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- PDB-2es7: Crystal structure of Q8ZP25 from Salmonella typhimurium LT2. NESG... -

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Basic information

Entry
Database: PDB / ID: 2es7
TitleCrystal structure of Q8ZP25 from Salmonella typhimurium LT2. NESG TARGET STR70
Componentsputative thiol-disulfide isomerase and thioredoxin
KeywordsISOMERASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG
Function / homology
Function and homology information


[NiFe]-hydrogenase maturation factor HyaE / Hydrogenase-1 expression protein HyaE / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Thiol-disulfide isomerase and thioredoxin
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsBenach, J. / Su, M. / Forouhar, F. / Chen, Y. / Ho, C.K. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Rong, X. / Liu, J. ...Benach, J. / Su, M. / Forouhar, F. / Chen, Y. / Ho, C.K. / Janjua, H. / Cunningham, K. / Ma, L.-C. / Rong, X. / Liu, J. / Baran, M. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of Q8ZP25 from Salmonella typhimurium LT2 NESG target STR70.
Authors: Benach, J. / Su, M. / Forouhar, F. / Chen, Y. / Janjua, H. / Rong, B.X. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionOct 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative thiol-disulfide isomerase and thioredoxin
B: putative thiol-disulfide isomerase and thioredoxin
C: putative thiol-disulfide isomerase and thioredoxin
D: putative thiol-disulfide isomerase and thioredoxin


Theoretical massNumber of molelcules
Total (without water)65,1474
Polymers65,1474
Non-polymers00
Water10,088560
1
A: putative thiol-disulfide isomerase and thioredoxin


Theoretical massNumber of molelcules
Total (without water)16,2871
Polymers16,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: putative thiol-disulfide isomerase and thioredoxin


Theoretical massNumber of molelcules
Total (without water)16,2871
Polymers16,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: putative thiol-disulfide isomerase and thioredoxin


Theoretical massNumber of molelcules
Total (without water)16,2871
Polymers16,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: putative thiol-disulfide isomerase and thioredoxin


Theoretical massNumber of molelcules
Total (without water)16,2871
Polymers16,2871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.549, 71.156, 95.004
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
putative thiol-disulfide isomerase and thioredoxin / Q8ZP25_SALTY


Mass: 16286.870 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: STM1790 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: GenBank: 16420320, UniProt: Q8ZP25*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 560 / 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: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97925, 0.97955, 0.96782
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2005
RadiationMonochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979251
20.979551
30.967821
ReflectionResolution: 2.8→20 Å / Num. obs: 25130 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 85.1 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 35.37
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 9.5 / % possible all: 97.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNS1.1refinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→19.9 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 364563.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.338 2372 9.6 %RANDOM
Rwork0.285 ---
obs0.285 24633 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 98.4149 Å2 / ksol: 0.159752 e/Å3
Displacement parametersBiso mean: 36.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.26 Å20 Å2-0.42 Å2
2---4.69 Å20 Å2
3----0.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 0 560 3840
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
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_deg2.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 379 9.5 %
Rwork0.327 3629 -
obs--95.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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