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- PDB-2gf6: CRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE (SSO2295) FROM SULFO... -

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Basic information

Entry
Database: PDB / ID: 2gf6
TitleCRYSTAL STRUCTURE OF A PUTATIVE THIOESTERASE (SSO2295) FROM SULFOLOBUS SOLFATARICUS AT 1.91 A RESOLUTION
ComponentsConserved hypothetical protein
KeywordsHYDROLASE / PUTATIVE THIOESTERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


fatty acyl-CoA hydrolase activity
Similarity search - Function
: / Thioesterase-like superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Thioesterase superfamily protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Conserved hypothetical protein (13815598) from Sulfolobus solfataricus at 1.91 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE 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: Conserved hypothetical protein
B: Conserved hypothetical protein
C: Conserved hypothetical protein
D: Conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6789
Polymers63,5684
Non-polymers3,1105
Water4,774265
1
A: Conserved hypothetical protein
B: Conserved hypothetical protein
hetero molecules

A: Conserved hypothetical protein
B: Conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6388
Polymers63,5684
Non-polymers3,0704
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7330 Å2
ΔGint-50 kcal/mol
Surface area23870 Å2
MethodPISA, PQS
2
C: Conserved hypothetical protein
D: Conserved hypothetical protein
hetero molecules

C: Conserved hypothetical protein
D: Conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,71810
Polymers63,5684
Non-polymers3,1506
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7500 Å2
ΔGint-49 kcal/mol
Surface area23260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.690, 57.690, 194.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein
Conserved hypothetical protein


Mass: 15892.006 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: 13815598 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97WD2
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2945.89
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop828.0% PEG-400, 0.2M CaCl2, 0.1M TRIS, PH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
2932vapor diffusion, sitting drop, nanodrop828.0% PEG-400, 0.2M CaCl2, 0.1M TRIS, PH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL1-510.918381
SYNCHROTRONSSRL BL1-520.979267, 0.918381
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDJan 21, 20061m long Rh coated bent cylindrical mirror for horizontal and vertical focussing
ADSC QUANTUM 3152CCDJan 21, 20061m long Rh coated bent cylindrical mirror for horizontal and vertical focussing
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Double-crystal monochromatorMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9183811
20.9792671
ReflectionResolution: 1.91→28.84 Å / Num. obs: 47208 / % possible obs: 89.8 % / Biso Wilson estimate: 28.618 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.91-1.980.7141.414613755881.4
1.98-2.060.6711.514966773684.5
2.06-2.150.5781.814533756487.5
2.15-2.260.52.115268791889.8
2.26-2.410.4252.517036876991.3
2.41-2.590.3423.115680805392
2.59-2.850.257416443834492.4
2.85-3.260.1376.716796844893.5
3.260.061317123853393.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.701data extraction
XDSdata reduction
SHELXphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.91→28.84 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.857 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. COENZYME A MODELED BASED ON PROPOSED FUNCTION, DENSITY AND SIMILARITY TO HOMOLOG 1NNG. 4. CA MODELED BASED ON DENSITY AND CRYSTALLIZATION CONDITIONS. 5. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2395 5.1 %RANDOM
Rwork0.217 ---
obs0.219 47207 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.746 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--1.03 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.91→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4237 0 193 265 4695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224544
X-RAY DIFFRACTIONr_bond_other_d0.0010.024118
X-RAY DIFFRACTIONr_angle_refined_deg1.572.0096190
X-RAY DIFFRACTIONr_angle_other_deg0.7939607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5255512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66224.497189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52215785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.061512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024735
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02867
X-RAY DIFFRACTIONr_nbd_refined0.1980.2823
X-RAY DIFFRACTIONr_nbd_other0.1770.24137
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22201
X-RAY DIFFRACTIONr_nbtor_other0.0850.22662
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2258
X-RAY DIFFRACTIONr_metal_ion_refined0.1720.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.2141
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.216
X-RAY DIFFRACTIONr_mcbond_it0.6631.52704
X-RAY DIFFRACTIONr_mcbond_other0.1491.51033
X-RAY DIFFRACTIONr_mcangle_it0.99924231
X-RAY DIFFRACTIONr_scbond_it1.61332186
X-RAY DIFFRACTIONr_scangle_it2.4734.51959
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 191 -
Rwork0.345 3291 -
obs-3482 99.89 %
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)
10.89330.295-0.17521.25260.41811.3239-0.00950.00750.0253-0.0152-0.02920.32290.0279-0.37550.0387-0.1373-0.0055-0.0262-0.10340.01-0.0829-13.235220.136838.0207
21.19470.09250.40292.7754-0.28051.3904-0.04550.26440.1802-0.25760.0217-0.2557-0.11180.42930.0238-0.1131-0.05660.0084-0.09680.0225-0.11248.501430.246234.0179
31.10290.41260.44480.83841.08233.32290.1985-0.2003-0.32630.1865-0.0313-0.15990.6330.0596-0.1673-0.0288-0.0193-0.0248-0.0548-0.0093-0.0667-21.4811-8.54987.0265
41.84260.20410.6430.8479-0.23374.1320.18840.029-0.4806-0.0053-0.08630.06160.6203-0.3514-0.1021-0.0529-0.0277-0.0149-0.0154-0.0597-0.0488-46.0647-10.5538-1.5925
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 1342 - 135
22BB1 - 1342 - 135
33CC6 - 1307 - 131
44DD6 - 1287 - 129

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