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- PDB-5xkb: Crystal Structure of HasAp with Fe-5,15-bisethynyl-10,20-diphenyl... -

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Basic information

Entry
Database: PDB / ID: 5xkb
TitleCrystal Structure of HasAp with Fe-5,15-bisethynyl-10,20-diphenylporphyrin
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
Chem-WVP / Heme acquisition protein HasAp
Similarity search - Component
Biological speciesPseudomonas aeruginosa str. PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 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
DepositionMay 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)38,9324
Polymers37,8032
Non-polymers1,1292
Water5,837324
1
A: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4662
Polymers18,9021
Non-polymers5641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4662
Polymers18,9021
Non-polymers5641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)153.330, 153.330, 36.919
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: UNP 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-WVP / 5,15-Bisethynyl-10,20-diphenylporphyrin containing FE


Mass: 564.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H20FeN4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 3.31 Å3/Da / Density % sol: 62.89 % / Mosaicity: 0.549 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50mM Tris-HCl (pH7.0), 50mM KPi buffer (pH7.0), 100mM lithium sulfate, 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: Nov 9, 2016
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 40002 / % possible obs: 99.9 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.014 / Rrim(I) all: 0.045 / Χ2: 0.917 / Net I/σ(I): 17.5 / Num. measured all: 422418
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.9780.21139250.9740.0780.2260.9799
1.97-2.0510.70.15539780.9930.050.1630.965100
2.05-2.1410.90.11539480.9960.0370.1210.926100
2.14-2.2510.90.08739610.9980.0280.0910.895100
2.25-2.3910.90.06939600.9980.0220.0720.874100
2.39-2.5810.90.05539850.9990.0170.0580.828100
2.58-2.8410.90.04140290.9990.0130.0430.775100
2.84-3.2510.90.03439850.9990.0110.0360.805100
3.25-4.0910.90.0440580.9990.0130.0421.348100
4.09-5010.50.02841730.9990.0090.030.79999.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
MOLREPphasing
RefinementResolution: 1.9→19.17 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.1893 / WRfactor Rwork: 0.1688 / FOM work R set: 0.888 / SU B: 2.331 / SU ML: 0.068 / SU R Cruickshank DPI: 0.113 / SU Rfree: 0.1046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1888 1986 5 %RANDOM
Rwork0.1671 ---
obs0.1682 37648 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.32 Å2 / Biso mean: 19.714 Å2 / Biso min: 7.24 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.9→19.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2659 0 82 324 3065
Biso mean--16.12 28.12 -
Num. residues----366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022845
X-RAY DIFFRACTIONr_bond_other_d0.0040.022404
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9683889
X-RAY DIFFRACTIONr_angle_other_deg0.8953.0055580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7675372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26925.135111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.45915372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.881154
X-RAY DIFFRACTIONr_chiral_restr0.0690.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023328
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02612
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 127 -
Rwork0.212 2721 -
all-2848 -
obs--98.65 %

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