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- PDB-2qs7: CRYSTAL STRUCTURE OF a putative oxidoreductase of the DsrE/DsrF-l... -

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Basic information

Entry
Database: PDB / ID: 2qs7
TitleCRYSTAL STRUCTURE OF a putative oxidoreductase of the DsrE/DsrF-like family (SSO1126) FROM SULFOLOBUS SOLFATARICUS P2 AT 2.09 A RESOLUTION
ComponentsUncharacterized protein
KeywordsOXIDOREDUCTASE / PUTATIVE OXIDOREDUCTASE OF THE DSRE/DSRF-LIKE FAMILY / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyDsrE2-like family / DsrE/DsrF/DrsH-like family / DsrEFH-like / DsrEFH-like / Hypothetical Protein Ychn; Chain: A, / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesSulfolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.09 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of protein of unknown function (NP_342590.1) from Sulfolobus solfataricus at 2.09 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 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: 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
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 WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TRIMER AS A 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,0109
Polymers66,4274
Non-polymers5835
Water1,53185
1
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0945
Polymers49,8213
Non-polymers2742
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-59 kcal/mol
Surface area16700 Å2
MethodPISA
2
D: Uncharacterized protein
hetero molecules

D: Uncharacterized protein
hetero molecules

D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,74812
Polymers49,8213
Non-polymers9289
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8380 Å2
ΔGint-36 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.360, 112.360, 293.284
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11D-144-

CL

21D-146-

EPE

31D-146-

EPE

41D-147-

HOH

51D-148-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: LYS / End label comp-ID: ILE / Refine code: 2 / Auth seq-ID: 7 - 143 / Label seq-ID: 8 - 144

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TRIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Uncharacterized protein


Mass: 16606.840 Da / Num. of mol.: 4
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_342590.1, SSO1126 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q97Z17
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6854.13
2
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2931vapor diffusion, sitting dropNANODROP, 23.1% PEG 3350, 0.193M Potassium dihydrogen phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2932vapor diffusion, sitting dropNANODROP, 22.2% PEG 3350, 0.193M Potassium dihydrogen phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-111
SYNCHROTRONSSRL BL11-120.91837, 0.97937
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDJun 30, 2007Flat mirror (vertical focusing)
MARMOSAIC 325 mm CCD2CCDJun 30, 2007Flat mirror (vertical focusing)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single crystal Si(111) bent (horizontal focusing)SINGLE WAVELENGTHMx-ray1
2Single crystal Si(111) bent (horizontal focusing)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.918371
30.979371
ReflectionResolution: 2.09→48.737 Å / Num. obs: 42142 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 48.55 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 21.12
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.09-2.160.8012.241999832671,288.8
2.16-2.250.6173.32597441711,295
2.25-2.350.4424.62484739961,296.3
2.35-2.480.3356.22677042941,297.3
2.48-2.630.3589.63605440291,298.3
2.63-2.830.25615.44632641431,299
2.83-3.120.14924.65104043331,299.5
3.12-3.570.085384952442471,299.6
3.57-48.7370.05650.64923942991,299.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.09→48.737 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 9.09 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.144
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. CL IONS FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. HEPES (EPE) MOLECULES WERE MODELED BASED ON DENSITY. 5. WATERS 6,7,8,10 COULD BE LIGHT METAL IONS SUCH AS MAGNESIUM. 6. DENSITIES FOR RESIDUES 59-61 ARE POOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2098 5 %RANDOM
Rwork0.176 ---
all0.177 ---
obs0.177 42142 99.62 %-
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: 49.899 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20.31 Å20 Å2
2--0.62 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.09→48.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4222 0 33 85 4340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224451
X-RAY DIFFRACTIONr_bond_other_d0.0030.023014
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9656028
X-RAY DIFFRACTIONr_angle_other_deg1.04837401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1225574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70624.471170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37715778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2521512
X-RAY DIFFRACTIONr_chiral_restr0.1010.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024897
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02915
X-RAY DIFFRACTIONr_nbd_refined0.2310.2902
X-RAY DIFFRACTIONr_nbd_other0.1870.22898
X-RAY DIFFRACTIONr_nbtor_refined0.1910.22214
X-RAY DIFFRACTIONr_nbtor_other0.0910.22248
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3330.211
X-RAY DIFFRACTIONr_mcbond_it1.97733012
X-RAY DIFFRACTIONr_mcbond_other0.32331137
X-RAY DIFFRACTIONr_mcangle_it2.69554474
X-RAY DIFFRACTIONr_scbond_it5.23781872
X-RAY DIFFRACTIONr_scangle_it6.971111541
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A802TIGHT POSITIONAL0.060.05
2B802TIGHT POSITIONAL0.040.05
3C802TIGHT POSITIONAL0.060.05
4D802TIGHT POSITIONAL0.050.05
1A847MEDIUM POSITIONAL0.340.5
2B847MEDIUM POSITIONAL0.420.5
3C847MEDIUM POSITIONAL0.40.5
4D847MEDIUM POSITIONAL0.350.5
1A802TIGHT THERMAL0.170.5
2B802TIGHT THERMAL0.150.5
3C802TIGHT THERMAL0.160.5
4D802TIGHT THERMAL0.190.5
1A847MEDIUM THERMAL1.172
2B847MEDIUM THERMAL0.962
3C847MEDIUM THERMAL1.172
4D847MEDIUM THERMAL1.182
LS refinement shellResolution: 2.09→2.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 148 -
Rwork0.269 2813 -
obs-2961 95.64 %
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)
12.8170.7470.21136.2030.47864.1435-0.10110.13130.0472-0.5629-0.15171.0288-0.0619-0.82410.2528-0.2306-0.0567-0.15580.097-0.1055-0.024-36.6354-6.1981-24.2314
24.8558-0.62340.56084.9436-0.02515.14-0.00140.1655-0.9176-0.2155-0.21340.04381.06470.00480.21470.0002-0.09580.0529-0.1535-0.03030.0407-23.8253-25.8199-20.8535
32.9349-1.12490.09164.86271.24644.4857-0.1707-0.5571-0.75520.7864-0.20220.7950.9065-0.93930.37290.0254-0.27820.1860.2306-0.01140.0437-37.4425-17.2914-3.4358
44.65440.1437-0.11723.9115-0.35332.5236-0.10010.6061-0.7183-0.6441-0.0040.06950.42580.00340.1041-0.0855-0.01020.0343-0.1586-0.1333-0.2064-0.6803-13.5808-41.6236
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 1437 - 144
2X-RAY DIFFRACTION2BB6 - 1437 - 144
3X-RAY DIFFRACTION3CC6 - 1437 - 144
4X-RAY DIFFRACTION4DD6 - 1437 - 144

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