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- PDB-6ar7: Crystal structure of a putative uncharacterized protein from Burk... -

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Basic information

Entry
Database: PDB / ID: 6ar7
TitleCrystal structure of a putative uncharacterized protein from Burkholderia thailandensis
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / SSGCID / Burkholderia thailandensis / unknown protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyLysozyme inhibitor LprI, N-terminal / Lysozyme inhibitor LprI / Lysozyme inhibitor LprI-like N-terminal domain-containing protein
Function and homology information
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a Putative uncharacterized protein from Burkholderia thailandensis
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionAug 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)105,1684
Polymers105,1684
Non-polymers00
Water10,233568
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,2921
Polymers26,2921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,2921
Polymers26,2921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,2921
Polymers26,2921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)26,2921
Polymers26,2921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.690, 77.580, 80.860
Angle α, β, γ (deg.)65.46, 90.03, 83.51
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESID 33 THROUGH 47 OR RESID 49...
211(CHAIN B AND (RESID 33 THROUGH 47 OR RESID 49...
311(CHAIN C AND (RESID 33 THROUGH 47 OR RESID 49...
411(CHAIN D AND (RESID 33 THROUGH 47 OR RESID 49...

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Components

#1: Protein
Uncharacterized protein / ButhA.18069.a.A2


Mass: 26291.902 Da / Num. of mol.: 4 / Fragment: UNP residues 35-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264) (bacteria)
Strain: ATCC 700388 / DSM 13276 / CIP 106301 / E264 / Gene: BTH_I0862, DR63_2637 / Plasmid: ButhA.17069.a.A2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2T081
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54 %
Preparation: For the anomalous data set, two 360-degree scans were merged to solve the structure at 2.5 Angstrom resolution, while the structure was refined against the first 360-degree scan at 2.1 Angstrom resolution.
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.26
Details: 21.4 mg/mL ButhA.17069.a.A2.PS38198 (SeMet protein) against RigakuReagents JCSG+ A2 optimization screen (20.2% PEG3350, 100 mM sodium citrate tribasic / citric acid, pH 5.26) cryoprotectant: ...Details: 21.4 mg/mL ButhA.17069.a.A2.PS38198 (SeMet protein) against RigakuReagents JCSG+ A2 optimization screen (20.2% PEG3350, 100 mM sodium citrate tribasic / citric acid, pH 5.26) cryoprotectant: 20% glycerol (2 steps), tray 249240c7, puck pcm7-6

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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-300 / Detector: CCD / Date: Apr 18, 2017
RadiationMonochromator: Diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→48.311 Å / Num. obs: 61171 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.872 % / Biso Wilson estimate: 36.03 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 10.07
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.57 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.21 / % possible all: 96.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.7.17phasing
ARPmodel building
Cootmodel building
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.1→48.31 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 22.19
RfactorNum. reflection% reflection
Rfree0.206 1964 3.21 %
Rwork0.171 --
obs0.172 61152 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.26 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6389 0 0 568 6957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086662
X-RAY DIFFRACTIONf_angle_d0.8429033
X-RAY DIFFRACTIONf_dihedral_angle_d16.7864178
X-RAY DIFFRACTIONf_chiral_restr0.045954
X-RAY DIFFRACTIONf_plane_restr0.0061212
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A3302X-RAY DIFFRACTIONPOSITIONAL
12B3302X-RAY DIFFRACTIONPOSITIONAL
13C3302X-RAY DIFFRACTIONPOSITIONAL
14D3302X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.27941500.26344112X-RAY DIFFRACTION97
2.1525-2.21070.27751360.22314214X-RAY DIFFRACTION97
2.2107-2.27580.2541310.19814190X-RAY DIFFRACTION97
2.2758-2.34920.22811500.1924232X-RAY DIFFRACTION98
2.3492-2.43320.21381220.18134217X-RAY DIFFRACTION98
2.4332-2.53060.23991470.18384208X-RAY DIFFRACTION98
2.5306-2.64580.22141340.18854188X-RAY DIFFRACTION98
2.6458-2.78520.23631560.18574268X-RAY DIFFRACTION98
2.7852-2.95970.24441460.19044230X-RAY DIFFRACTION98
2.9597-3.18820.23541410.18614238X-RAY DIFFRACTION99
3.1882-3.5090.20851490.17794288X-RAY DIFFRACTION99
3.509-4.01650.17991330.14544250X-RAY DIFFRACTION99
4.0165-5.05950.17861480.1344282X-RAY DIFFRACTION99
5.0595-48.32390.16261210.16564271X-RAY DIFFRACTION99
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)
11.4627-0.05860.2091.90680.94873.9737-0.1569-0.0893-0.01560.10090.05860.08260.4196-0.06230.13310.2413-0.03210.03310.18160.00150.22499.713735.569819.0453
22.69320.24990.65823.23580.01324.4999-0.089-0.35030.27010.3614-0.1050.02030.04350.05390.1430.25880.013-0.00290.3279-0.06190.250213.902947.233432.8572
31.20350.044-0.34891.9772-0.52523.2984-0.01050.0835-0.1534-0.13520.0461-0.00630.6235-0.1132-0.0230.303-0.00210.00290.1632-0.00920.21962.584330.921464.1839
42.4383-0.09450.65782.6360.60594.02110.00020.37290.2901-0.4046-0.02120.10140.0175-0.0745-0.02340.24860.02220.01440.27920.04960.23911.667943.957150.7532
53.45550.53571.29091.57560.20962.3075-0.1641-0.05920.39660.0475-0.01240.2213-0.1924-0.25270.15230.25150.04010.01950.1977-0.06750.2753-4.835759.005371.0479
63.5268-0.15741.41982.9008-0.02564.10610.061-0.08820.0197-0.1654-0.0910.4970.2466-0.5373-0.02590.1751-0.0306-0.0220.3841-0.05550.3302-17.282848.276762.5684
73.3545-0.91781.10871.5092-0.23442.1836-0.28130.14240.4659-0.10670.1166-0.2919-0.25080.30280.16720.3024-0.0798-0.02170.22320.04740.356323.162760.935611.9946
84.21570.26111.4512.7224-0.03534.42520.05740.0778-0.1290.0882-0.0118-0.45980.46470.581-0.12130.26650.0843-0.00670.42390.02750.3933.045847.990421.3235
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID 33 THROUGH 150)
2X-RAY DIFFRACTION2(CHAIN 'A' AND RESID 151 THROUGH 237)
3X-RAY DIFFRACTION3(CHAIN 'B' AND RESID 32 THROUGH 155)
4X-RAY DIFFRACTION4(CHAIN 'B' AND RESID 156 THROUGH 237)
5X-RAY DIFFRACTION5(CHAIN 'C' AND RESID 32 THROUGH 150)
6X-RAY DIFFRACTION6(CHAIN 'C' AND RESID 151 THROUGH 238)
7X-RAY DIFFRACTION7(CHAIN 'D' AND RESID 32 THROUGH 148)
8X-RAY DIFFRACTION8(CHAIN 'D' AND RESID 152 THROUGH 237)

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