62.91 % / Mosaicity: 0.497 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50mM MES (pH6.0), 50mM KPi buffer (pH7.0), 500mM Potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 28, 2015
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 122191 / % possible obs: 99.5 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.015 / Rrim(I) all: 0.046 / Χ2: 0.92 / Net I/σ(I): 14.8 / Num. measured all: 1060408
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.3-1.355.80.303117850.9260.1330.3320.84996.9
1.35-1.48.50.232122000.9740.0830.2470.90299.6
1.4-1.468.90.175121430.9860.0610.1850.89199.7
1.46-1.5490.125121570.9930.0440.1330.91499.8
1.54-1.6490.09121990.9960.0310.0950.959100
1.64-1.7690.067122190.9980.0230.0710.957100
1.76-1.949.10.05122660.9980.0170.0530.899100
1.94-2.229.10.044122980.9980.0150.0470.856100
2.22-2.89.20.049123880.9980.0170.0520.906100
2.8-5090.033125360.9990.0120.0351.0399.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W8O

3w8o


Resolution: 1.3→19.05 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.1945 / WRfactor Rwork: 0.1773 / FOM work R set: 0.8893 / SU B: 0.626 / SU ML: 0.027 / SU R Cruickshank DPI: 0.0406 / SU Rfree: 0.0415 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1829 6109 5 %RANDOM
Rwork0.1683 ---
obs0.169 115462 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.62 Å2 / Biso mean: 15.876 Å2 / Biso min: 8.21 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.3→19.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2670 0 80 481 3231
Biso mean--15.01 27.28 -
Num. residues----368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192978
X-RAY DIFFRACTIONr_bond_other_d0.0060.022523
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.9664083
X-RAY DIFFRACTIONr_angle_other_deg0.88535873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0845399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44125.088114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.72815397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.541155
X-RAY DIFFRACTIONr_chiral_restr0.0730.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023524
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02642
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 385 -
Rwork0.239 7668 -
all-8053 -
obs--89.96 %

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