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

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Basic information

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


Oxidoreductases; Acting on the CH-CH group of donors; With oxygen as acceptor / 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 D/UW-3/CX (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.61 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

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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)55,7586
Polymers55,5392
Non-polymers2204
Water1,09961
1
A: 4-aminobenzoate synthase
hetero molecules

B: 4-aminobenzoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7586
Polymers55,5392
Non-polymers2204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_444-x-1,-x+y-1,-z-1/31
Buried area2270 Å2
ΔGint-26 kcal/mol
Surface area17480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.668, 91.668, 117.602
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 D/UW-3/CX (bacteria)
Gene: CT_610 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O84616
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.57 Å3/Da / Density % sol: 52.11 % / 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 31, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.61→17.14 Å / Num. obs: 17762 / % possible obs: 99.17 % / Redundancy: 9.1 % / Biso Wilson estimate: 46.83 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.0484 / Rrim(I) all: 0.1464 / Net I/σ(I): 11.96
Reflection shellResolution: 2.61→2.703 Å / Redundancy: 9 % / Rmerge(I) obs: 0.8696 / Mean I/σ(I) obs: 2.54 / Num. unique obs: 1761 / CC1/2: 0.792 / CC star: 0.94 / Rpim(I) all: 0.306 / Rrim(I) all: 0.9226 / % possible all: 99.89

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisPro42.90adata reduction
Aimless1.12.15data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→17.14 Å / SU ML: 0.4591 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.0141
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2976 1761 9.93 %
Rwork0.222 15968 -
obs0.2297 17729 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.5 Å2
Refinement stepCycle: LAST / Resolution: 2.61→17.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 4 61 3380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793418
X-RAY DIFFRACTIONf_angle_d0.9564629
X-RAY DIFFRACTIONf_chiral_restr0.0484479
X-RAY DIFFRACTIONf_plane_restr0.0073609
X-RAY DIFFRACTIONf_dihedral_angle_d5.3252469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.680.40841310.34381213X-RAY DIFFRACTION99.85
2.68-2.760.43631360.32761212X-RAY DIFFRACTION99.7
2.76-2.850.39581310.30621206X-RAY DIFFRACTION99.63
2.85-2.950.40521350.29111221X-RAY DIFFRACTION99.78
2.95-3.070.34931300.31031204X-RAY DIFFRACTION99.63
3.07-3.210.35331360.28321206X-RAY DIFFRACTION99.7
3.21-3.370.35521390.25471232X-RAY DIFFRACTION99.64
3.37-3.580.31121310.24021217X-RAY DIFFRACTION99.93
3.58-3.860.28071390.20591225X-RAY DIFFRACTION99.78
3.86-4.240.23411370.18131228X-RAY DIFFRACTION99.78
4.24-4.840.25991400.1741247X-RAY DIFFRACTION99.36
4.84-6.050.3211390.2021251X-RAY DIFFRACTION99.57
6.05-17.140.21341370.16591306X-RAY DIFFRACTION99.18

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