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- PDB-3k8n: Crystal structure of E. Coli CCMG -

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Basic information

Entry
Database: PDB / ID: 3k8n
TitleCrystal structure of E. Coli CCMG
ComponentsCytochrome c biogenesis protein ccmG
KeywordsOXIDOREDUCTASE / N-terminal transmembrane helix / C-terminal thioredoxin-like domain / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP / Cell inner membrane / Cell membrane / Cytochrome c-type biogenesis / Disulfide bond / Membrane / Redox-active center / Transmembrane
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 / Thioredoxin-like superfamily ...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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSavage, D. / Newby, Z. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: To be Published
Title: Crystal structure of E. Coli CCMG
Authors: Savage, D. / Newby, Z. / Stroud, R.M.
History
DepositionOct 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c biogenesis protein ccmG


Theoretical massNumber of molelcules
Total (without water)20,8311
Polymers20,8311
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.696, 67.403, 159.374
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 20830.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b2195, ccmG, dsbE, JW2183, yejQ / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA86
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.73 Å3/Da / Density % sol: 67.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: drops contained 1:1 protein:precipitant, where precipitant solution was 30% (w/v) PEG 4000, 0.2M ammonium sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 27, 2006 / Details: monochrometer
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.1→62.1 Å / Num. all: 17017 / Num. obs: 17017 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 5.56 % / Biso Wilson estimate: 25.3 Å2 / Rsym value: 0.152 / Net I/σ(I): 14.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 2323 / Rsym value: 0.917 / % possible all: 95.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ELVESrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KNG

1kng


Resolution: 2.3→62.08 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.764 / SU ML: 0.38 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): -3.7 / Phase error: 29.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.255 634 4.9 %random
Rwork0.228 ---
obs0.23 12940 99.29 %-
all-13032 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.257 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso max: 92.64 Å2 / Biso mean: 34.065 Å2 / Biso min: 16.36 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→62.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 0 98 1314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111250
X-RAY DIFFRACTIONf_angle_d1.2881700
X-RAY DIFFRACTIONf_chiral_restr0.082178
X-RAY DIFFRACTIONf_plane_restr0.006224
X-RAY DIFFRACTIONf_dihedral_angle_d20.803454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.4780.3451130.3372388250198
2.478-2.7270.3011050.28124552560100
2.727-3.1220.3271220.2624522574100
3.122-3.9330.2481620.19624332595100
3.933-62.1020.1821320.1782578271099

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