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- PDB-3gja: CytC3 -

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Basic information

Entry
Database: PDB / ID: 3gja
TitleCytC3
ComponentsCytC3
KeywordsBIOSYNTHETIC PROTEIN / CytC3 / halogenase / beta barrel
Function / homology
Function and homology information


2-oxoglutarate-dependent dioxygenase activity / iron ion binding
Similarity search - Function
Chlorinating enzyme / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / q2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsWong, C. / Drennan, C.L.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Structural analysis of an open active site conformation of nonheme iron halogenase CytC3
Authors: Wong, C. / Fujimori, D.G. / Walsh, C.T. / Drennan, C.L.
History
DepositionMar 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CytC3
B: CytC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2056
Polymers72,9692
Non-polymers2364
Water4,143230
1
A: CytC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6624
Polymers36,4851
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CytC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5442
Polymers36,4851
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: CytC3
B: CytC3
hetero molecules

A: CytC3
B: CytC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,41112
Polymers145,9384
Non-polymers4728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area12150 Å2
ΔGint-53 kcal/mol
Surface area40570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.024, 90.024, 249.187
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CytC3


Mass: 36484.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces (bacteria) / Strain: pSPHE02 / Gene: cytC3 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0VX22*PLUS
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 3.46 Å3/Da / Density % sol: 64.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.8 M sodium acetate trihydrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 1, 2006 / Details: inter-image dead time 5s
RadiationMonochromator: side scattering bent cube-root I-beam single crystal
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 50903 / % possible obs: 95.9 % / Rmerge(I) obs: 0.056 / Χ2: 1.136
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.280.19942130.911181.5
2.28-2.370.18445540.98186.9
2.37-2.480.15748811.072194.1
2.48-2.610.15652031.152199.6
2.61-2.770.12352321.2131100
2.77-2.990.0952701.1491100
2.99-3.290.06852671.124199.8
3.29-3.760.05353171.212199.5
3.76-4.740.04653101.136198.2
4.74-500.03956561.103199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å14.92 Å
Translation3 Å14.92 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FCT

2fct


Resolution: 2.2→44.52 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.806 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.261 4840 9.1 %
Rwork0.226 --
obs-49459 93.3 %
Solvent computationBsol: 50.807 Å2
Displacement parametersBiso max: 96.75 Å2 / Biso mean: 45.732 Å2 / Biso min: 25.51 Å2
Baniso -1Baniso -2Baniso -3
1--9.801 Å20 Å20 Å2
2---9.801 Å20 Å2
3---19.601 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3558 Å0.3072 Å
Luzzati d res low-5 Å
Luzzati sigma a0.356 Å0.307 Å
Refinement stepCycle: LAST / Resolution: 2.2→44.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4300 0 16 230 4546
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3171.5
X-RAY DIFFRACTIONc_scbond_it1.9972
X-RAY DIFFRACTIONc_mcangle_it2.1562
X-RAY DIFFRACTIONc_scangle_it2.8752.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ACT.par
X-RAY DIFFRACTION3water_rep.param

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