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- PDB-4mp4: Crystal structure of a glutathione transferase family member from... -

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Basic information

Entry
Database: PDB / ID: 4mp4
TitleCrystal structure of a glutathione transferase family member from Acinetobacter baumannii, Target EFI-501785, apo structure
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / GST / glutathione S-transferase fold / Enzyme Function Initiative / EFI / structural genomics
Function / homology
Function and homology information


Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutaredoxin / Glutaredoxin / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutathione S-transferase / Glutathione S-transferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.498 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Scott Glenn, A. / Chowdhury, S. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Armstrong, R.N. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of a glutathione transferase family member from Acinetobacter baumannii, Target EFI-501785, apo structure
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Armstrong, R.N. / Almo, S.C.
History
DepositionSep 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase
B: Glutathione S-transferase
C: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0434
Polymers74,9473
Non-polymers961
Water2,900161
1
A: Glutathione S-transferase
B: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0613
Polymers49,9652
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-21 kcal/mol
Surface area18270 Å2
MethodPISA
2
C: Glutathione S-transferase

C: Glutathione S-transferase


Theoretical massNumber of molelcules
Total (without water)49,9652
Polymers49,9652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area2880 Å2
ΔGint-15 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.198, 103.358, 51.057
Angle α, β, γ (deg.)90.000, 91.090, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glutathione S-transferase / GST


Mass: 24982.426 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: ACICU / Gene: ACICU_01452 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B2HYC1, UniProt: A0A7U4DD23*PLUS, glutathione transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.22 Å3/Da / Density % sol: 61.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: protein in 10 mM HEPES, pH 7.5, 5 mM GSH, reservoir: MCSG2(E10) (0.8 M lithium sulfate, 0.1 M sodium acetate, pH 4.6), cryoprotection: 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 8, 2012 / Details: mirrors
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.498→50 Å / Num. all: 32775 / Num. obs: 32775 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 11.2
Reflection shellResolution: 2.498→2.54 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1605 / % possible all: 98.9

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
HKL-3000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JBB

