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- PDB-3gjb: CytC3 with Fe(II) and alpha-ketoglutarate -

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Basic information

Entry
Database: PDB / ID: 3gjb
TitleCytC3 with Fe(II) and alpha-ketoglutarate
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
ACETATE ION / 2-OXOGLUTARIC ACID / : / CytC3
Similarity search - Component
Biological speciesStreptomyces sp. (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 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_sheet.number_strands / _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

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Assembly

Deposited unit
A: CytC3
B: CytC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,18417
Polymers72,9692
Non-polymers1,21415
Water3,909217
1
A: CytC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1068
Polymers36,4851
Non-polymers6217
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CytC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0789
Polymers36,4851
Non-polymers5938
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: CytC3
B: CytC3
hetero molecules

A: CytC3
B: CytC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,36734
Polymers145,9384
Non-polymers2,42930
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area17800 Å2
ΔGint-169 kcal/mol
Surface area37450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.988, 88.988, 248.442
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CytC3


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

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Non-polymers , 5 types, 232 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.37 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 298 K / 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
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 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: 50583 / % possible obs: 97.6 % / Redundancy: 11 % / Rmerge(I) obs: 0.082
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.48 / % possible all: 81.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→44.49 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.259 4978 9.6 %
Rwork0.227 --
obs0.227 49189 95.1 %
Solvent computationBsol: 62.81 Å2
Displacement parametersBiso mean: 48.04 Å2
Baniso -1Baniso -2Baniso -3
1--10.263 Å20 Å20 Å2
2---10.263 Å20 Å2
3---20.525 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.2→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4239 0 74 217 4530
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.2861.5
X-RAY DIFFRACTIONc_mcangle_it2.1132
X-RAY DIFFRACTIONc_scbond_it2.0552
X-RAY DIFFRACTIONc_scangle_it2.9492.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1Fe_Cytc3_repCLD.par
X-RAY DIFFRACTION2WATER_REP.PARAM

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