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- PDB-2in3: Crystal structure of a putative protein disulfide isomerase from ... -

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Basic information

Entry
Database: PDB / ID: 2in3
TitleCrystal structure of a putative protein disulfide isomerase from Nitrosomonas europaea
ComponentsHypothetical protein
KeywordsISOMERASE / DsbA family / FrnE-like subfamily / disulfide isomerase / structural genomics / Nitrosomonas europaea / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


protein-disulfide reductase activity
Similarity search - Function
putative protein disulfide isomerase domain / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Cyclin A; domain 1 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DSBA domain-containing protein
Similarity search - Component
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsCuff, M.E. / Skarina, T. / Onopriyenko, O. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a putative protein disulfide isomerase from Nitrosomonas europaea
Authors: Cuff, M.E. / Skarina, T. / Onopriyenko, O. / Edwards, A. / Savchenko, A. / Joachimiak, A.
History
DepositionOct 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.
Remark 400 COMPOUND AUTHORS STATE THAT THIS PROTEIN IS A PUTATIVE ISOMERASE, SINCE NO EXPERIMENTS HAVE BEEN ... COMPOUND AUTHORS STATE THAT THIS PROTEIN IS A PUTATIVE ISOMERASE, SINCE NO EXPERIMENTS HAVE BEEN DONE SO FAR TO VERIFY THAT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8777
Polymers24,4411
Non-polymers4356
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.844, 59.642, 84.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein / putative protein disulfide isomerase


Mass: 24441.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Gene: NE2553 / Plasmid: p11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82S11
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25mM Potassium phosphate, 20% PEG 8000, 2% Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97930, 0.97946
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.979461
ReflectionResolution: 1.85→31.9 Å / Num. all: 20391 / Num. obs: 20391 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 47.8 Å2 / Rsym value: 0.057 / Net I/σ(I): 11.5
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4.4 % / Rsym value: 0.33 / % possible all: 67.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
autoSHARPphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.85→31.9 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.494 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.136
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22731 1050 5.1 %RANDOM
Rwork0.1886 ---
all0.19053 19340 --
obs0.19053 19340 93.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48 Å2
Baniso -1Baniso -2Baniso -3
1--2.77 Å20 Å20 Å2
2--2.2 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.85→31.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 0 27 180 1838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221734
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9532361
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1755210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40923.67179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79715269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6441510
X-RAY DIFFRACTIONr_chiral_restr0.0930.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021331
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.2846
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21182
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9571.51075
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27621693
X-RAY DIFFRACTIONr_scbond_it2.1173767
X-RAY DIFFRACTIONr_scangle_it3.2614.5667
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 63 -
Rwork0.261 941 -
obs--64.4 %
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)
12.59771.17790.5247.1242-2.56034.51370.03380.1881-0.07880.04060.0970.30510.1506-0.2802-0.1308-0.16860.00990.0013-0.1426-0.0756-0.213440.057246.28512.9556
25.22752.29341.40813.1771.63042.9234-0.29870.79140.1758-0.28110.1643-0.0234-0.48170.03220.1344-0.1429-0.0051-0.0318-0.074-0.0222-0.189244.048758.48523.6554
33.5012-0.25761.65221.9384-1.11134.2047-0.09740.1592-0.21480.19810.09570.1018-0.1605-0.49950.0017-0.21020.0151-0.0049-0.1129-0.0905-0.112835.062947.60211.3117
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 516 - 53
2X-RAY DIFFRACTION2AA52 - 13054 - 132
3X-RAY DIFFRACTION3AA131 - 211133 - 213

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