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- PDB-5ixu: Crystal structure of an uncharacterized NIPSNAP domain protein fr... -

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Basic information

Entry
Database: PDB / ID: 5ixu
TitleCrystal structure of an uncharacterized NIPSNAP domain protein from Burkholderia xenovorans
ComponentsUncharacterized protein
KeywordsStructural Genomics/Unknown Function / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Structural Genomics-Unknown Function complex
Function / homologyNIPSNAP / NIPSNAP / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / NIPSNAP domain-containing protein
Function and homology information
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of an uncharacterized protein from Burkholderia xenovorans
Authors: Mayclin, S.J. / Delker, S.L. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)13,8442
Polymers13,7481
Non-polymers961
Water28816
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6874
Polymers27,4952
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_556y,x,-z+11
Buried area2890 Å2
ΔGint-46 kcal/mol
Surface area10150 Å2
MethodPISA
2
A: Uncharacterized protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)110,74916
Polymers109,9808
Non-polymers7698
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_556-y,-x,-z+11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
Buried area19670 Å2
ΔGint-247 kcal/mol
Surface area32490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.620, 94.620, 94.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number207
Space group name H-MP432

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Components

#1: Protein Uncharacterized protein


Mass: 13747.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (strain LB400) (bacteria)
Strain: LB400 / Gene: Bxe_B0070 / Plasmid: BuxeA.00127.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13J81
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.57 Å3/Da / Density % sol: 52 % / Mosaicity: 0.27 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: JCSG+ E4: 1.26 M Ammonium sulfate, 0.1 M Tris pH 8.5; protein conc. 19.1mg/mL; 20% EG cryo; puck bbt8-3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 16, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 5419 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 26.79 % / Biso Wilson estimate: 50.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.063 / Net I/σ(I): 43.75
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-2.570.5696.651100
2.57-2.640.4838.081100
2.64-2.710.38510.051100
2.71-2.80.31212.581100
2.8-2.890.21618.181100
2.89-2.990.19919.421100
2.99-3.10.1427.141100
3.1-3.230.10934.211100
3.23-3.370.08144.911100
3.37-3.540.06552.871100
3.54-3.730.06557.04196.1
3.73-3.950.05563.51199.6
3.95-4.230.04279199.6
4.23-4.570.03488.981100
4.57-50.0397.81100
5-5.590.03192.341100
5.59-6.460.03484.351100
6.46-7.910.0386.011100
7.91-11.180.02397.49199.2
11.18-500.02366.23195.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vqs

1vqs


Resolution: 2.5→50 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.59
RfactorNum. reflection% reflectionSelection details
Rfree0.2646 542 10.02 %Random selection
Rwork0.1923 ---
obs0.199 5407 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.82 Å2 / Biso mean: 50.0019 Å2 / Biso min: 25 Å2
Refinement stepCycle: final / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms811 0 5 16 832
Biso mean--134.61 44.44 -
Num. residues----102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008846
X-RAY DIFFRACTIONf_angle_d0.931163
X-RAY DIFFRACTIONf_chiral_restr0.053125
X-RAY DIFFRACTIONf_plane_restr0.006149
X-RAY DIFFRACTIONf_dihedral_angle_d16.426484
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5004-2.7520.33861310.240411661297100
2.752-3.150.32461480.24411731321100
3.15-3.96810.28761260.18661214134099
3.9681-38.6330.20941370.17091312144999
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)
13.3279-2.2019-2.47757.40073.79586.5130.13391.0602-0.4253-0.3796-0.5948-0.7212-0.281-0.31030.5670.40210.10550.06650.55840.12960.41113.0388.69129.6747
27.4203-4.2640.59837.58050.45612.87580.16530.12320.9179-0.6413-0.1944-0.8022-0.30210.54070.02540.3859-0.04950.05060.54440.12260.548915.452322.090334.0384
35.1044-5.8828-0.92459.16840.43430.42780.34860.16950.2554-0.3789-0.4671-0.27730.00740.05370.0210.3728-0.0187-0.01150.44060.12840.360313.386211.085740.5855
46.1317-2.9662.23592.5372-3.97719.05360.0122-0.45770.99720.8496-0.0132-0.6647-0.7155-0.4417-0.01410.53880.17-0.01440.5095-0.00730.59364.676429.13643.2589
51.9578-0.79320.12545.39461.91782.58190.46320.43790.3646-0.5811-0.3695-0.9488-0.4687-0.4966-0.07720.67880.176-0.05350.62570.18210.49655.441225.280927.2278
62.48590.2968-0.18512.74281.66935.57210.14870.1957-0.09860.0481-0.1462-0.45550.2429-0.1386-0.0160.44820.0618-0.06790.37180.04360.37618.473715.233641.5622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 28 )A15 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 46 )A29 - 46
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 62 )A47 - 62
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 72 )A63 - 72
5X-RAY DIFFRACTION5chain 'A' and (resid 73 through 86 )A73 - 86
6X-RAY DIFFRACTION6chain 'A' and (resid 87 through 116 )A87 - 116

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