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- PDB-4gb5: Crystal structure of Kfla4162 protein from Kribbella flavida -

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Basic information

Entry
Database: PDB / ID: 4gb5
TitleCrystal structure of Kfla4162 protein from Kribbella flavida
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG / SnoaL-like domain
Function / homology
Function and homology information


SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / PHOSPHATE ION / SnoaL-like domain-containing protein
Similarity search - Component
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsMichalska, K. / Chhor, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of Kfla4162 protein from Kribbella flavida (CASP Target)
Authors: Michalska, K. / Chhor, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionJul 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9365
Polymers17,3911
Non-polymers5454
Water2,252125
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,80915
Polymers52,1723
Non-polymers1,63612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6850 Å2
ΔGint-31 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.948, 57.948, 81.605
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-340-

HOH

21A-352-

HOH

31A-401-

HOH

DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Uncharacterized protein


Mass: 17390.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kribbella flavida (bacteria) / Strain: DSM 17836 / Gene: Kfla_4162 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Magic / References: UniProt: D2PTS5
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2 M NaCl, 0.1 M NaH2PO4/K2HPO4, pH 6.2, 50% PEG200, 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: 0.9791 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 28, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 22603 / Num. obs: 22441 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 24.3
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1110 / % possible all: 98.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
PHENIX(phenix.refine: dev_1096)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→28.974 Å / SU ML: 0.13 / Isotropic thermal model: isotropic / Cross valid method: Rfree / σ(F): 0 / Phase error: 16.09 / Stereochemistry target values: ML
Details: HYDROGEN ATOMS HAVE BEEN ADDED AT THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1798 1138 5.07 %random
Rwork0.1441 ---
all0.1458 22433 --
obs0.1458 22433 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→28.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1152 0 35 125 1312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131259
X-RAY DIFFRACTIONf_angle_d1.3911712
X-RAY DIFFRACTIONf_dihedral_angle_d13.298457
X-RAY DIFFRACTIONf_chiral_restr0.086185
X-RAY DIFFRACTIONf_plane_restr0.007224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5504-1.6210.19461360.17862646X-RAY DIFFRACTION99
1.621-1.70640.17431580.15782626X-RAY DIFFRACTION99
1.7064-1.81330.20271380.14562646X-RAY DIFFRACTION99
1.8133-1.95330.16611440.13172650X-RAY DIFFRACTION99
1.9533-2.14980.16311480.12052648X-RAY DIFFRACTION100
2.1498-2.46070.16811460.12322665X-RAY DIFFRACTION100
2.4607-3.09970.18431400.14232686X-RAY DIFFRACTION100
3.0997-28.9790.18721280.15742728X-RAY DIFFRACTION100
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)
12.65640.28920.48283.00011.49810.7916-0.02550.61150.1086-0.8615-0.00360.0193-0.28060.0102-0.1280.17530.00260.00920.1519-0.01490.08282.431726.98522.5831
20.2701-0.15070.20750.1902-0.22981.45060.02680.0201-0.1715-0.0291-0.0053-0.12720.1734-0.08860.09310.0799-0.00180.00060.0591-0.01570.1106-2.227317.023517.1668
32.35240.81431.39532.15081.51372.18360.0707-0.2702-0.34330.44580.0464-0.26650.5812-0.05750.12370.22240.04460.0170.08080.01890.12411.589514.091618.814
40.3221-0.05890.13780.05930.10810.4233-0.133-0.16110.01340.12910.1101-0.05080.0744-0.08250.02320.21650.06950.03220.1025-0.01330.14094.91839.379621.8485
51.42050.12380.03781.357-0.16340.2049-0.0007-0.0671-0.1708-0.04460.0068-0.08770.07310.02580.02680.045200.00420.02380.00510.05175.349623.123719.7447
63.23680.2479-0.94520.9320.61811.2321-0.0734-0.5864-0.46530.2271-0.0983-0.05450.3970.2393-0.16050.14950.0217-0.01750.14890.04410.175610.278923.751432.2943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:12)
2X-RAY DIFFRACTION2(chain A and resid 13:30)
3X-RAY DIFFRACTION3(chain A and resid 31:51)
4X-RAY DIFFRACTION4(chain A and resid 52:67)
5X-RAY DIFFRACTION5(chain A and resid 68:134)
6X-RAY DIFFRACTION6(chain A and resid 135:149)

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