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- PDB-3p2a: Crystal Structure of Thioredoxin 2 from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 3p2a
TitleCrystal Structure of Thioredoxin 2 from Yersinia pestis
ComponentsPutative thioredoxin-like protein
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta-alpha sandwich / Energy metabolism / cytosol
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / glycerol ether metabolic process / protein-disulfide reductase (NAD(P)H) activity / protein-disulfide reductase activity / cell redox homeostasis / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Zn-finger domain of Sec23/24 / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / SH3 type barrels. ...Zn-finger domain of Sec23/24 / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / SH3 type barrels. / Thioredoxin-like superfamily / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Thioredoxin 2 / Thioredoxin 2
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.195 Å
AuthorsKim, Y. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Thioredoxin 2 from Yersinia pestis
Authors: Kim, Y. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative thioredoxin-like protein
B: Putative thioredoxin-like protein
C: Putative thioredoxin-like protein
D: Putative thioredoxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2649
Polymers66,9574
Non-polymers3085
Water6,359353
1
A: Putative thioredoxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8513
Polymers16,7391
Non-polymers1112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative thioredoxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8052
Polymers16,7391
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative thioredoxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8052
Polymers16,7391
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative thioredoxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8052
Polymers16,7391
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Putative thioredoxin-like protein
hetero molecules

C: Putative thioredoxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6555
Polymers33,4782
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_745-x+2,y-1/2,-z1
Buried area1360 Å2
ΔGint-9 kcal/mol
Surface area14150 Å2
MethodPISA
6
B: Putative thioredoxin-like protein
D: Putative thioredoxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6094
Polymers33,4782
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-5 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.970, 75.582, 81.512
Angle α, β, γ (deg.)90.00, 90.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative thioredoxin-like protein / Thioredoxin 2


Mass: 16739.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: trxC, y0919, YPO3270, YP_0661 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q7CK81, UniProt: A0A3N4B5I2*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium chloride, 0.1 M HEPES pH 7.5, 25 % w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 22, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 33346 / Num. obs: 33346 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 26.56 Å2 / Rsym value: 0.131 / Net I/σ(I): 7.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1649 / Rsym value: 0.777 / % possible all: 98.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.195→34.285 Å / SU ML: 0.33 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 1692 5.09 %random
Rwork0.184 ---
all0.187 33249 --
obs0.187 33249 98.86 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.867 Å2 / ksol: 0.312 e/Å3
Displacement parametersBiso mean: 37.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.1135 Å20 Å21.5781 Å2
2--3.5356 Å20 Å2
3----6.6491 Å2
Refinement stepCycle: LAST / Resolution: 2.195→34.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4450 0 7 353 4810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144558
X-RAY DIFFRACTIONf_angle_d1.5646172
X-RAY DIFFRACTIONf_dihedral_angle_d16.6431707
X-RAY DIFFRACTIONf_chiral_restr0.1681
X-RAY DIFFRACTIONf_plane_restr0.008816
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.195-2.27340.32831600.2373036319695
2.2734-2.36440.27911770.22443144332199
2.3644-2.4720.28441510.21423124327599
2.472-2.60230.31191810.21463138331999
2.6023-2.76520.29841520.21433166331899
2.7652-2.97860.29371710.22373170334199
2.9786-3.27820.2651550.198732003355100
3.2782-3.7520.22831710.192231723343100
3.752-4.72520.19781890.1431863375100
4.7252-34.28890.15521850.14483221340699
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)
10.4576-0.0008-0.28421.0705-0.65551.20.02870.0401-0.02920.08880.0247-0.0694-0.0561-0.0152-0.03550.0145-0.0069-0.00420.0698-0.03620.059163.1071-2.931728.2322
20.09670.10820.24551.10740.3171.0269-0.0090.157-0.0144-0.17340.0157-0.012-0.04730.1236-0.00950.1558-0.03610.00630.23740.00050.164736.14998.645810.6211
32.17980.6605-1.60172.2142-0.74561.24960.2693-0.5370.03160.6424-0.25350.0423-0.35370.3762-0.01990.3669-0.1160.00160.2928-0.0010.135542.563535.52058.102
40.7990.43590.59661.59360.97651.58210.0819-0.16420.02740.3206-0.05090.01450.3524-0.1683-0.02220.2086-0.05390.02110.15160.02470.162737.9218.036746.9249
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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