4jbb


Resolution: 2.498→36.317 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.7978 / SU ML: 0.31 / σ(F): 0 / σ(I): 0 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2546 1608 5.05 %RANDOM
Rwork0.1911 ---
all0.1943 31838 --
obs0.1943 31838 96.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.63 Å2 / Biso mean: 35.3232 Å2 / Biso min: 1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.498→36.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4778 0 5 161 4944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084908
X-RAY DIFFRACTIONf_angle_d1.0316656
X-RAY DIFFRACTIONf_chiral_restr0.067735
X-RAY DIFFRACTIONf_plane_restr0.005849
X-RAY DIFFRACTIONf_dihedral_angle_d15.8231813
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.498-2.5790.29551010.21342131223275
2.579-2.67120.28791300.21422556268690
2.6712-2.77810.28271590.21972733289298
2.7781-2.90450.31461570.207228523009100
2.9045-3.05750.28361340.220428492983100
3.0575-3.2490.30821490.205928332982100
3.249-3.49970.2811530.199828452998100
3.4997-3.85150.26291530.164728432996100
3.8515-4.4080.20151490.161128523001100
4.408-5.55040.2131460.16728673013100
5.5504-36.32110.2371770.21092869304699
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)
11.2772-0.1359-0.23011.35960.13161.2604-0.29180.28020.4938-0.30490.13080.5033-0.1251-0.0192-0.04680.1852-0.0546-0.06910.18890.07960.236155.80598.573123.7812
20.8730.7226-0.24941.74030.07990.9311-0.18270.38380.5579-0.1957-0.00270.3539-0.23440.1372-0.34520.3194-0.1132-0.12410.10420.28070.252949.79627.973219.1506
30.98980.18490.24840.91210.08590.4046-0.05570.0864-0.1063-0.1084-0.1074-0.22740.1768-0.155-0.00250.2091-0.07760.08340.176-0.02850.080654.9596-5.911928.9029
43.1647-0.2771-0.87182.92710.66594.48110.235-0.1836-0.43080.346-0.13110.02770.3761-0.00790.09590.2518-0.0277-0.10290.11080.12930.414156.6251-16.30236.5195
50.90310.67220.77160.98810.26092.9070.15430.0592-0.4317-0.16430.2492-0.41630.32920.42690.18190.14210.01680.01490.1308-0.00050.227765.1865-8.152429.2484
60.78940.01150.61293.57021.24451.0612-0.15810.04790.4515-0.0244-0.06710.1153-0.2970.0243-0.04740.2047-0.0523-0.01610.190.08950.292363.123413.80430.2637
71.162-0.05760.21441.1311-0.28861.1308-0.1478-0.2975-0.38360.27760.15630.00760.16140.02120.00760.24470.0673-0.01980.12210.06620.219339.769-19.56219.107
81.158-0.14790.29781.2191-0.08880.6664-0.1212-0.04330.3741-0.1764-0.126-0.85420.05270.15910.12030.38760.03270.06640.19550.01930.403234.844-5.21925.355
90.3250.0532-0.30771.384-0.20181.15780.06430.07910.7116-0.15360.2087-0.9454-0.52840.31530.44210.2799-0.09340.02840.04790.03111.145426.64-0.88224.423
100.33660.6367-0.31763.75810.87331.1619-0.1684-0.1151-0.4554-0.13660.1259-0.12510.12530.0895-0.180.15540.008-0.08310.26470.10890.740626.405-25.03325.08
111.0197-0.03230.57271.23370.23631.1329-0.15080.53550.0761-0.24420.0622-0.0684-0.29610.289-0.08820.0598-0.0617-0.1560.45960.09470.042282.705716.076835.7225
120.9643-0.21480.23241.67450.04232.0427-0.16950.40560.1188-0.3180.1444-0.164-0.06760.37130.08670.2034-0.0839-0.0270.4040.10980.134989.673219.676436.8849
132.43750.7504-3.6770.9677-0.72915.9742-0.12790.06440.4370.168-0.0691-0.0318-0.4727-0.009-0.05650.27810.0546-0.11130.24340.06240.404581.685829.994447.9985
140.8796-0.14350.27170.6057-0.06470.96610.2369-0.2017-0.30150.34120.1641-0.12850.29970.0656-0.06280.12890.0446-0.0770.23010.04670.194780.16986.999450.8452
150.2626-0.1988-0.4981.6353-0.29882.0968-0.0875-0.2091-0.08470.36210.02520.00120.19150.11210.19250.2297-0.12160.03980.72460.2888-0.044775.53425.882160.3859
163.3306-0.19510.2093.03920.22112.7331-0.0718-0.3421-0.04070.3420.01550.45030.1538-0.4019-0.00070.20040.1130.03520.47240.00510.267370.458922.004554.262
170.50290.08520.25221.3923-0.0270.8180.0349-0.09080.09110.1352-0.04010.27110.0277-0.3122-0.02660.0914-0.0331-0.00290.2550.05070.114970.727511.193545.2967
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ( resid 5 through 29 )A5 - 29
2X-RAY DIFFRACTION2chain 'A' and ( resid 30 through 83 )A30 - 83
3X-RAY DIFFRACTION3chain 'A' and ( resid 84 through 133 )A84 - 133
4X-RAY DIFFRACTION4chain 'A' and ( resid 134 through 150 )A134 - 150
5X-RAY DIFFRACTION5chain 'A' and ( resid 151 through 197 )A151 - 197
6X-RAY DIFFRACTION6chain 'A' and ( resid 198 through 216 )A198 - 216
7X-RAY DIFFRACTION7chain 'B' and ( resid 5 through 83 )B5 - 83
8X-RAY DIFFRACTION8chain 'B' and ( resid 84 through 133 )B84 - 133
9X-RAY DIFFRACTION9chain 'B' and ( resid 134 through 197 )B134 - 197
10X-RAY DIFFRACTION10chain 'B' and ( resid 198 through 216 )B198 - 216
11X-RAY DIFFRACTION11chain 'C' and ( resid 5 through 29 )C5 - 29
12X-RAY DIFFRACTION12chain 'C' and ( resid 30 through 83 )C30 - 83
13X-RAY DIFFRACTION13chain 'C' and ( resid 84 through 93 )C84 - 93
14X-RAY DIFFRACTION14chain 'C' and ( resid 94 through 133 )C94 - 133
15X-RAY DIFFRACTION15chain 'C' and ( resid 134 through 151 )C134 - 151
16X-RAY DIFFRACTION16chain 'C' and ( resid 152 through 163 )C152 - 163
17X-RAY DIFFRACTION17chain 'C' and ( resid 164 through 209 )C164 - 209

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