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- PDB-3bby: Crystal structure of glutathione S-transferase (NP_416804.1) from... -

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Basic information

Entry
Database: PDB / ID: 3bby
TitleCrystal structure of glutathione S-transferase (NP_416804.1) from Escherichia coli K12 at 1.85 A resolution
ComponentsUncharacterized GST-like protein yfcF
KeywordsTRANSFERASE / NP_416804.1 / glutathione S-transferase / N-terminal domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


maleylacetoacetate isomerase activity / L-phenylalanine catabolic process / glutathione transferase / glutathione transferase activity / glutathione metabolic process / peroxidase activity / response to hydrogen peroxide
Similarity search - Function
Glutathione S-transferases, subfamily 4, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...Glutathione S-transferases, subfamily 4, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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, C-terminal-like / Soluble glutathione S-transferase C-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
ACETATE ION / 2-ETHOXYETHANOL / Glutathione S-transferase YfcF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of glutathione S-transferase (NP_416804.1) from Escherichia coli K12 at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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 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: Uncharacterized GST-like protein yfcF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9176
Polymers24,5971
Non-polymers3195
Water4,143230
1
A: Uncharacterized GST-like protein yfcF
hetero molecules

A: Uncharacterized GST-like protein yfcF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,83412
Polymers49,1952
Non-polymers63910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area1930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.960, 69.960, 92.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-216-

CA

21A-220-

HOH

31A-229-

HOH

41A-242-

HOH

51A-307-

HOH

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Components

#1: Protein Uncharacterized GST-like protein yfcF


Mass: 24597.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yfcF, b2301, JW2298 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: P77544
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ETX / 2-ETHOXYETHANOL / 2-Ethoxyethanol


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: NANODROP, 40.0% 2-ethoxyethanol, 0.05M Ca(OAc)2, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9184, 0.9795, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.97951
30.97961
ReflectionResolution: 1.85→28.772 Å / Num. obs: 22750 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.99 % / Biso Wilson estimate: 16.68 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 8.16
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.85-1.920.7912208404428198
1.92-1.990.6762.41894339801100
1.99-2.080.5133.22011842191100
2.08-2.190.3734.32087743721100
2.19-2.330.3055.22108144121100
2.33-2.510.2466.52060543031100
2.51-2.760.1838.42044642761100
2.76-3.160.12611.52063543161100
3.16-3.980.07517.32047443101100
3.98-28.7720.05920.5204694329199.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.85→28.772 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.371 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.109
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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. CALCIUM IONS, ACETATE (ACT) AND 2-ETHOXYETHANOL (ETX) MODELED ARE PRESENT IN THE CRYSTALLIZATION/CRYO CONDITIONS. 5. RAMACHANDRAN OUTLIER A71 AND ROTAMER OUTLIER A197 ARE SUPPORTED BY CLEARLY DEFINED DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1768 7.8 %RANDOM
Rwork0.158 ---
obs0.161 22714 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: 16.365 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.23 Å20 Å2
2--0.45 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.85→28.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 18 230 1768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221611
X-RAY DIFFRACTIONr_bond_other_d0.0020.021099
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9612197
X-RAY DIFFRACTIONr_angle_other_deg0.92532677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5195203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81623.51474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83915264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9521512
X-RAY DIFFRACTIONr_chiral_restr0.0750.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021785
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02337
X-RAY DIFFRACTIONr_nbd_refined0.2180.2334
X-RAY DIFFRACTIONr_nbd_other0.2010.21166
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2791
X-RAY DIFFRACTIONr_nbtor_other0.0860.2774
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2144
X-RAY DIFFRACTIONr_metal_ion_refined0.1840.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3250.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.220
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0360.21
X-RAY DIFFRACTIONr_mcbond_it1.84531014
X-RAY DIFFRACTIONr_mcbond_other0.4953383
X-RAY DIFFRACTIONr_mcangle_it2.73551582
X-RAY DIFFRACTIONr_scbond_it4.5498695
X-RAY DIFFRACTIONr_scangle_it6.14511608
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 127 -
Rwork0.21 1522 -
all-1649 -
obs--99.94 %

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