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- PDB-2nuj: Crystal structure of thioesterase superfamily (YP_509914.1) from ... -

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Entry
Database: PDB / ID: 2nuj
TitleCrystal structure of thioesterase superfamily (YP_509914.1) from Jannaschia Sp. CCS1 at 2.00 A resolution
ComponentsThioesterase superfamily
KeywordsHYDROLASE / YP_509914.1 / thioesterase superfamily / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homologyHotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / Thioesterase superfamily
Function and homology information
Biological speciesJannaschia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of thioesterase superfamily (YP_509914.1) from Jannaschia Sp. CCS1 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 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 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioesterase superfamily
B: Thioesterase superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0297
Polymers36,4382
Non-polymers5915
Water3,981221
1
A: Thioesterase superfamily
B: Thioesterase superfamily
hetero molecules

A: Thioesterase superfamily
B: Thioesterase superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,05814
Polymers72,8764
Non-polymers1,18210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Buried area10780 Å2
ΔGint-134 kcal/mol
Surface area25470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.401, 78.401, 151.418
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: LEU / End label comp-ID: ALA / Refine code: 5 / Auth seq-ID: 3 - 161 / Label seq-ID: 4 - 162

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Thioesterase superfamily


Mass: 18219.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jannaschia (bacteria) / Genus: Jannaschia / Strain: CCS1 / Gene: YP_509914.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q28QX3
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 9
Details: 65.0% MPD, 0.1M Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97922
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 19, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 1.9→28.796 Å / Num. obs: 32500 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 23.96 Å2 / Rmerge(I) obs: 0.193 / Rsym value: 0.193 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.057.21.3851.61712223681.385100
2.05-2.117.20.0140.71666723100.01064100
2.11-2.177.30.0140.81636522510.861100
2.17-2.247.20.01411571221820.7499.9
2.24-2.317.20.0141.11548221360.63999.9
2.31-2.397.20.0141.31476120410.54899.9
2.39-2.487.20.0141.61438619880.45199.8
2.48-2.587.30.0141.81387119110.4199.8
2.58-2.77.20.0142.31335918520.31999.8
2.7-2.837.20.0142.91260417480.25199.7
2.83-2.987.20.0143.71215116820.299.6
2.98-3.167.20.0144.61143615890.15799.5
3.16-3.387.20.0145.21074914900.13399.4
3.38-3.657.10.0145.9992913970.11499.3
3.65-470.0146.7917013010.199
4-4.477.10.0147.9839911770.08198.8
4.47-5.1670.0149.3742110530.0798.9
5.16-6.3270.0148.561948910.07898.2
6.32-8.946.70.0149.348317180.0798.2
8.94-28.86.10.0148.425274150.06194.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→28.796 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.811 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.115
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 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 ...Details: 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. FIVE MPD MOLCULES FROM CRYSTALLIZATION SOLUTION ARE INCLUDED IN THE MODEL. 5. THERE IS SOME UNKNOWN DENSITY NEAR HIS64B, BUT THE EQUIVALENT DENSITY WAS NOT FOUND IN HIS64A.
RfactorNum. reflection% reflectionSelection details
Rfree0.187 1648 5.1 %RANDOM
Rwork0.155 ---
obs0.157 32500 99.29 %-
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: 26.852 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2→28.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 40 221 2746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222681
X-RAY DIFFRACTIONr_bond_other_d0.0010.022476
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9663670
X-RAY DIFFRACTIONr_angle_other_deg0.83435683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.335333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19521.017118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98215393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1081530
X-RAY DIFFRACTIONr_chiral_restr0.0940.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023015
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02617
X-RAY DIFFRACTIONr_nbd_refined0.2070.2474
X-RAY DIFFRACTIONr_nbd_other0.1950.22492
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21313
X-RAY DIFFRACTIONr_nbtor_other0.0860.21663
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2165
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.216
X-RAY DIFFRACTIONr_mcbond_it2.08931659
X-RAY DIFFRACTIONr_mcbond_other0.7713662
X-RAY DIFFRACTIONr_mcangle_it3.09552651
X-RAY DIFFRACTIONr_scbond_it4.89981150
X-RAY DIFFRACTIONr_scangle_it6.947111019
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
893MEDIUM POSITIONAL0.340.5
1406LOOSE POSITIONAL0.555
893MEDIUM THERMAL1.122
1406LOOSE THERMAL2.8710
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 116 -
Rwork0.227 2254 -
obs-2370 100 %
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)
10.61870.1004-0.0241.02970.36831.11580.0213-0.0512-0.0250.01840.0633-0.08410.08320.131-0.0846-0.05840.0223-0.0107-0.0447-0.0032-0.062150.99550.07736.0758
21.0672-0.622-0.22911.64790.60981.4608-0.0569-0.07190.0910.16670.0654-0.0715-0.07230.0486-0.0085-0.0045-0.0156-0.0082-0.0768-0.0155-0.025243.869278.420812.3838
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 3 - 161 / Label seq-ID: 4 - 162

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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