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- PDB-4nar: Crystal Structure of the Q9WYS3 protein from Thermotoga maritima.... -

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Basic information

Entry
Database: PDB / ID: 4nar
TitleCrystal Structure of the Q9WYS3 protein from Thermotoga maritima. Northeast Structural Genomics Consortium Target VR152
ComponentsPutative uronate isomerase
KeywordsISOMERASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / VR152 / PF09861 / DUF2088
Function / homology
Function and homology information


lactate racemase activity
Similarity search - Function
LarA, C-terminal domain / LarA, N-terminal domain / LarA-like, C-terminal domain / LarA-like, N-terminal / : / Lactate racemase N-terminal domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / LarA-like N-terminal domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.388 Å
AuthorsVorobiev, S. / Lew, S. / Seetharaman, J. / Chi, Y. / Xiao, R. / Maglaqui, M. / Lee, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S. / Lew, S. / Seetharaman, J. / Chi, Y. / Xiao, R. / Maglaqui, M. / Lee, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Q9WYS3 protein from Thermotoga maritima.
Authors: Vorobiev, S. / Lew, S. / Seetharaman, J. / Chi, Y. / Xiao, R. / Maglaqui, M. / Lee, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uronate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0145
Polymers50,6661
Non-polymers3474
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative uronate isomerase
hetero molecules

A: Putative uronate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,02710
Polymers101,3332
Non-polymers6948
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area3350 Å2
ΔGint-124 kcal/mol
Surface area32910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.903, 144.605, 49.612
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-503-

SO4

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Components

#1: Protein Putative uronate isomerase


Mass: 50666.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589/MSB8/DSM 3109/JCM 10099 / Gene: Tmari_0439, TM_0442 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9WYS3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 291 K / Method: microbatch crystallization under oil / pH: 4.6
Details: 30% PEG MME 2000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, Microbatch crystallization under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 10, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. all: 18378 / Num. obs: 18360 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 26.84 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 22.8
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 8 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1807 / % possible all: 98.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.388→47.023 Å / Occupancy max: 1 / Occupancy min: 0.21 / SU ML: 0.62 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1733 5.09 %RANDOM
Rwork0.165 ---
obs0.168 34027 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.168 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 166.92 Å2 / Biso mean: 31.386 Å2 / Biso min: 10.78 Å2
Baniso -1Baniso -2Baniso -3
1--2.929 Å20 Å20 Å2
2--2.073 Å20 Å2
3---0.857 Å2
Refinement stepCycle: LAST / Resolution: 2.388→47.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 19 160 3585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013504
X-RAY DIFFRACTIONf_angle_d1.1274730
X-RAY DIFFRACTIONf_chiral_restr0.08504
X-RAY DIFFRACTIONf_plane_restr0.004607
X-RAY DIFFRACTIONf_dihedral_angle_d19.1861306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.388-2.4580.3091610.2022572273397
2.458-2.5380.3441390.20926942833100
2.538-2.6290.2921580.19327092867100
2.629-2.7340.2761630.19326982861100
2.734-2.8580.3031340.17626552789100
2.858-3.0090.1921490.18127192868100
3.009-3.1970.261570.15826872844100
3.197-3.4440.2071300.15827462876100
3.444-3.7910.2051360.14926952831100
3.791-4.3390.1661650.13626612826100
4.339-5.4650.2051310.14127162847100
5.465-47.0320.2221100.17927422852100
Refinement TLS params.Method: refined / Origin x: -17.1145 Å / Origin y: 23.9907 Å / Origin z: -13.4147 Å
111213212223313233
T0.1102 Å2-0.0006 Å2-0.0131 Å2-0.1483 Å2-0.0209 Å2--0.1326 Å2
L0.6564 °20.2677 °2-0.1882 °2-1.0328 °2-0.2914 °2--0.9787 °2
S0.0354 Å °-0.0332 Å °0.0041 Å °0.076 Å °-0.0521 Å °-0.0101 Å °0.057 Å °0.0026 Å °0.0114 Å °
Refinement TLS groupSelection details: chain A

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