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- PDB-2q78: Crystal structure of a thioesterase-like protein (tm0581) from th... -

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Basic information

Entry
Database: PDB / ID: 2q78
TitleCrystal structure of a thioesterase-like protein (tm0581) from thermotoga maritima msb8 at 2.20 A resolution
ComponentsUncharacterized protein
KeywordsHYDROLASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Fluoroacetyl-CoA thioesterase / : / Fluoroacetyl-CoA-specific thioesterase / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
MALONYL-COENZYME A / Fluoroacetyl-CoA-specific thioesterase-like domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Uncharacterized protein TM0581 (TM0581) from Thermotoga maritima at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jul 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 1.6Jan 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 1.7Oct 16, 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: 1,2,3,4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 ... BIOMOLECULE: 1,2,3,4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 8 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH 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: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,96818
Polymers141,0688
Non-polymers6,90010
Water5,080282
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9744
Polymers35,2672
Non-polymers1,7072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-33 kcal/mol
Surface area12430 Å2
MethodPISA
2
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0105
Polymers35,2672
Non-polymers1,7433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-42 kcal/mol
Surface area12030 Å2
MethodPISA
3
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0105
Polymers35,2672
Non-polymers1,7433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-43 kcal/mol
Surface area12440 Å2
MethodPISA
4
G: Uncharacterized protein
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9744
Polymers35,2672
Non-polymers1,7072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-32 kcal/mol
Surface area12050 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30100 Å2
ΔGint-191 kcal/mol
Surface area41990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.347, 90.706, 230.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 5 / Auth seq-ID: 3 - 130 / Label seq-ID: 15 - 142

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Uncharacterized protein


Mass: 17633.559 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Species: Thermotoga maritima / Strain: MSB8, DSM 3109, JCM 10099 / Gene: TM_0581 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9WZ50
#2: Chemical
ChemComp-MLC / MALONYL-COENZYME A


