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- PDB-7abw: Crystal structure of siderophore reductase FoxB -

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Basic information

Entry
Database: PDB / ID: 7abw
TitleCrystal structure of siderophore reductase FoxB
ComponentsPepSY domain-containing protein
KeywordsMEMBRANE PROTEIN / Membrane protein Reductase Siderophore
Function / homologyPepSY-associated TM protein / PepSY-associated TM region / membrane / PROTOPORPHYRIN IX CONTAINING FE / PepSY domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 3.35 Å
AuthorsJosts, I. / Tidow, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structural insights into a novel family of integral membrane siderophore reductases.
Authors: Josts, I. / Veith, K. / Normant, V. / Schalk, I.J. / Tidow, H.
History
DepositionSep 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PepSY domain-containing protein
B: PepSY domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,69815
Polymers86,2252
Non-polymers5,47313
Water00
1
A: PepSY domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8408
Polymers43,1121
Non-polymers2,7277
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PepSY domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8597
Polymers43,1121
Non-polymers2,7466
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)237.065, 114.321, 64.382
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PepSY domain-containing protein / Peptidase


Mass: 43112.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: ALP65_03579, CAZ10_13355, DY930_33720, ECC04_000260, F7O90_26595, IPC36_29360, IPC669_34100, NCTC12951_00372, NCTC13621_01916, PaeAG1_03004, RW109_RW109_03547
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C7CRS7
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#4: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestY

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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: 5.06 Å3/Da / Density % sol: 75.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 30% PEG600 100 mm Bicine pH9 100 mM ZnSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.35→47.4 Å / Num. obs: 15384 / % possible obs: 92.5 % / Redundancy: 19.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.021 / Rrim(I) all: 0.066 / Net I/σ(I): 22.7
Reflection shellResolution: 3.35→3.717 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 759 / CC1/2: 0.839 / Rpim(I) all: 0.99 / Rrim(I) all: 1.48 / % possible all: 73.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
SHELXCDphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 3.35→46.36 Å / Cor.coef. Fo:Fc: 0.812 / Cor.coef. Fo:Fc free: 0.754 / SU B: 53.98 / SU ML: 0.422 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.78 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2988 767 5 %RANDOM
Rwork0.2646 ---
obs0.2663 14617 59.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.11 Å2 / Biso mean: 40.871 Å2 / Biso min: 5.97 Å2
Baniso -1Baniso -2Baniso -3
1--2.83 Å2-0 Å20 Å2
2--2.78 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 3.35→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5774 0 273 0 6047
Biso mean--29.5 --
Num. residues----725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136263
X-RAY DIFFRACTIONr_bond_other_d0.0170.0175731
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.6958553
X-RAY DIFFRACTIONr_angle_other_deg1.8111.62313149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5225721
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.36119.91332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72615872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7951552
X-RAY DIFFRACTIONr_chiral_restr0.2440.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027041
X-RAY DIFFRACTIONr_gen_planes_other0.0220.021575
LS refinement shellResolution: 3.354→3.441 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 4 -
Rwork0.291 83 -
all-87 -
obs--4.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.22860.53590.77091.02230.30850.80480.0219-0.09130.1969-0.0379-0.0022-0.0758-0.1890.0289-0.01970.22060.00530.03530.016-0.01830.0443.887924.10832.0802
23.47140.0015-0.63280.4150.18251.22710.059-0.39740.06050.00470.00760.03970.0342-0.0164-0.06660.2405-0.08990.03390.10510.03120.089161.863624.737726.7178
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 505
2X-RAY DIFFRACTION2B1 - 504

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