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- PDB-2qzc: Crystal structure of a putative tena-like thiaminase (tena-1, sso... -

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Basic information

Entry
Database: PDB / ID: 2qzc
TitleCrystal structure of a putative tena-like thiaminase (tena-1, sso2206) from sulfolobus solfataricus p2 at 1.50 A resolution
ComponentsTranscriptional activator TenA-1
KeywordsLYASE / Heme oxygenase-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


small molecule metabolic process / sulfur compound metabolic process / cytosol
Similarity search - Function
: / Thiaminase-2/PQQC / TENA/THI-4/PQQC family / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
IMIDAZOLE / Transcriptional activator (TenA-1)
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative TenA-like thiaminase II (NP_343586.1) from Sulfolobus solfataricus at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: 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: pdbx_struct_special_symmetry / 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 1.4Jan 25, 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 13, 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: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional activator TenA-1
B: Transcriptional activator TenA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,90111
Polymers50,1182
Non-polymers7839
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
MethodPISA
2
A: Transcriptional activator TenA-1
B: Transcriptional activator TenA-1
hetero molecules

A: Transcriptional activator TenA-1
B: Transcriptional activator TenA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,80222
Polymers100,2374
Non-polymers1,56618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.862, 88.862, 135.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-258-

HOH

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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 6 / Auth seq-ID: 5 - 213 / Label seq-ID: 6 - 214

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

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Components

#1: Protein Transcriptional activator TenA-1


Mass: 25059.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Species: Sulfolobus solfataricus / Strain: P2, DSM 1617, JCM 11322 / Gene: NP_343586.1, tenA-1 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q97WL0
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: NANODROP, 2.4M (NH4)2SO4, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.918381, 0.979310, 0.978921
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 16, 2007
Details: 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing
RadiationMonochromator: Double-crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9183811
20.979311
30.9789211
ReflectionResolution: 1.5→38.152 Å / Num. obs: 87321 / % possible obs: 99.8 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.544.80.6880.92980562280.68898.1
1.54-1.5860.631.23733662190.6399.9
1.58-1.637.20.5531.24366960460.553100
1.63-1.687.20.4651.64256758920.465100
1.68-1.737.20.372.14122956910.37100
1.73-1.797.20.2732.83998555260.273100
1.79-1.867.20.2213.53873753530.221100
1.86-1.947.20.1614.13723051400.161100
1.94-2.027.20.1355.33591249630.135100
2.02-2.127.20.1244.43387547150.124100
2.12-2.247.20.1065.83248245170.106100
2.24-2.377.20.0935.83088542820.093100
2.37-2.547.90.0817.43204140570.081100
2.54-2.7410.80.0699.24021937350.069100
2.74-310.70.05710.53765235070.057100
3-3.3510.70.04413.43359031500.044100
3.35-3.8710.50.03616.53006628530.036100
3.87-4.7410.30.02920.62492224100.029100
4.74-6.71100.02720.81914819160.027100
6.71-38.1528.50.02523.2955211210.02598.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SHARPphasing
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→38.152 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.342 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.06
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. RESIDUES 1-2, 81-82 IN CHAIN A AND 1-4, 81-85 IN CHAIN B ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 5. IMIDAZOLE MOLECULES FROM THE PURIFICATION SOLUTION ARE MODELED. 6. GLYCEROL MOLECULES FROM THE CRYO SOLUTION ARE MODELED. 7. IMIDAZOLE AND ONE GLYCEROL MOLECULES OCCUPY THE ACTIVE SITE OF THE PROTEIN.
RfactorNum. reflection% reflectionSelection details
Rfree0.184 4372 5 %RANDOM
Rwork0.165 ---
all0.166 ---
obs0.166 87230 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.706 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.5→38.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3329 0 52 312 3693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223657
X-RAY DIFFRACTIONr_bond_other_d0.0040.022427
X-RAY DIFFRACTIONr_angle_refined_deg1.51.965015
X-RAY DIFFRACTIONr_angle_other_deg1.34435926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6085468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44923.455165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.18615597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2661518
X-RAY DIFFRACTIONr_chiral_restr0.1050.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024066
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02817
X-RAY DIFFRACTIONr_nbd_refined0.2080.2770
X-RAY DIFFRACTIONr_nbd_other0.1410.22364
X-RAY DIFFRACTIONr_nbtor_refined0.180.21827
X-RAY DIFFRACTIONr_nbtor_other0.0740.21599
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0690.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1370.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.211
X-RAY DIFFRACTIONr_mcbond_it1.66732204
X-RAY DIFFRACTIONr_mcbond_other0.4393868
X-RAY DIFFRACTIONr_mcangle_it2.53953502
X-RAY DIFFRACTIONr_scbond_it3.83981723
X-RAY DIFFRACTIONr_scangle_it5.437111482
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2642 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.25
LOOSE THERMAL7.2210
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 326 -
Rwork0.235 5899 -
obs-6225 97.72 %
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)
10.33010.1831-0.1020.1823-0.14470.6458-0.02360.03470.0167-0.02640.03550.0072-0.0401-0.0755-0.0119-0.0266-0.00220.0059-0.01430.0205-0.0228.10224.901-10.537
20.53320.4824-0.18920.4373-0.19870.915-0.07320.12250.0952-0.2420.1121-0.06170.4093-0.4372-0.0390.0955-0.2612-0.05960.164-0.0102-0.0826-11.993-4.782-14.598
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA3 - 804 - 81
21AA83 - 21384 - 214
32BB5 - 806 - 81
42BB86 - 21387 - 214

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