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- PDB-2onf: Crystal structure of a putative osmotically inducible protein c (... -

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Basic information

Entry
Database: PDB / ID: 2onf
TitleCrystal structure of a putative osmotically inducible protein c (ta0195) from thermoplasma acidophilum at 1.70 A resolution
ComponentsHypothetical protein Ta0195
KeywordsOXIDOREDUCTASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


: / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Uncharacterized protein
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_393673.1) from Thermoplasma acidophilum at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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 1.5Jan 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
Revision 1.6Oct 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 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 DIMER AS A BIOLOGICALLY 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

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein Ta0195
B: Hypothetical protein Ta0195
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4827
Polymers32,4662
Non-polymers1,0165
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-33 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.070, 68.550, 48.670
Angle α, β, γ (deg.)90.000, 98.290, 90.000
Int Tables number4
Space group name H-MP1211
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Hypothetical protein Ta0195


Mass: 16232.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: AMRC-C165, DSM1728, IFO15155, JCM9062 / Gene: NP_393673.1, Ta0195 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9HLN2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: NANODROP, 30.0% PEG-6000, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97910
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 18, 2006 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.97911
ReflectionResolution: 1.7→27.929 Å / Num. obs: 33417 / % possible obs: 94.4 % / Biso Wilson estimate: 28.911 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 14.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.7-1.760.3152.69345570287.6
1.76-1.830.2683.39851594689.8
1.83-1.910.214.19374567388.5
1.91-2.020.1416.211442693395.6
2.02-2.140.0988.59922600496.1
2.14-2.310.07211.210968660896.7
2.31-2.540.04415.210704641598.2
2.54-2.90.03220.510782644298.6
2.90.0213011048653097.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SOLVEphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.7→27.929 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.534 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.103
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN 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 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. ONE COENZYME A (COA) MONOMER WAS MODELED IN THE ACTIVE SITE BASED ON THE PRESENCE OF CLEAR AND CONCLUSIVE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1697 5.1 %RANDOM
Rwork0.162 ---
all0.164 ---
obs0.164 33399 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.658 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å20.96 Å2
2---0.42 Å20 Å2
3---2.09 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2260 0 64 306 2630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222507
X-RAY DIFFRACTIONr_bond_other_d0.0030.021765
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.9843415
X-RAY DIFFRACTIONr_angle_other_deg0.97234307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8795315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42924.08125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78415440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2141517
X-RAY DIFFRACTIONr_chiral_restr0.1030.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022767
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02511
X-RAY DIFFRACTIONr_nbd_refined0.2140.2413
X-RAY DIFFRACTIONr_nbd_other0.2060.21836
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21137
X-RAY DIFFRACTIONr_nbtor_other0.0850.21299
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2244
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2530.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.211
X-RAY DIFFRACTIONr_mcbond_it2.31931621
X-RAY DIFFRACTIONr_mcbond_other0.5723579
X-RAY DIFFRACTIONr_mcangle_it2.88652391
X-RAY DIFFRACTIONr_scbond_it5.09281154
X-RAY DIFFRACTIONr_scangle_it6.907111005
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 121 -
Rwork0.24 2292 -
obs-2413 96.91 %
Refinement TLS params.Method: refined / Origin x: 24.8092 Å / Origin y: 12.05 Å / Origin z: 10.5566 Å
111213212223313233
T-0.0425 Å20.0134 Å2-0.0007 Å2--0.0208 Å2-0.0105 Å2---0.057 Å2
L1.0474 °20.6326 °2-0.178 °2-0.959 °2-0.1927 °2--0.3031 °2
S-0.017 Å °-0.1015 Å °0.027 Å °0.0081 Å °0.0109 Å °0.0178 Å °0.0103 Å °0.0121 Å °0.0061 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL / Auth seq-ID: 0 - 139 / Label seq-ID: 1 - 140

IDAuth asym-IDLabel asym-ID
1AA
2BB

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