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- PDB-8vai: Crystal structure of apo CtCADD from Chlamydia trachomatis -

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Basic information

Entry
Database: PDB / ID: 8vai
TitleCrystal structure of apo CtCADD from Chlamydia trachomatis
Components4-aminobenzoate synthase
KeywordsOXIDOREDUCTASE
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 D/UW-3/CX (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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)55,6313
Polymers55,5392
Non-polymers921
Water4,540252
1
B: 4-aminobenzoate synthase

A: 4-aminobenzoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6313
Polymers55,5392
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_454-x-1,-x+y,-z-1/31
Buried area1970 Å2
ΔGint-7 kcal/mol
Surface area17820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.528, 94.528, 120.673
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-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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.8 Å3/Da / Density % sol: 56.11 % / 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: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00005 Å
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 wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 2.07→48.57 Å / Num. obs: 38531 / % possible obs: 99.94 % / Redundancy: 9.3 % / Biso Wilson estimate: 38.37 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1481 / Rpim(I) all: 0.0517 / Rrim(I) all: 0.1571 / Net I/σ(I): 7.57
Reflection shellResolution: 2.07→2.144 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.18 / Num. unique obs: 3795 / CC1/2: 0.903 / CC star: 0.974 / Rpim(I) all: 0.1754 / Rrim(I) all: 0.5529 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimless1.12.15data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→48.57 Å / SU ML: 0.2432 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.8524
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2191 1990 5.17 %
Rwork0.1835 36537 -
obs0.1854 38527 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.03 Å2
Refinement stepCycle: LAST / Resolution: 2.07→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3451 0 6 252 3709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693590
X-RAY DIFFRACTIONf_angle_d0.79134867
X-RAY DIFFRACTIONf_chiral_restr0.0448520
X-RAY DIFFRACTIONf_plane_restr0.0061631
X-RAY DIFFRACTIONf_dihedral_angle_d5.3815480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.120.26271430.2052571X-RAY DIFFRACTION99.96
2.12-2.180.2371410.19862558X-RAY DIFFRACTION100
2.18-2.240.21081420.20172603X-RAY DIFFRACTION100
2.24-2.320.24641400.18612583X-RAY DIFFRACTION100
2.32-2.40.23891390.19972553X-RAY DIFFRACTION100
2.4-2.490.23951450.19892582X-RAY DIFFRACTION100
2.49-2.610.24341380.22122596X-RAY DIFFRACTION100
2.61-2.750.25691400.20242603X-RAY DIFFRACTION100
2.75-2.920.23921450.20782584X-RAY DIFFRACTION99.96
2.92-3.140.25841450.20572625X-RAY DIFFRACTION100
3.14-3.460.26451420.20462603X-RAY DIFFRACTION99.93
3.46-3.960.19461410.15922634X-RAY DIFFRACTION99.82
3.96-4.990.18961380.15212673X-RAY DIFFRACTION99.82
4.99-48.570.18241510.17742769X-RAY DIFFRACTION99.79

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