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- PDB-3h3h: Crystal structure of a snoal-like protein of unknown function (bt... -

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Basic information

Entry
Database: PDB / ID: 3h3h
TitleCrystal structure of a snoal-like protein of unknown function (bth_ii0226) from burkholderia thailandensis e264 at 1.60 A resolution
Componentsuncharacterized SnoaL-like protein
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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 / Unknown ligand / SnoaL-like domain-containing protein
Function and homology information
Biological speciesBurkholderia thailandensis E264 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of SnoaL-like protein of unknown function (YP_438428.1) from Burkholderia thailandensis E264 at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized SnoaL-like protein
B: uncharacterized SnoaL-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9945
Polymers27,7982
Non-polymers1953
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-17 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.746, 73.399, 97.049
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-124-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 2 / Auth seq-ID: 3 - 121 / Label seq-ID: 4 - 122

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsTHE RESULTS FROM SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein uncharacterized SnoaL-like protein


Mass: 13899.132 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis E264 (bacteria)
Gene: BTH_II0226, YP_438428.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2T8S1
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 1.98 Å3/Da / Density % sol: 37.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 27.6000% polyethylene glycol 6000, 0.1M MES pH 5.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97889,0.97833
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 22, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978891
30.978331
ReflectionResolution: 1.6→29.424 Å / Num. obs: 29144 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.594 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 10.17
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.6-1.660.5631.492975056185.1
1.66-1.720.391296835137199.4
1.72-1.80.2952.8108695737199.2
1.8-1.90.1844.2112425925199.4
1.9-2.020.1097107615648198.7
2.02-2.170.0779.9102325374198.1
2.17-2.390.0612.6105985556196.9
2.39-2.730.04515.8103195416196.6
2.73-3.440.03220.7104305433194.7
3.44-29.4240.02525.5104715352193.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→29.424 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 3.824 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.093
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY OTHER REFINEMENT REMARKS: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY OTHER REFINEMENT REMARKS: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.UNKNOWN LIGANDS(UNL) ARE MODELED IN PUTATIVE ACTIVE SITES COMPRISED OF RESIDUES 16, 20, 32, 42, 64, 92, 102, 104 AND 119 IN EACH SUBUNIT. 5.ONE MES MOLECULE FROM CRYSTALLIZATION CONDITION IS MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1478 5.1 %RANDOM
Rwork0.179 ---
obs0.18 29133 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.49 Å2 / Biso mean: 19.436 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2--0.53 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1867 0 35 171 2073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212071
X-RAY DIFFRACTIONr_bond_other_d0.0050.021398
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9232828
X-RAY DIFFRACTIONr_angle_other_deg0.84633365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7875263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.20222.475101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92115315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8191518
X-RAY DIFFRACTIONr_chiral_restr0.0840.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022424
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02482
X-RAY DIFFRACTIONr_mcbond_it1.96931263
X-RAY DIFFRACTIONr_mcbond_other0.7683515
X-RAY DIFFRACTIONr_mcangle_it2.95452016
X-RAY DIFFRACTIONr_scbond_it4.9348808
X-RAY DIFFRACTIONr_scangle_it6.2611812
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
639TIGHT POSITIONAL0.360.05
779MEDIUM POSITIONAL0.760.5
639TIGHT THERMAL1.280.5
779MEDIUM THERMAL1.662
LS refinement shellResolution: 1.599→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 108 -
Rwork0.332 1898 -
all-2006 -
obs--94.4 %
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)
10.960.1281-0.13670.49710.20791.713-0.00080.15360.0635-0.0689-0.02920.0106-0.0791-0.03910.030.030.0084-0.00870.03520.00170.030513.40725.487711.3512
21.5046-0.11150.29680.3056-0.30012.7874-0.0148-0.04170.02990.0298-0.05450.0192-0.00110.12170.06920.0127-0.00610.00130.017-0.01040.03917.21430.320834.0707
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 121
2X-RAY DIFFRACTION2B2 - 121

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