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

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Basic information

Entry
Database: PDB / ID: 8vab
TitleCrystal structure of FeII/FeII CtCADD from Chlamydia trachomatis
Components4-aminobenzoate synthase
KeywordsOXIDOREDUCTASE / FeII 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 / MOLECULAR REPLACEMENT / Resolution: 2.65 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8813
Polymers27,7691
Non-polymers1122
Water57632
1
A: 4-aminobenzoate synthase
hetero molecules

A: 4-aminobenzoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7626
Polymers55,5392
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area2400 Å2
ΔGint-65 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.882, 92.882, 122.743
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

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Components

#1: Protein 4-aminobenzoate synthase


Mass: 27769.285 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.75 Å3/Da / Density % sol: 55.3 % / 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: Apr 18, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.65→18.11 Å / Num. obs: 9563 / % possible obs: 98.04 % / Redundancy: 18.2 % / Biso Wilson estimate: 53.6 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.2071 / Rpim(I) all: 0.04942 / Rrim(I) all: 0.213 / Net I/σ(I): 8.77
Reflection shellResolution: 2.65→2.744 Å / Rmerge(I) obs: 1.008 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.912 / CC star: 0.977 / Rpim(I) all: 0.2437 / Rrim(I) all: 1.038 / % possible all: 95.61

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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: 2.65→18.11 Å / SU ML: 0.425 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3205
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2749 943 10.01 %
Rwork0.2039 8482 -
obs0.2107 9425 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.6 Å2
Refinement stepCycle: LAST / Resolution: 2.65→18.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1652 0 2 32 1686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751694
X-RAY DIFFRACTIONf_angle_d0.88072299
X-RAY DIFFRACTIONf_chiral_restr0.0476247
X-RAY DIFFRACTIONf_plane_restr0.0067298
X-RAY DIFFRACTIONf_dihedral_angle_d5.2465231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.790.45461270.29061151X-RAY DIFFRACTION96.45
2.79-2.960.35591300.28441162X-RAY DIFFRACTION97.29
2.96-3.190.33681320.27471185X-RAY DIFFRACTION98.36
3.19-3.510.35251330.22361200X-RAY DIFFRACTION99.26
3.51-4.010.25721350.1841208X-RAY DIFFRACTION98.97
4.01-5.040.21241380.1651242X-RAY DIFFRACTION99.57
5.04-18.110.23351480.18581334X-RAY DIFFRACTION99.8

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