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- PDB-1rcw: Crystal structure of CT610 from Chlamydia trachomatis -

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Basic information

Entry
Database: PDB / ID: 1rcw
TitleCrystal structure of CT610 from Chlamydia trachomatis
ComponentsCT610
KeywordsOXIDOREDUCTASE / TOXIN / iron / di-iron / redox enzyme / metallo enzyme
Function / homology
Function and homology information


Oxidoreductases / : / toxin activity / host cell cytoplasm / oxidoreductase activity / extracellular region / metal ion binding
Similarity search - Function
Putative folate metabolism protein, CADD family / Pyrroloquinoline-quinone synthase-like / Thiaminase-2/PQQC / TENA/THI-4/PQQC family / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Probable oxidoreductase CT_610
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsSchwarzenbacher, R. / Liddington, R.C.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure of the Chlamydia protein CADD reveals a redox enzyme that modulates host cell apoptosis.
Authors: Schwarzenbacher, R. / Stenner-Liewen, F. / Liewen, H. / Robinson, H. / Yuan, H. / Bossy-Wetzel, E. / Reed, J.C. / Liddington, R.C.
History
DepositionNov 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CT610
B: CT610
C: CT610
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1969
Polymers80,8613
Non-polymers3356
Water3,045169
1
A: CT610
B: CT610
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1316
Polymers53,9082
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-62 kcal/mol
Surface area17820 Å2
MethodPISA
2
C: CT610
hetero molecules

C: CT610
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1316
Polymers53,9082
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Unit cell
Length a, b, c (Å)77.553, 192.966, 93.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C

NCS domain segments:

Ens-ID: 1 / Beg label comp-ID: ASN

Dom-IDComponent-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEU1AA7 - 2197 - 219
21ASP1BB7 - 2207 - 220
31LEU1CC7 - 2197 - 219
42LEU1AA7 - 2197 - 219
52ASP1BB7 - 2207 - 220
62LEU1CC7 - 2197 - 219
73LEU4AA7 - 2197 - 219
83ASP4BB7 - 2207 - 220
93LEU4CC7 - 2197 - 219

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Components

#1: Protein CT610 / CADD


Mass: 26953.797 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: CT610 / Plasmid: pet21d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O84616
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% (v/v) PEG 6K, 20mM cacodylate, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.998, 0.9791, 0.925, 0.9794
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9981
20.97911
30.9251
40.97941
ReflectionResolution: 2.5→29.88 Å / Num. obs: 24069 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.061 / Net I/σ(I): 11.2
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.401 / % possible all: 94.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.88 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.898 / SU B: 19.855 / SU ML: 0.221 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.081 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The density adjacent to the iron ions in copy A and B could not be identified and has been modeled as Waters 501 and 503. It may also ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The density adjacent to the iron ions in copy A and B could not be identified and has been modeled as Waters 501 and 503. It may also resemble a bound oxide ion, or hydroxide ion, or reactive oxygen species.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1226 5.1 %RANDOM
Rwork0.191 ---
obs0.195 22843 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.53 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å20 Å2
2--1.93 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5186 0 6 169 5361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225372
X-RAY DIFFRACTIONr_bond_other_d0.0020.024718
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9487260
X-RAY DIFFRACTIONr_angle_other_deg0.928311009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4275637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53924.7283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.23115937
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7561524
X-RAY DIFFRACTIONr_chiral_restr0.0940.2769
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025990
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021117
X-RAY DIFFRACTIONr_nbd_refined0.260.21432
X-RAY DIFFRACTIONr_nbd_other0.1880.24690
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0920.23013
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3560.2208
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1850.24
X-RAY DIFFRACTIONr_metal_ion_refined0.0890.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3830.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3130.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4140.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.80333194
X-RAY DIFFRACTIONr_mcbond_other0.35931292
X-RAY DIFFRACTIONr_mcangle_it3.48355108
X-RAY DIFFRACTIONr_scbond_it6.17582178
X-RAY DIFFRACTIONr_scangle_it9.173112152
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A6424tight positional0.130.05
2B6424tight positional0.130.05
3C6424tight positional0.250.05
1A3212medium positional0.130.5
2B3212medium positional0.130.5
3C3212medium positional0.250.5
1A6424tight thermal1.660.5
2B6424tight thermal1.620.5
3C6424tight thermal3.260.5
1A3212medium thermal1.662
2B3212medium thermal1.622
3C3212medium thermal3.262
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.341 80
Rwork0.25 1585
Refinement TLS params.Method: refined / Origin x: 28.18 Å / Origin y: 71.555 Å / Origin z: -8.173 Å
111213212223313233
T-0.017 Å2-0.001 Å20.0264 Å2--0.0234 Å2-0.0134 Å2---0.0503 Å2
L0.31 °2-0.0447 °20.0284 °2-0.1645 °2-0.1649 °2--0.2893 °2
S0.0149 Å °0.0168 Å °0.0913 Å °0.0317 Å °0.0232 Å °0.0268 Å °-0.0743 Å °-0.0282 Å °-0.0381 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 2197 - 219
2X-RAY DIFFRACTION1BB7 - 2207 - 220
3X-RAY DIFFRACTION1CC7 - 2197 - 219

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