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- PDB-3cbu: Crystal structure of a putative glutathione s-transferase (reut_a... -

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Basic information

Entry
Database: PDB / ID: 3cbu
TitleCrystal structure of a putative glutathione s-transferase (reut_a1011) from ralstonia eutropha jmp134 at 2.05 A resolution
ComponentsProbable gst-related protein
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


: / 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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / 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
PHOSPHATE ION / Probable gst-related protein
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative glutathione S-transferase (YP_295234.1) from Ralstonia eutropha JMP134 at 2.05 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable gst-related protein
B: Probable gst-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4589
Polymers47,9902
Non-polymers4677
Water6,557364
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-25.1 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.840, 106.840, 113.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 1 - 210 / Label seq-ID: 2 - 211

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

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Components

#1: Protein Probable gst-related protein


Mass: 23995.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Species: Cupriavidus necator / Strain: JMP134 / Gene: YP_295234.1, Reut_A1011 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q473P3
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE 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: 3.38 Å3/Da / Density % sol: 63.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 11
Details: NANODROP, 0.2M Lithium sulfate, 0.79M Sodium dihydrogen phosphate, 0.891M Di-potassium hydrogen phosphate, 0.1M CAPS pH 11.0, 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, 0.97879, 0.97935
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 22, 2008 / 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
20.978791
30.979351
ReflectionResolution: 2.05→29.683 Å / Num. obs: 41838 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.954 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.28
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.05-2.120.6052.4289357234195.8
2.12-2.210.4793.23404583661100
2.21-2.310.3684.13204778741100
2.31-2.430.2815.4318497805199.9
2.43-2.580.21373178477821100
2.58-2.780.178.63265179771100
2.78-3.060.10812.9326507958199.9
3.06-3.50.05921.8323137861199.9
3.5-4.40.03434.73258579191100
4.4-29.6830.02642323477960199.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→29.683 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.23 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.131
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. THERE IS UNMODELED DENSITY NEAR SER 10 IN EACH CHAIN, WHICH IS THE PUTATIVE GLUTATHIONE BINDING SITE. 5. PO4 AND EDO WERE MODELED BASED ON CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 2110 5 %RANDOM
Rwork0.171 ---
obs0.173 41801 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.519 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 29 364 3653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223361
X-RAY DIFFRACTIONr_bond_other_d0.0010.022262
X-RAY DIFFRACTIONr_angle_refined_deg1.5252.0024568
X-RAY DIFFRACTIONr_angle_other_deg1.48735554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6635426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54424.219128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14815558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4691516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213678
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02644
X-RAY DIFFRACTIONr_mcbond_it1.80632133
X-RAY DIFFRACTIONr_mcbond_other0.6443840
X-RAY DIFFRACTIONr_mcangle_it2.87153440
X-RAY DIFFRACTIONr_scbond_it4.6981228
X-RAY DIFFRACTIONr_scangle_it6.346111126
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1233MEDIUM POSITIONAL0.150.5
2B1449LOOSE POSITIONAL0.335
1A1233MEDIUM THERMAL0.922
2B1449LOOSE THERMAL1.0810
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 136 -
Rwork0.202 2823 -
all-2959 -
obs--97.5 %
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)
10.64710.0779-0.12430.5365-0.12820.7681-0.0082-0.0015-0.12540.0375-0.01320.01620.08690.03930.0214-0.0639-0.00140.0243-0.03540.0128-0.038484.14742.4579.564
20.7826-0.28220.26580.7102-0.28730.92280.02590.0956-0.0186-0.10830.01650.0358-0.04720.0503-0.0424-0.06160.0070.026-0.01520.0221-0.060285.1458.324-8.059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2112 - 212
2X-RAY DIFFRACTION2BB1 - 2122 - 213

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