Mass: 853.580 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H38N7O19P3S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NANODROP, 0.8M Lithium chloride, 10.0% PEG 6000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97913 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2007 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 2.2→29.975 Å / Num. obs: 65127 / % possible obs: 99.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.263.90.7521.61788246040.75296.8
2.26-2.324.80.6921.12242046460.692100
2.32-2.3950.6191.22236345020.619100
2.39-2.4650.5711.32178843830.571100
2.46-2.5450.4691.62116042430.469100
2.54-2.6350.3652.12070241490.365100
2.63-2.7350.2892.61986639930.289100
2.73-2.8450.2233.41902338280.223100
2.84-2.9750.184.21827936860.18100
2.97-3.1150.1551761535450.15100
3.11-3.2850.126.11669033650.12100
3.28-3.4850.0897.91577531860.089100
3.48-3.724.90.0794.61491730190.079100
3.72-4.024.90.0738.61388528310.073100
4.02-4.44.90.0679.21259225930.067100
4.4-4.924.80.06110.41142323660.061100
4.92-5.684.80.0699.21010921200.069100
5.68-6.964.60.0729.2837418080.072100
6.96-9.844.50.0637.9644014380.063100
9.84-29.984.10.0541033458220.05496.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.975 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.66 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.193
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. RESIDUES A/B/C/D/E/G131-141 AND F134-141 AND MOST OF THE N_TERMINAL PURIFICATION TAG ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. RESIDUES A/B/C/D/E/G131-141 AND F134-141 AND MOST OF THE N_TERMINAL PURIFICATION TAG ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. ONE MALONYL-COA (MCL) IS MODELED FOR EACH MONOMER BASED ON DENSITY AND STRUCTURAL HOMOLOGY (PDB ID: 2F3X). THE OCCUPANCY OF OF MCL IN CHAIN H IS LIKELY LESS THAN 1.0. 5. CL MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3296 5.1 %RANDOM
Rwork0.175 ---
obs0.177 65047 99.73 %-
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: 43.94 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2---0.45 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8219 0 434 282 8935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228989
X-RAY DIFFRACTIONr_bond_other_d0.0010.025998
X-RAY DIFFRACTIONr_angle_refined_deg1.5722.02312277
X-RAY DIFFRACTIONr_angle_other_deg0.883314549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43351104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57121.721366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.733151535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9215104
X-RAY DIFFRACTIONr_chiral_restr0.080.21466
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029713
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021907
X-RAY DIFFRACTIONr_nbd_refined0.2080.21560
X-RAY DIFFRACTIONr_nbd_other0.2050.26541
X-RAY DIFFRACTIONr_nbtor_refined0.1710.24246
X-RAY DIFFRACTIONr_nbtor_other0.0850.25139
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2281
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0760.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.219
X-RAY DIFFRACTIONr_mcbond_it1.85535465
X-RAY DIFFRACTIONr_mcbond_other0.58532173
X-RAY DIFFRACTIONr_mcangle_it2.76158649
X-RAY DIFFRACTIONr_scbond_it5.36783944
X-RAY DIFFRACTIONr_scangle_it7.379113601
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A717MEDIUM POSITIONAL0.290.5
2B717MEDIUM POSITIONAL0.240.5
3C717MEDIUM POSITIONAL0.390.5
4D717MEDIUM POSITIONAL0.270.5
5E717MEDIUM POSITIONAL0.220.5
6F717MEDIUM POSITIONAL0.310.5
7G717MEDIUM POSITIONAL0.250.5
8H717MEDIUM POSITIONAL0.240.5
1A704LOOSE POSITIONAL0.515
2B704LOOSE POSITIONAL0.475
3C704LOOSE POSITIONAL0.645
4D704LOOSE POSITIONAL0.685
5E704LOOSE POSITIONAL0.455
6F704LOOSE POSITIONAL0.645
7G704LOOSE POSITIONAL0.55
8H704LOOSE POSITIONAL0.465
1A717MEDIUM THERMAL1.422
2B717MEDIUM THERMAL0.962
3C717MEDIUM THERMAL0.842
4D717MEDIUM THERMAL1.152
5E717MEDIUM THERMAL0.642
6F717MEDIUM THERMAL0.852
7G717MEDIUM THERMAL0.752
8H717MEDIUM THERMAL0.692
1A704LOOSE THERMAL3.4410
2B704LOOSE THERMAL2.710
3C704LOOSE THERMAL3.2510
4D704LOOSE THERMAL4.9910
5E704LOOSE THERMAL2.6110
6F704LOOSE THERMAL3.1810
7G704LOOSE THERMAL2.1910
8H704LOOSE THERMAL2.3610
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 223 -
Rwork0.224 4350 -
obs-4573 96.31 %
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)
10.7325-0.20880.01330.90570.1560.03510.11460.01090.1456-0.0049-0.003-0.0177-0.16020.1013-0.1116-0.1636-0.001-0.0171-0.07560.0373-0.103626.285-4.401-19.378
20.485-0.19720.40341.3754-0.86672.9992-0.03010.2427-0.0078-0.2843-0.0807-0.00020.15690.09380.1108-0.0860.02310.0156-0.04080.0213-0.115724.565-11.908-36.297
32.2962-0.1676-0.52881.1419-0.06112.61540.07280.27910.2455-0.00140.01330.1974-0.2141-0.302-0.0861-0.14770.05030.0081-0.07840.11390.023356.2141.695-12.229
41.22580.0323-0.02390.5842-0.56412.02750.0627-0.05390.12860.13930.01230.1386-0.1539-0.2367-0.075-0.1524-0.00350.0439-0.10910.0383-0.05155.715-8.8982.761
50.98340.3608-0.48771.8405-1.85465.7846-0.1474-0.31010.30490.7726-0.1925-0.2396-1.1110.29770.33990.4706-0.0788-0.1489-0.0108-0.07930.145576.34212.75133.28
61.48410.44580.84611.9869-0.49263.7037-0.0268-0.15880.04420.3138-0.2052-0.4844-0.44020.54710.232-0.0571-0.087-0.0562-0.01680.03660.11782.2055.70316.854
71.34220.3320.11044.14890.05383.4307-0.08470.08710.1232-0.2914-0.0984-0.2625-0.20010.3440.18320.0381-0.02090.04850.01950.1351-0.011823.55715.174-66.237
80.8411-0.15450.01132.3623-1.73744.4355-0.0475-0.12810.10580.2760.10030.1676-0.6465-0.3177-0.05280.03890.05140.02210.03340.0571-0.035811.41214.283-52.11
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-4 - 1308 - 142
2X-RAY DIFFRACTION2BB0 - 13012 - 142
3X-RAY DIFFRACTION3CC0 - 13012 - 142
4X-RAY DIFFRACTION4DD1 - 13013 - 142
5X-RAY DIFFRACTION5EE0 - 13012 - 142
6X-RAY DIFFRACTION6FF-2 - 13310 - 145
7X-RAY DIFFRACTION7GG0 - 13012 - 142
8X-RAY DIFFRACTION8HH0 - 13012 - 142

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