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- PDB-2b1l: Crystal structure of N-terminal 57 residue deletion mutant of E. ... -

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Basic information

Entry
Database: PDB / ID: 2b1l
TitleCrystal structure of N-terminal 57 residue deletion mutant of E. coli CcmG protein(residues 58-185)
ComponentsThiol:disulfide interchange protein dsbE
KeywordsOXIDOREDUCTASE / Comparison with the E.coli CcmG / folding topology 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 / 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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionSep 16, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein dsbE
B: Thiol:disulfide interchange protein dsbE


Theoretical massNumber of molelcules
Total (without water)29,4412
Polymers29,4412
Non-polymers00
Water2,504139
1
A: Thiol:disulfide interchange protein dsbE


Theoretical massNumber of molelcules
Total (without water)14,7211
Polymers14,7211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol:disulfide interchange protein dsbE


Theoretical massNumber of molelcules
Total (without water)14,7211
Polymers14,7211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.691, 43.349, 78.986
Angle α, β, γ (deg.)90.00, 94.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14720.697 Da / Num. of mol.: 2 / Mutation: N-terminal 57 residue deletion mutant
Source method: isolated from a genetically manipulated source
Details: N-terminal 57 residue deletion mutant / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ccmg / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA86
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 41.56 %
Crystal growTemperature: 293 K / Method: seeding / pH: 7.8
Details: HEPES buffer, ammonium sulfate, PEG 4000, pH 7.8, Seeding, temperature 293.0K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 20230 / Num. obs: 19846 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.053
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.233 / Num. unique all: 1722 / % possible all: 85.2

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: structure of E.coli CcmG

Resolution: 1.9→29.14 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 285770.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1891 9.8 %RANDOM
Rwork0.193 ---
all0.196 20283 --
obs0.193 19228 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.0236 Å2 / ksol: 0.309022 e/Å3
Displacement parametersBiso mean: 27.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.82 Å20 Å2-4.33 Å2
2---2.78 Å20 Å2
3----3.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 0 139 2205
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.322
X-RAY DIFFRACTIONc_scbond_it2.282
X-RAY DIFFRACTIONc_scangle_it3.442.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.299 149 9.8 %
Rwork0.265 1379 -
obs-1528 75.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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