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- PDB-2fno: Crystal structure of a glutathione s-transferase (atu5508) from a... -

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Basic information

Entry
Database: PDB / ID: 2fno
TitleCrystal structure of a glutathione s-transferase (atu5508) from agrobacterium tumefaciens str. c58 at 2.00 A resolution
ComponentsAGR_pAT_752p
KeywordsTRANSFERASE / Thioredoxin fold / gst c-terminal domain-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


transferase activity
Similarity search - Function
Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich ...Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / : / Glutathione S-transferase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2006
Title: Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 A resolution.
Authors: Kosloff, M. / Han, G.W. / Krishna, S.S. / Schwarzenbacher, R. / Fasnacht, M. / Elsliger, M.A. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Astakhova, T. / Axelrod, H.L. / Canaves, J.M. / ...Authors: Kosloff, M. / Han, G.W. / Krishna, S.S. / Schwarzenbacher, R. / Fasnacht, M. / Elsliger, M.A. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Astakhova, T. / Axelrod, H.L. / Canaves, J.M. / Carlton, D. / Chiu, H.J. / Clayton, T. / DiDonato, M. / Duan, L. / Feuerhelm, J. / Grittini, C. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Haugen, J. / Jaroszewski, L. / Jin, K.K. / Johnson, H. / Klock, H.E. / Knuth, M.W. / Koesema, E. / Kreusch, A. / Kuhn, P. / Levin, I. / McMullan, D. / Miller, M.D. / Morse, A.T. / Moy, K. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Page, R. / Paulsen, J. / Quijano, K. / Reyes, R. / Rife, C.L. / Sims, E. / Spraggon, G. / Sridhar, V. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / White, A. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionJan 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
SupersessionMar 21, 2006ID: 1ZGM
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 1.3Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AGR_pAT_752p
B: AGR_pAT_752p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0306
Polymers55,7972
Non-polymers2324
Water7,098394
1
A: AGR_pAT_752p
hetero molecules

A: AGR_pAT_752p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0306
Polymers55,7972
Non-polymers2324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4180 Å2
ΔGint-23 kcal/mol
Surface area18520 Å2
MethodPISA, PQS
2
B: AGR_pAT_752p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0153
Polymers27,8991
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: AGR_pAT_752p
hetero molecules

B: AGR_pAT_752p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0306
Polymers55,7972
Non-polymers2324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)110.204, 50.261, 117.660
Angle α, β, γ (deg.)90.000, 115.720, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-250-

HOH

21B-241-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ASP / End label comp-ID: SER / Refine code: 2 / Auth seq-ID: 3 - 236 / Label seq-ID: 15 - 248

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

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Components

#1: Protein AGR_pAT_752p


Mass: 27898.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: str. C58 / Gene: 15162326 / Production host: Escherichia coli (E. coli) / References: GenBank: 15162326, UniProt: Q7D2W7*PLUS
#2: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.67 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 18.00% PEG 3350, 0.2M Potassium Thiocyanate, 10.00% Glycerol, additive - 0.01M spermine tetra-HCL, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979127, 0.964062, 0.979291
DetectorType: SBC / Detector: CCD / Date: Feb 22, 2004
Details: Water cooled, Sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791271
20.9640621
30.9792911
ReflectionResolution: 2→44.6 Å / Num. obs: 37755 / % possible obs: 95 % / Redundancy: 3.1 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.191 / Net I/σ(I): 18.9
Reflection shellResolution: 2→2.07 Å / % possible obs: 64.8 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 5.1 / Num. measured obs: 5008 / Χ2: 0.998 / % possible all: 78.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
SCALEPACKdata scaling
PDB_EXTRACT1.601data extraction
DENZOdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→44.55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.607 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.152
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THERE ARE LARGE DIFFERENCE FOURIER PEAKS ON THE CRYSTALLOGRAPHIC 2-FOLD AXIS BETWEEN NEAR ASP 107 AND ASP 110 AND SYMMETRY COPIES ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THERE ARE LARGE DIFFERENCE FOURIER PEAKS ON THE CRYSTALLOGRAPHIC 2-FOLD AXIS BETWEEN NEAR ASP 107 AND ASP 110 AND SYMMETRY COPIES FORMING THE BIOLOGICAL UNIT IN BOTH MONOMERS (A AND B). THESE PEAKS WERE LEFT UNMODELED. 3. THE N-TERMINAL REGION OF MOLECULE B IS LESS WELL ORDERED A PEAK IS OBSERVED IN THE DIFFERENCE MAP FOR THE SE ATOM FROM RESIDUE B1 WHICH WAS NOT MODELED. 4. RESIDUE GLN 73 IS A RAMACHANDRAN OUTLIER IN BOTH CHAINS. THE ELECTRON DENSITY IS GOOD IN THIS REGION AND CLEARLY SUPPORTS THIS BACKBONE CONFORMATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1871 5 %RANDOM
Rwork0.181 ---
all0.183 ---
obs0.18306 35858 94.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.467 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å21.25 Å2
2---0.32 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3617 0 12 394 4023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223713
X-RAY DIFFRACTIONr_bond_other_d0.0020.022479
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9555047
X-RAY DIFFRACTIONr_angle_other_deg1.0736029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8585471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92223.677155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11915590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1611525
X-RAY DIFFRACTIONr_chiral_restr0.0920.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024164
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02759
X-RAY DIFFRACTIONr_nbd_refined0.2660.2889
X-RAY DIFFRACTIONr_nbd_other0.2210.22514
X-RAY DIFFRACTIONr_nbtor_refined0.180.21839
X-RAY DIFFRACTIONr_nbtor_other0.0840.21738
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.225
X-RAY DIFFRACTIONr_mcbond_it1.64232355
X-RAY DIFFRACTIONr_mcbond_other0.4523962
X-RAY DIFFRACTIONr_mcangle_it2.59153770
X-RAY DIFFRACTIONr_scbond_it4.92181358
X-RAY DIFFRACTIONr_scangle_it6.369111277
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
1370TIGHT POSITIONAL0.030.05
1618MEDIUM POSITIONAL0.250.5
1370TIGHT THERMAL0.190.5
1618MEDIUM THERMAL0.842
LS refinement shellResolution: 2→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 98 -
Rwork0.21 1985 -
obs--71.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.2409-0.0327-1.32650.73670.06453.18710.01340.21220.02590.0260.00170.12170.1592-0.4813-0.015-0.2055-0.0287-0.0278-0.14890.0004-0.1016-11.1569-6.14055.2334
21.669-0.1298-2.02090.68980.13344.54-0.06460.29520.0424-0.06760.05970.09350.1385-0.64020.0049-0.0284-0.0314-0.0014-0.09710.0092-0.1126-27.9587-1.087141.1423
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-2 - 23610 - 248
22BB3 - 23615 - 248

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