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- PDB-3gl3: Crystal structure of a putative Thiol:disulfide interchange prote... -

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Basic information

Entry
Database: PDB / ID: 3gl3
TitleCrystal structure of a putative Thiol:disulfide interchange protein DsbE from Chlorobium tepidum
ComponentsPutative Thiol:disulfide interchange protein DsbE
KeywordsOXIDOREDUCTASE / PSI-II / 11210h / Thiol:disulfide interchange protein DsbE / putative / Chlorobium tepidum / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / New York Structural GenomiX Research Consortium
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
: / Redoxin / Redoxin / 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, putative
Similarity search - Component
Biological speciesChlorobium tepidum TLS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsDamodharan, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative Thiol:disulfide interchange protein DsbE from Chlorobium tepidum
Authors: Damodharan, L. / Burley, S.K. / Swaminathan, S.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative Thiol:disulfide interchange protein DsbE
B: Putative Thiol:disulfide interchange protein DsbE
C: Putative Thiol:disulfide interchange protein DsbE
D: Putative Thiol:disulfide interchange protein DsbE


Theoretical massNumber of molelcules
Total (without water)67,9234
Polymers67,9234
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative Thiol:disulfide interchange protein DsbE


Theoretical massNumber of molelcules
Total (without water)16,9811
Polymers16,9811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Putative Thiol:disulfide interchange protein DsbE


Theoretical massNumber of molelcules
Total (without water)16,9811
Polymers16,9811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Putative Thiol:disulfide interchange protein DsbE


Theoretical massNumber of molelcules
Total (without water)16,9811
Polymers16,9811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Putative Thiol:disulfide interchange protein DsbE


Theoretical massNumber of molelcules
Total (without water)16,9811
Polymers16,9811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.197, 42.067, 82.522
Angle α, β, γ (deg.)90.00, 108.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative Thiol:disulfide interchange protein DsbE


Mass: 16980.709 Da / Num. of mol.: 4 / Fragment: UNP residues 30-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum TLS (bacteria) / Strain: TLS / DSM 12025 / Gene: CT1072 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KDH8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M Sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 27, 2009 / Details: mirrors
RadiationMonochromator: Si(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.09→39.07 Å / Num. all: 29179 / Num. obs: 29179 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.2
Reflection shellResolution: 2.09→2.22 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2 / Num. unique all: 5321 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.09→39.07 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 115348.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1488 5.1 %RANDOM
Rwork0.263 ---
all0.272 29179 --
obs0.272 29179 90.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.072 Å2 / ksol: 0.389351 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1--7.52 Å20 Å21.25 Å2
2--7.99 Å20 Å2
3----0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.09→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 0 0 201 4492
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it2.852.5
LS refinement shellResolution: 2.09→2.22 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 231 5.2 %
Rwork0.305 4175 -
obs-5321 83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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