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- PDB-3gnj: The crystal structure of a thioredoxin-related protein from Desul... -

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Basic information

Entry
Database: PDB / ID: 3gnj
TitleThe crystal structure of a thioredoxin-related protein from Desulfitobacterium hafniense DCB
ComponentsThioredoxin domain protein
Keywordsstructural genomics / unknown function / APC92103 / thioredoxin / Desulfitobacterium hafniense DCB / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


protein-disulfide reductase activity / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin domain protein
Similarity search - Component
Biological speciesDesulfitobacterium hafniense DCB-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 Å
AuthorsTan, K. / Volkart, L. / Gu, M. / Kinney, J.N. / Babnigg, G. / Kerfeld, C. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a thioredoxin-related protein from Desulfitobacterium hafniense DCB
Authors: Tan, K. / Volkart, L. / Gu, M. / Kinney, J.N. / Babnigg, G. / Kerfeld, C. / Joachimiak, A.
History
DepositionMar 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin domain protein
B: Thioredoxin domain protein
C: Thioredoxin domain protein
D: Thioredoxin domain protein


Theoretical massNumber of molelcules
Total (without water)52,5094
Polymers52,5094
Non-polymers00
Water1,62190
1
A: Thioredoxin domain protein

B: Thioredoxin domain protein


Theoretical massNumber of molelcules
Total (without water)26,2542
Polymers26,2542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area1570 Å2
ΔGint-4 kcal/mol
Surface area10630 Å2
MethodPISA
2
C: Thioredoxin domain protein

D: Thioredoxin domain protein


Theoretical massNumber of molelcules
Total (without water)26,2542
Polymers26,2542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_647-x+1,y-1/2,-z+21
Buried area1550 Å2
ΔGint-3 kcal/mol
Surface area10810 Å2
MethodPISA
3
A: Thioredoxin domain protein
B: Thioredoxin domain protein


Theoretical massNumber of molelcules
Total (without water)26,2542
Polymers26,2542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Thioredoxin domain protein
D: Thioredoxin domain protein


Theoretical massNumber of molelcules
Total (without water)26,2542
Polymers26,2542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.167, 66.341, 70.163
Angle α, β, γ (deg.)90.00, 105.67, 90.00
Int Tables number4
Space group name H-MP1211
DetailsExperimentally unknown. It is predicted that the chains A and B, C and D form dimers respectively.

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Components

#1: Protein
Thioredoxin domain protein


Mass: 13127.140 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense DCB-2 (bacteria)
Strain: DCB / Gene: Desulfitobacterium hafniense, Dhaf_4889 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: B8G0E7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.84 Å3/Da / Density % sol: 33.23 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG400 0.1M MES, 0.1M MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921, 0.97942
DetectorType: SBC-3 / Detector: CCD / Date: Oct 8, 2008 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.979421
ReflectionResolution: 1.99→26 Å / Num. all: 26104 / Num. obs: 26104 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 22.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.3 / % possible all: 97.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.99→25.92 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.343 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26605 1322 5.1 %RANDOM
Rwork0.19605 ---
obs0.19949 24697 98.39 %-
all-24698 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.23 Å2
2--0.09 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.99→25.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3592 0 0 90 3682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223706
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9754989
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9915450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20725.911203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.22615707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6461513
X-RAY DIFFRACTIONr_chiral_restr0.1260.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022823
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8611.52204
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58823560
X-RAY DIFFRACTIONr_scbond_it2.9531502
X-RAY DIFFRACTIONr_scangle_it4.2844.51423
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.986→2.037 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 87 -
Rwork0.252 1601 -
obs--86.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.72491.156-0.37014.8884-0.04113.10560.0808-0.2251-0.21610.1533-0.1576-0.0750.0270.07620.07680.0869-0.017-0.0140.06430.01280.012514.33333.59837.507
24.97950.0650.89773.78280.07271.84330.3155-0.01660.3201-0.0749-0.2425-0.40510.13110.1258-0.0730.0976-0.01240.01310.06310.01920.158230.02251.59834.192
34.19661.5598-0.04125.324-0.28992.8695-0.0114-0.17080.01210.3323-0.1579-0.11740.06840.04230.16930.0843-0.0087-0.03780.04980.00460.03274.73836.70971.096
45.21640.39890.71323.5580.20811.8740.16640.0711-0.1831-0.07030.0235-0.64420.00890.2205-0.18980.05620.0006-0.02740.0619-0.01870.178420.57554.50667.531
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 108
2X-RAY DIFFRACTION2B0 - 107
3X-RAY DIFFRACTION3C-2 - 108
4X-RAY DIFFRACTION4D-1 - 108

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