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- PDB-5evh: Crystal structure of known function protein from Kribbella flavid... -

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Basic information

Entry
Database: PDB / ID: 5evh
TitleCrystal structure of known function protein from Kribbella flavida DSM 17836
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / unkown function
Function / homologySnoaL-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 / SnoaL-like domain-containing protein
Function and homology information
Biological speciesKribbella flavida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.852 Å
AuthorsChang, C. / Duke, N. / Endres, M. / Chhor, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal structure of known function protein from Kribbella flavida DSM 17836
Authors: Chang, C. / Duke, N. / Endres, M. / Chhor, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionNov 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1542
Polymers14,0621
Non-polymers921
Water2,216123
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3094
Polymers28,1242
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2530 Å2
ΔGint-20 kcal/mol
Surface area11260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.908, 45.908, 140.479
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Uncharacterized protein


Mass: 14062.239 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399) (bacteria)
Strain: DSM 17836 / JCM 10339 / NBRC 14399 / Gene: Kfla_2811 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D2Q084
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Ammonium Actate, Sodium Acetate pH 4.6, PEG4000, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 13604 / % possible obs: 99.8 % / Redundancy: 17.9 % / Biso Wilson estimate: 18.75 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.022 / Rrim(I) all: 0.092 / Χ2: 0.954 / Net I/av σ(I): 34.75 / Net I/σ(I): 8.8 / Num. measured all: 243644
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.8815.61.4426470.8740.3681.4890.836100
1.88-1.9216.41.1256680.9530.281.160.826100
1.92-1.9517.81.0286520.9150.2481.0580.86100
1.95-1.9918.10.8256750.9460.1970.8490.866100
1.99-2.0418.40.6856550.9770.1630.7050.892100
2.04-2.0818.80.5786680.970.1360.5940.935100
2.08-2.1418.80.4456440.9860.1050.4570.919100
2.14-2.1918.60.3446730.9910.0820.3540.969100
2.19-2.2618.80.2936570.9910.0690.3010.986100
2.26-2.3318.60.2386880.9940.0560.2450.991100
2.33-2.4118.70.2316750.9920.0550.2381.003100
2.41-2.5118.50.1836630.9970.0440.1880.988100
2.51-2.6318.60.1346750.9960.0320.1380.971100
2.63-2.7618.40.1116810.9980.0270.1150.96100
2.76-2.9418.30.0956840.9920.0230.0970.987100
2.94-3.1618.20.086840.9950.0190.0821.117100
3.16-3.48180.0736910.9970.0180.0751.315100
3.48-3.9917.50.067070.9980.0150.0621.23100
3.99-5.0216.90.0377320.9990.0090.0380.747100
5.02-5015.60.0327850.9980.0080.0330.6397.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.852→32.462 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.89 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1997 545 4.16 %
Rwork0.1717 22277 -
obs0.1729 12892 95.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.24 Å2 / Biso mean: 28.8752 Å2 / Biso min: 8.49 Å2
Refinement stepCycle: final / Resolution: 1.852→32.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms912 0 6 123 1041
Biso mean--70.89 38.69 -
Num. residues----121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018991
X-RAY DIFFRACTIONf_angle_d1.5821356
X-RAY DIFFRACTIONf_chiral_restr0.107151
X-RAY DIFFRACTIONf_plane_restr0.01180
X-RAY DIFFRACTIONf_dihedral_angle_d14.22579
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8515-1.94910.2963890.25122282237168
1.9491-2.07120.2711250.21343344346999
2.0712-2.23110.22721550.182233223477100
2.2311-2.45560.2391390.177933313470100
2.4556-2.81070.19261450.176533413486100
2.8107-3.54050.2111580.164433453503100
3.5405-32.46680.15341560.14633312346899
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)
13.5264-0.9956-0.0854.21440.52623.2645-0.0730.22420.329-0.03020.1014-0.0157-0.0064-0.1754-0.01760.13590.0088-0.01990.14120.04490.124911.6111-4.528822.4774
21.9347-0.34280.88371.5236-0.63440.76120.02190.33830.0305-0.0942-0.2249-0.4392-0.05850.63090.02240.1302-0.0311-0.05840.25530.03030.207622.8399-4.450123.7841
30.96890.32420.47230.95120.63450.65350.02160.3107-0.0029-0.05840.0177-0.3973-0.01490.3643-0.01270.1298-0.0029-0.00290.3053-0.02720.251421.9229-11.941920.3643
41.62460.1396-0.06970.91820.22131.0489-0.00970.1991-0.00870.0394-0.02510.13850.0010.05450.03420.14880.0371-0.02210.1345-0.02470.093611.2733-13.726328.1847
52.275-0.46090.19034.2515-1.62671.9721-0.02560.15850.33270.1863-0.1122-0.1646-0.180.34050.11410.131-0.0115-0.02580.15070.01710.115718.1287-5.607230.8705
62.4021-3.304-0.42745.56880.4170.1010.2630.5615-0.2919-0.2997-0.0946-0.57620.47440.63270.26150.37750.3433-0.06360.5274-0.18770.362126.646-29.542528.1071
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 20 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 46 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 66 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 91 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 112 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 113 through 125 )A0

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