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- PDB-8va9: Crystal structure of FeII/MnII CtCADD from Chlamydia trachomatis -

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Basic information

Entry
Database: PDB / ID: 8va9
TitleCrystal structure of FeII/MnII CtCADD from Chlamydia trachomatis
Components4-aminobenzoate synthase
KeywordsOXIDOREDUCTASE / Fe/Mn reconstituted form
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With oxygen as acceptor / symbiont-mediated suppression of host tumor necrosis factor-mediated signaling pathway / small molecule metabolic process / sulfur compound metabolic process / toxin activity / host cell cytoplasm / oxidoreductase activity / extracellular region / metal ion binding
Similarity search - Function
Putative folate metabolism protein, CADD family / Iron-containing redox enzyme / Pyrroloquinoline-quinone synthase-like / Thiaminase-2/PQQC / TENA/THI-4/PQQC family / Haem oxygenase-like, multi-helical
Similarity search - Domain/homology
: / : / 4-aminobenzoate synthase
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsPhan, H.N. / Swartz, P.D. / Makris, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135315 United States
CitationJournal: Biochemistry / Year: 2024
Title: Assembly of a Heterobimetallic Fe/Mn Cofactor in the para -Aminobenzoate Synthase Chlamydia Protein Associating with Death Domains (CADD) Initiates Long-Range Radical Hole-Hopping.
Authors: Phan, H.N. / Swartz, P.D. / Gangopadhyay, M. / Guo, Y. / Smirnov, A.I. / Makris, T.M.
History
DepositionDec 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-aminobenzoate synthase
B: 4-aminobenzoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8527
Polymers55,5392
Non-polymers3145
Water1,17165
1
A: 4-aminobenzoate synthase
hetero molecules

B: 4-aminobenzoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8527
Polymers55,5392
Non-polymers3145
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_444-x-1,-x+y-1,-z-1/31
Buried area2500 Å2
ΔGint-48 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.124, 93.124, 121.046
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein 4-aminobenzoate synthase


Mass: 27769.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: Strain D/UW-3/Cx / Gene: CT_610 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O84616
#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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.73 Å3/Da / Density % sol: 54.91 % / Description: Hexagonal plates
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.2M Lithium citrate tribasic tetrahydrate, 20% w/v PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.000, 1.729, 1.860
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.7291
31.861
ReflectionResolution: 2.35→48.41 Å / Num. obs: 25830 / % possible obs: 99.87 % / Redundancy: 9.5 % / Biso Wilson estimate: 60.64 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07512 / Rpim(I) all: 0.026 / Rrim(I) all: 0.07961 / Net I/σ(I): 14.53
Reflection shellResolution: 2.35→2.434 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.7978 / Mean I/σ(I) obs: 2.25 / CC1/2: 0.97 / CC star: 0.992 / Rpim(I) all: 0.2652 / Rrim(I) all: 0.8414 / % possible all: 99.84

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimless1.12.15data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→46.56 Å / SU ML: 0.5444 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.6894
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3074 1998 7.74 %
Rwork0.2455 23809 -
obs0.2502 25807 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.1 Å2
Refinement stepCycle: LAST / Resolution: 2.35→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3333 0 10 65 3408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00883432
X-RAY DIFFRACTIONf_angle_d0.91124652
X-RAY DIFFRACTIONf_chiral_restr0.0471486
X-RAY DIFFRACTIONf_plane_restr0.0083613
X-RAY DIFFRACTIONf_dihedral_angle_d5.7044468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.53961410.42071665X-RAY DIFFRACTION99.78
2.41-2.470.51991420.41421685X-RAY DIFFRACTION100
2.47-2.550.47651380.41871667X-RAY DIFFRACTION99.89
2.55-2.630.48491400.39311668X-RAY DIFFRACTION99.72
2.63-2.720.41151390.37331690X-RAY DIFFRACTION99.95
2.72-2.830.381410.35171704X-RAY DIFFRACTION99.89
2.83-2.960.41191420.38151658X-RAY DIFFRACTION99.83
2.96-3.120.46491430.37871701X-RAY DIFFRACTION99.95
3.12-3.310.41911450.3291690X-RAY DIFFRACTION99.89
3.31-3.570.32691460.24791701X-RAY DIFFRACTION99.89
3.57-3.920.2581420.23921694X-RAY DIFFRACTION99.95
3.93-4.490.20611440.18481728X-RAY DIFFRACTION100
4.5-5.660.27161440.18651728X-RAY DIFFRACTION99.89
5.66-46.560.24721510.17631830X-RAY DIFFRACTION99.95

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