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- PDB-8w1q: Aerobic crystal structure of iron-bound FlcD from Pseudomonas aer... -

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Basic information

Entry
Database: PDB / ID: 8w1q
TitleAerobic crystal structure of iron-bound FlcD from Pseudomonas aeruginosa
ComponentsPyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C
KeywordsOXIDOREDUCTASE / mono-iron dioxygenase
Function / homology
Function and homology information


pyrroloquinoline-quinone synthase / hydrolase activity, hydrolyzing O-glycosyl compounds / periplasmic space / oxidoreductase activity
Similarity search - Function
Haem-oxygenase-associated, N-terminal helices / Haem-oxygenase-associated N-terminal helices / Iron-containing redox enzyme / Iron-containing redox enzyme / Pyrroloquinoline-quinone synthase-like / Lytic transglycosylase, superhelical linker domain superfamily / Haem oxygenase-like, multi-helical
Similarity search - Domain/homology
: / : / Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsWalker, M.E. / Grove, T.L. / Li, B. / Redinbo, M.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM148685 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137286 United States
CitationJournal: Acs Cent.Sci. / Year: 2024
Title: Structural Basis for Methine Excision by a Heme Oxygenase-like Enzyme
Authors: Simke, W.C. / Walker, M.E. / Calderone, L.A. / Putz, A.T. / Patteson, J.B. / Vitro, C.N. / Zizola, C.F. / Redinbo, M.R. / Pandelia, M.E. / Grove, T.L. / Li, B.
History
DepositionFeb 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C
B: Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7878
Polymers80,4802
Non-polymers3066
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-50 kcal/mol
Surface area26530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.461, 83.551, 68.829
Angle α, β, γ (deg.)90.000, 97.702, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C / Pyrroloquinoline-quinone synthase


Mass: 40240.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: pqqC_2, CAZ10_19980, DT376_18990, NCTC13621_03444, PAERUG_P19_London_7_VIM_2_05_10_05324
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0C7AN42, pyrroloquinoline-quinone synthase

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Non-polymers , 5 types, 552 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O

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Details

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 % sol: 33.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium chloride, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→31.57 Å / Num. obs: 79607 / % possible obs: 95.19 % / Redundancy: 3 % / Biso Wilson estimate: 18.17 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.09696 / Rpim(I) all: 0.0637 / Rrim(I) all: 0.1166 / Net I/σ(I): 6.46
Reflection shellResolution: 1.56→1.616 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.4948 / Mean I/σ(I) obs: 1.32 / Num. unique obs: 7453 / CC1/2: 0.508 / CC star: 0.821 / Rpim(I) all: 0.373 / Rrim(I) all: 0.6235 / % possible all: 89.23

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→31.57 Å / SU ML: 0.1861 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4771
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2083 2000 2.51 %
Rwork0.1758 77799 -
obs0.1766 79607 94.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.44 Å2
Refinement stepCycle: LAST / Resolution: 1.56→31.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5077 0 3 546 5626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00585257
X-RAY DIFFRACTIONf_angle_d0.82457157
X-RAY DIFFRACTIONf_chiral_restr0.0444793
X-RAY DIFFRACTIONf_plane_restr0.0055942
X-RAY DIFFRACTIONf_dihedral_angle_d15.4706742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.590.33151210.27244734X-RAY DIFFRACTION80.54
1.59-1.640.28881400.25075414X-RAY DIFFRACTION91.86
1.64-1.690.32131400.22595416X-RAY DIFFRACTION93.43
1.69-1.740.28571400.21795485X-RAY DIFFRACTION93.8
1.74-1.80.2411420.2095521X-RAY DIFFRACTION94.05
1.8-1.870.22151430.19985546X-RAY DIFFRACTION94.41
1.87-1.960.25021400.18755488X-RAY DIFFRACTION94.57
1.96-2.060.20431440.1775585X-RAY DIFFRACTION95.34
2.06-2.190.21491470.17265694X-RAY DIFFRACTION96.4
2.19-2.360.20421460.17335667X-RAY DIFFRACTION97.01
2.36-2.60.22071460.17115718X-RAY DIFFRACTION97.2
2.6-2.970.22441490.17125780X-RAY DIFFRACTION98.15
2.98-3.750.17231490.15915830X-RAY DIFFRACTION98.66
3.75-31.570.16681530.1585921X-RAY DIFFRACTION98.99

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