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- PDB-3efg: Structure of SlyX protein from Xanthomonas campestris pv. campest... -

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Basic information

Entry
Database: PDB / ID: 3efg
TitleStructure of SlyX protein from Xanthomonas campestris pv. campestris str. ATCC 33913
ComponentsProtein slyX homolog
Keywordsstructural genomics / unknown function / Xanthomonas campestris pv. campestris / coiled-coil / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologySlyX / SlyX / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha / Protein SlyX homolog
Function and homology information
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsCuff, M.E. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of SlyX protein from Xanthomonas campestris pv. campestris str. ATCC 33913
Authors: Cuff, M.E. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionSep 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein slyX homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8942
Polymers8,8321
Non-polymers621
Water43224
1
A: Protein slyX homolog
hetero molecules

A: Protein slyX homolog
hetero molecules

A: Protein slyX homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6826
Polymers26,4953
Non-polymers1863
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 area6210 Å2
ΔGint-39 kcal/mol
Surface area9530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.945, 35.945, 81.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-81-

HOH

21A-94-

HOH

Detailslikely a trimer: x,y,z, x-y,x,z+1/2, -y+1,x-y+1,z

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Components

#1: Protein Protein slyX homolog


Mass: 8831.825 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Strain: ATCC 33913 / Gene: slyX, XCC1504 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PAH9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.73 Å3/Da / Density % sol: 28.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 0.2M Ammonium Sulfate, 20% PEG 3350, 4% Glycerol, 1/60 cymotrypsin, then soaked in Na Bromide for phasing, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931, 0.91966, 0.91948
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 15, 2008
ADSC QUANTUM 3152CCDApr 21, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)MADMx-ray1
2SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979311
20.919661
30.919481
ReflectionRedundancy: 12.4 % / Av σ(I) over netI: 58.47 / Number: 58725 / Rmerge(I) obs: 0.051 / Χ2: 1.08 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 4751 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.685095.610.030.94112.2
3.724.6810010.0351.28812
3.253.7210010.0532.09812.3
2.953.2510010.0631.91512.3
2.742.9510010.0621.46912.5
2.582.7410010.0731.13512.6
2.452.5810010.0761.0312.4
2.342.4510010.0990.96912.6
2.252.3410010.1120.89612.5
2.172.2510010.1340.83512.5
2.112.1710010.1810.78912.5
2.052.1110010.2790.76912.4
1.992.0510010.3140.69312.4
1.941.9910010.450.67112.4
1.91.9410010.5330.59811.9
ReflectionResolution: 1.9→50 Å / Num. all: 4751 / Num. obs: 4751 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.051 / Χ2: 1.075 / Net I/σ(I): 58.469
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.533 / Num. unique all: 298 / Χ2: 0.598 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.9 Å / D res low: 20 Å / FOM : 0.319 / FOM acentric: 0.325 / FOM centric: 0.056 / Reflection: 4701 / Reflection acentric: 4593 / Reflection centric: 108
Phasing MAD set

Highest resolution: 1.9 Å / Lowest resolution: 20 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.33100004593108
20.990.974.24.60.160.114262102
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
19.13-202.2600.4000310
15.92-9.131.4210.20.2001034
14.37-5.921.110.20.1002276
13.47-4.370.9510.10.10038211
12.88-3.471.1810.100056917
12.46-2.882.251000080718
12.14-2.463.2710000107724
11.9-2.141.6210000139728
29.13-200.8305.700.960310
25.92-9.130.980.827.511.80.490.41034
24.37-5.920.970.9810.310.10.230.132266
23.47-4.370.990.998.910.20.160.0738211
22.88-3.470.990.995.24.10.150.1356917
22.46-2.880.9913.63.50.130.0880718
22.14-2.46112.92.30.080.06107724
21.9-2.14112.32.60.060.02106722
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Br32.55734-0.344-0.659-0.0590
2Br254.77559-0.328-0.31-0.0340
3Br169.20793-0.328-0.31-0.0340
4Br63.40574-0.784-0.233-0.0580
5Br65.8746-0.808-0.622-0.4570
6Br36.23496-0.346-0.659-0.059-0.009
7Br329.80746-0.336-0.315-0.035-0.06
8Br260.60501-0.336-0.315-0.035-0.06
9Br112.28146-0.336-0.315-0.035-0.06
10Br90.6346-0.783-0.235-0.058-0.06
11Br40.691-0.805-0.624-0.458-0.015
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.13-200.8010.801031310
5.92-9.130.6480.6540.5011071034
4.37-5.920.5770.5880.1412332276
3.47-4.370.5050.5180.06639338211
2.88-3.470.4560.4680.05258656917
2.46-2.880.4270.4350.04882580718
2.14-2.460.2750.2810.0221101107724
1.9-2.140.1060.1080.0051425139728
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 4701
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
3.97-10061.80.822501
3.17-3.9760.50.841503
2.77-3.17640.798507
2.52-2.7759.60.809507
2.34-2.5260.40.837501
2.2-2.3466.90.836502
2.09-2.2730.795502
2-2.0976.30.756509
1.9-280.10.706669

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2→31.13 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.243 / WRfactor Rwork: 0.23 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.85 / SU B: 9.527 / SU ML: 0.112 / SU R Cruickshank DPI: 0.206 / SU Rfree: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.211 191 4.7 %RANDOM
Rwork0.204 ---
all0.204 4065 --
obs0.204 4065 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.78 Å2 / Biso mean: 38.483 Å2 / Biso min: 10.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20.81 Å20 Å2
2--1.62 Å20 Å2
3----2.43 Å2
Refinement stepCycle: LAST / Resolution: 2→31.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms404 0 4 24 432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021424
X-RAY DIFFRACTIONr_bond_other_d0.0060.02293
X-RAY DIFFRACTIONr_angle_refined_deg1.3892.006572
X-RAY DIFFRACTIONr_angle_other_deg0.9013712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.83554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.40124.425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.6431582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.087156
X-RAY DIFFRACTIONr_chiral_restr0.0630.269
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0283
X-RAY DIFFRACTIONr_mcbond_it0.881.5259
X-RAY DIFFRACTIONr_mcbond_other0.1551.5104
X-RAY DIFFRACTIONr_mcangle_it1.8722411
X-RAY DIFFRACTIONr_scbond_it2.9393165
X-RAY DIFFRACTIONr_scangle_it5.1674.5159
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 14 -
Rwork0.244 275 -
all-289 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -0.0591 Å / Origin y: 17.3655 Å / Origin z: 39.1731 Å
111213212223313233
T0.0021 Å2-0.0005 Å2-0.0019 Å2-0.0128 Å2-0.0021 Å2--0.0129 Å2
L0.6885 °2-0.0379 °2-1.8462 °2-0.3682 °20.2184 °2--9.2106 °2
S0.0325 Å °0.0169 Å °-0.0394 Å °0.0041 Å °-0.0677 Å °0.0158 Å °-0.0423 Å °-0.0937 Å °0.0352 Å °

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