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- PDB-2oaf: Crystal structure of thioesterase superfamily (YP_508616.1) from ... -

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Entry
Database: PDB / ID: 2oaf
TitleCrystal structure of thioesterase superfamily (YP_508616.1) from Jannaschia sp. CCS1 at 2.00 A resolution
ComponentsThioesterase superfamily
KeywordsHYDROLASE / YP_508616.1 / thioesterase superfamily / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / TRIETHYLENE GLYCOL / PHOSPHATE ION / Thioesterase superfamily
Similarity search - Component
Biological speciesJannaschia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of thioesterase superfamily (YP_508616.1) from Jannaschia sp. CCS1 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (-7), FOLLOWED BY THE TARGET SEQUENCE. CLONING WAS BASED ON A DRAFT ANNOTATION OF THE JANNASCHIA SP CCS1 GENOME AND THE EXPRESSED CONSTRUCT CONTAINS 7 RESIDUES (-6)MQGAGRL(0) AT THE N-TERMINUS NOT PRESENT IN THE CURRENT PREDICTED GENE PRODUCT.
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...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 INDICATES THAT THE TETRAMER IS 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)35,27911
Polymers34,1242
Non-polymers1,1559
Water3,747208
1
A: Thioesterase superfamily
B: Thioesterase superfamily
hetero molecules

A: Thioesterase superfamily
B: Thioesterase superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,55822
Polymers68,2484
Non-polymers2,31018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area14150 Å2
ΔGint-101 kcal/mol
Surface area21430 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.412, 68.412, 260.002
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 3 / Auth seq-ID: 3 - 143 / Label seq-ID: 11 - 151

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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thioesterase superfamily


Mass: 17061.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jannaschia sp. (bacteria) / Strain: CCS1 / Gene: YP_508616.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q28UM1

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Non-polymers , 5 types, 217 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.2
Details: 40.0% PEG-300, 0.1M Phosphate Citrate pH 4.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97932
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 5, 2006 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979321
ReflectionResolution: 2→29.617 Å / Num. obs: 25559 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 27.03 Å2 / Rmerge(I) obs: 0.142 / Rsym value: 0.142 / Net I/σ(I): 14
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.0510.52.21931618351.121100
2.05-2.1110.50.71874417781.052100
2.11-2.1710.511832317480.761100
2.17-2.2410.51.21784416940.626100
2.24-2.3110.41.51712616400.531100
2.31-2.3910.51.61668515920.469100
2.39-2.4810.41.81624415570.424100
2.48-2.5810.52.21559614900.348100
2.58-2.710.42.91497314390.27100
2.7-2.8310.43.41446313910.22100
2.83-2.9810.44.81360413100.157100
2.98-3.1610.35.81277712430.128100
3.16-3.3810.26.91213711860.105100
3.38-3.6510.27.81124211020.085100
3.65-410.19.81051210430.066100
4-4.47101294139430.054100
4.47-5.169.89.783618540.061100
5.16-6.329.610.270307360.059100
6.32-8.94914.554206020.042100
8.94-29.627.813.829243760.04297.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.617 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.968 / SU B: 6.835 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.129
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. CHLORIDE, PEG, CITRATE AND PHOSPHATE ARE MODELED BASED ON THE CRYSTALLIZATION CONDITIONS. 5. THERE ARE SOME DISORDERED DENSITIES BETWEEN RESIDUE 17 AND RESIDUE 52 FROM SYMMETRICAL RELATED DIMER (DIMER/DIMER INTERFACE). PARTS OF DENSITY ARE INTERPRETED AS PHOSPHATE AND WATER MOLECULES.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1297 5.1 %RANDOM
Rwork0.167 ---
obs0.168 25455 99.94 %-
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: 29.134 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20.52 Å20 Å2
2--1.05 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2→29.617 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2284 0 72 208 2564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222483
X-RAY DIFFRACTIONr_bond_other_d0.0020.021678
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.953403
X-RAY DIFFRACTIONr_angle_other_deg0.95734069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1985301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.47822.589112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29715350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4861516
X-RAY DIFFRACTIONr_chiral_restr0.0930.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022745
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02529
X-RAY DIFFRACTIONr_nbd_refined0.2080.2483
X-RAY DIFFRACTIONr_nbd_other0.2060.21710
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21179
X-RAY DIFFRACTIONr_nbtor_other0.0870.21240
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2151
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.216
X-RAY DIFFRACTIONr_mcbond_it1.85231510
X-RAY DIFFRACTIONr_mcbond_other0.3993574
X-RAY DIFFRACTIONr_mcangle_it2.74552399
X-RAY DIFFRACTIONr_scbond_it4.98981129
X-RAY DIFFRACTIONr_scangle_it6.21211996
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
807TIGHT POSITIONAL0.070.05
1017LOOSE POSITIONAL0.385
807TIGHT THERMAL0.210.5
1017LOOSE THERMAL2.0710
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 90 -
Rwork0.232 1734 -
obs-1824 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)
10.4158-0.0936-0.50450.53680.02341.91430.08910.0244-0.00670.06420.0953-0.0816-0.13090.1383-0.1843-0.0760.0030.0109-0.0126-0.0457-0.020413.97338.0610.882
20.9083-0.02920.12161.02230.0111.43650.04110.0462-0.18880.18490.0268-0.02940.13510.0243-0.0679-0.02870.0159-0.0262-0.0713-0.0128-0.0132-1.2222.90819.092
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 1439 - 151
22BB0 - 1438 - 151

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