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- PDB-5xic: Crystal Structure of HasAp with Fe-5,10,15-triphenylporphyrin -

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Basic information

Entry
Database: PDB / ID: 5xic
TitleCrystal Structure of HasAp with Fe-5,10,15-triphenylporphyrin
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
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / 5,10,15-Triphenylporphyrin cpntaining FE / Heme acquisition protein HasAp
Similarity search - Component
Biological speciesPseudomonas aeruginosa str. PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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
DepositionApr 26, 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
C: Heme acquisition protein HasAp
D: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,45812
Polymers75,6064
Non-polymers3,8528
Water8,575476
1
A: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2354
Polymers18,9021
Non-polymers1,3333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8643
Polymers18,9021
Non-polymers9632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4942
Polymers18,9021
Non-polymers5921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8643
Polymers18,9021
Non-polymers9632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.652, 83.460, 83.489
Angle α, β, γ (deg.)90.000, 89.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Heme acquisition protein HasAp


Mass: 18901.535 Da / Num. of mol.: 4 / Fragment: UNP Residues 1-184 / Mutation: Wild-type
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-WXP / 5,10,15-Triphenylporphyrin cpntaining FE


Mass: 592.469 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H24FeN4
#3: Chemical
ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Polyethylene glycol


Mass: 370.436 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O9
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.1 Å3/Da / Density % sol: 41.53 % / Mosaicity: 0.831 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15% v/v PEG 400, 50mM Tris-HCl (pH8.5), 50mM KPi buffer (pH7.0), 100mM MgCl2, 15% v/v PEG 400

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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: 1.45→50 Å / Num. obs: 107752 / % possible obs: 96.2 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.019 / Rrim(I) all: 0.034 / Χ2: 0.796 / Net I/σ(I): 16.6 / Num. measured all: 330905
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.52.40.20488840.9140.1510.2550.90980
1.5-1.5630.158107900.9590.1060.1910.92196.3
1.56-1.633.10.114108740.9760.0750.1370.92397.3
1.63-1.723.10.083109280.9860.0550.10.89297.8
1.72-1.833.10.062109600.9910.0410.0740.86398
1.83-1.973.10.045109840.9940.0290.0540.77998.4
1.97-2.173.20.033110550.9960.0210.0390.66998.7
2.17-2.483.20.028110940.9970.0180.0330.60398.9
2.48-3.123.20.031111110.9960.020.0370.84198.9
3.12-503.20.023110720.9980.0150.0280.63597.4

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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: 1.45→19.48 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.2028 / FOM work R set: 0.8598 / SU B: 1.36 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0831 / SU Rfree: 0.0813 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2177 5347 5 %RANDOM
Rwork0.1928 ---
obs0.194 101412 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 46.14 Å2 / Biso mean: 13.68 Å2 / Biso min: 6.67 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.45→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5340 0 296 476 6112
Biso mean--18.69 23.86 -
Num. residues----736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196054
X-RAY DIFFRACTIONr_bond_other_d0.0070.025148
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9878276
X-RAY DIFFRACTIONr_angle_other_deg0.9293.00711979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8745794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.18124.825228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.69815774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0441511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2862
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217196
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021347
LS refinement shellResolution: 1.45→1.487 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 314 -
Rwork0.244 6105 -
all-6419 -
obs--78.48 %

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