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- PDB-2g0f: Crystal Structure of P144A mutant of E.coli CcmG protein -

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Basic information

Entry
Database: PDB / ID: 2g0f
TitleCrystal Structure of P144A mutant of E.coli CcmG protein
ComponentsThiol:disulfide interchange protein dsbE
KeywordsOXIDOREDUCTASE / E.coli CcmG / P144A mutant / cis-to-trans configuration change
Function / homology
Function and homology information


cytochrome complex assembly / disulfide oxidoreductase activity / outer membrane-bounded periplasmic space / plasma membrane
Similarity search - Function
Periplasmic protein thiol:disulphide oxidoreductase DsbE / : / Redoxin / Redoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Periplasmic protein thiol:disulphide oxidoreductase DsbE / : / Redoxin / Redoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsOuyang, N. / Gao, Y.G. / Hu, H.Y. / Xia, Z.X.
CitationJournal: Proteins / Year: 2006
Title: Crystal structures of E. coli CcmG and its mutants reveal key roles of the N-terminal beta-sheet and the fingerprint region
Authors: Ouyang, N. / Gao, Y.G. / Hu, H.Y. / Xia, Z.X.
History
DepositionFeb 12, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein dsbE


Theoretical massNumber of molelcules
Total (without water)18,9271
Polymers18,9271
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.416, 47.783, 85.432
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thiol:disulfide interchange protein dsbE / CcmG protein / Cytochrome c biogenesis protein ccmG


Mass: 18927.418 Da / Num. of mol.: 1 / Fragment: residues 36-184 / Mutation: P144A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ccmG / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA86
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 1.908668 Å3/Da / Density % sol: 35.557152 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.0M ammonium sulfate, 0.1M HEPES buffer (pH=8.0),2%(w/v) PEG 4K, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SEALED TUBE / Type: CONVENTIONAL Cu / Wavelength: 1.5418 Å
DetectorType: BRUKER APEX / Detector: CCD / Date: Dec 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 7948 / Num. obs: 7932 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.104
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.594 / Num. unique all: 762 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CNS1refinement
SMARTdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2B1K

2b1k


Resolution: 2.2→42.72 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 290283.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 782 10.7 %RANDOM
Rwork0.186 ---
all0.191 7801 --
obs0.186 7281 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.3868 Å2 / ksol: 0.340477 e/Å3
Displacement parametersBiso mean: 29 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2---0.22 Å20 Å2
3----0.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 0 58 1257
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.472
X-RAY DIFFRACTIONc_scbond_it2.452
X-RAY DIFFRACTIONc_scangle_it3.732.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.353 81 12.5 %
Rwork0.281 568 -
obs--86.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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