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- PDB-5k9f: Crystal structure of a NIPSNAP domain protein from Burkholderia x... -

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Basic information

Entry
Database: PDB / ID: 5k9f
TitleCrystal structure of a NIPSNAP domain protein from Burkholderia xenovorans
ComponentsNIPSNAP domain protein
KeywordsStructural Genomics / Unknown Function / SSGCID / NIPSNAP / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


NIPSNAP / NIPSNAP / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / OXAMIC ACID / NIPSNAP domain-containing protein
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a NIPSNAP domain protein from Burkholderia xenovorans
Authors: Mayclin, S.J. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMay 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 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_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: NIPSNAP domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8543
Polymers12,7061
Non-polymers1482
Water2,810156
1
A: NIPSNAP domain protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)102,83624
Polymers101,6518
Non-polymers1,18516
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area19850 Å2
ΔGint-98 kcal/mol
Surface area32840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.360, 95.360, 63.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein NIPSNAP domain protein


Mass: 12706.376 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_A1114 / Plasmid: BuxeA.00127.d.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13VQ7
#2: Chemical ChemComp-OXM / OXAMIC ACID / Oxamic acid


Mass: 89.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3NO3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 3.08 Å3/Da / Density % sol: 60 % / Mosaicity: 0.25 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MORPHEUS G2: 10% w/v PEG8000, 20% v/v ethylene glycol, 100mM MES/imidazole pH 6.5, 20mM citrate, 20mM tartrate, 20mM acetate, 20mM oxamate, 20mM formate; dc; protein 9.94mg/mL; fsu3-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 13, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 17813 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Biso Wilson estimate: 17.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 27.58
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.65-1.690.4266.261100
1.69-1.740.3567.371100
1.74-1.790.2799.261100
1.79-1.840.22911.021100
1.84-1.910.16914.861100
1.91-1.970.13417.971100
1.97-2.050.10821.521100
2.05-2.130.0925.251100
2.13-2.220.07729.751100
2.22-2.330.06932.71100
2.33-2.460.06135.661100
2.46-2.610.05739.161100
2.61-2.790.05240.481100
2.79-3.010.04746.331100
3.01-3.30.04349.831100
3.3-3.690.0453.91100
3.69-4.260.03755.51100
4.26-5.220.03457.07199.8
5.22-7.380.03354.641100
7.380.02951.39194.7

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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: 1.65→35.346 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.72
RfactorNum. reflection% reflection
Rfree0.1873 1831 10.28 %
Rwork0.1586 --
obs0.1615 17812 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.18 Å2 / Biso mean: 23.1097 Å2 / Biso min: 9.34 Å2
Refinement stepCycle: final / Resolution: 1.65→35.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms808 0 10 156 974
Biso mean--36.89 38.09 -
Num. residues----103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006887
X-RAY DIFFRACTIONf_angle_d0.8151214
X-RAY DIFFRACTIONf_chiral_restr0.047130
X-RAY DIFFRACTIONf_plane_restr0.005160
X-RAY DIFFRACTIONf_dihedral_angle_d17.671532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.69460.20611510.16311891340100
1.6946-1.74450.19371340.160311991333100
1.7445-1.80080.19931380.157612181356100
1.8008-1.86520.16751480.152212001348100
1.8652-1.93980.20181370.15812141351100
1.9398-2.02810.17921270.153612291356100
2.0281-2.1350.18121490.149312081357100
2.135-2.26880.1711530.15912131366100
2.2688-2.44390.1851420.164112251367100
2.4439-2.68980.19031290.163712421371100
2.6898-3.07880.19571420.170612471389100
3.0788-3.87820.18891290.163912721401100
3.8782-35.35370.18671520.14821325147799
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)
11.58010.1893-0.20642.64390.43111.7449-0.09080.1434-0.0904-0.22020.0117-0.1590.00120.2570.04780.1092-0.01730.0220.14910.01650.114218.43640.167-13.075
20.53410.1436-0.15741.4131-0.11210.858-0.04440.09140.01-0.25320.0575-0.1618-0.08430.168-0.00950.1367-0.03550.02520.15560.01550.126520.21166.3276-11.2415
34.2414-3.21192.95755.9211.24777.0426-0.0289-0.1015-0.040.0539-0.0259-1.092-0.14451.0857-0.10460.1669-0.0332-0.04790.32530.08380.32428.04714.60779.2303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 33 )A9 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 104 )A34 - 104
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 111 )A105 - 111

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