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- PDB-4hoj: Crystal structure of glutathione transferase homolog from Neisser... -

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Basic information

Entry
Database: PDB / ID: 4hoj
TitleCrystal structure of glutathione transferase homolog from Neisseria Gonorrhoeae, target EFI-501841, with bound glutathione
ComponentsRegF protein
KeywordsTRANSFERASE / GST / glutathione S-transferase / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


Stringent starvation protein A, 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, C-terminal / 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. ...Stringent starvation protein A, 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, C-terminal / 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 / GLUTATHIONE / Glutathione S-transferase, N-terminal domain protein
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of glutathione transferase homolog from Neisseria Gonorrhoeae, target EFI-501841, with bound glutathione
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Armstrong, R.N. / Gerlt, J.A. / Almo, S.C.
History
DepositionOct 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: RegF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7395
Polymers24,2921
Non-polymers4474
Water4,792266
1
A: RegF protein
hetero molecules

A: RegF protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,47710
Polymers48,5842
Non-polymers8938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4600 Å2
ΔGint-57 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.876, 49.876, 160.236
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-441-

HOH

21A-562-

HOH

31A-636-

HOH

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Components

#1: Protein RegF protein


Mass: 24292.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: regF / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O33374
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Protein (10 mM Hepes, pH 7.5, 100 mM NaCl), Reservoir (0.2 M Calcium Acetate, 0.1 M Imidazole:HCl, pH 8.0, 10% (w/v) PEG 8000), Cryoprotection (reservoir + 20% diethylene glycol), vapor ...Details: Protein (10 mM Hepes, pH 7.5, 100 mM NaCl), Reservoir (0.2 M Calcium Acetate, 0.1 M Imidazole:HCl, pH 8.0, 10% (w/v) PEG 8000), Cryoprotection (reservoir + 20% diethylene glycol), vapor diffusion, sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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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: Oct 13, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.4→160.236 Å / Num. obs: 46474 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.4-1.483.80.5151.548016125610.51597.8
1.48-1.5740.3412.347624119700.34198.3
1.57-1.674.20.2063.847318112790.20698.8
1.67-1.814.40.1355.746209104960.13599.3
1.81-1.984.70.09384550897610.09399.4
1.98-2.214.90.06211.24286387930.06299.5
2.21-2.565.20.04913.43979177220.04999.6
2.56-3.135.50.03915.73640166170.039100
3.13-4.435.60.029212825850430.02999.2
4.43-160.2365.40.02622.81404726130.02693.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YY7

1yy7


Resolution: 1.4→41.705 Å / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.8832 / SU ML: 0.14 / σ(F): 0 / σ(I): 0 / Phase error: 18.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 2351 5.06 %RANDOM
Rwork0.1757 ---
all0.1772 46474 --
obs0.1772 46474 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.34 Å2 / Biso mean: 21.4705 Å2 / Biso min: 6.28 Å2
Refinement stepCycle: LAST / Resolution: 1.4→41.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 26 266 1884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161684
X-RAY DIFFRACTIONf_angle_d1.7142276
X-RAY DIFFRACTIONf_chiral_restr0.104243
X-RAY DIFFRACTIONf_plane_restr0.01299
X-RAY DIFFRACTIONf_dihedral_angle_d14.186663
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.42860.27081330.240825572690100
1.4286-1.45970.25961500.22425392689100
1.4597-1.49360.2531450.206825452690100
1.4936-1.5310.21171310.193625392670100
1.531-1.57240.17661350.175425902725100
1.5724-1.61860.19321500.170625382688100
1.6186-1.67090.19041470.164925862733100
1.6709-1.73060.20581270.167225902717100
1.7306-1.79990.19421090.164326002709100
1.7999-1.88180.20661390.170225632702100
1.8818-1.9810.20081330.17426072740100
1.981-2.10510.21331350.166625942729100
2.1051-2.26770.21441320.166126512783100
2.2677-2.49580.20081400.167526162756100
2.4958-2.85690.19041510.173426112762100
2.8569-3.59910.20861580.168526832841100
3.5991-41.72370.21061360.18522714285096
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)
12.08770.4044-0.00271.1433-0.28272.13310.0334-0.03780.22840.04870.0380.1373-0.2997-0.1271-0.05050.09370.00070.02610.0754-0.00510.0984-2.372717.365412.3373
21.1651-2.2046-1.84414.54572.81064.164-0.0784-0.07470.4249-0.21760.2408-0.0691-0.04120.3808-0.1580.3908-0.16530.0770.3149-0.10540.306214.781424.02759.498
32.84642.1623-1.14712.9967-1.29083.3829-0.1002-0.04270.0452-0.14620.03750.09960.129-0.04880.06160.1215-0.0091-0.00050.1304-0.02870.1048.13554.63676.5413
42.74033.54380.54555.2498-0.01442.9128-0.16750.3689-0.9163-0.27860.1124-0.17580.9507-0.13980.00790.3997-0.02560.04040.1834-0.03890.25456.134-7.860913.5488
50.12510.1431-0.26882.2664-0.37630.5796-0.0767-0.0863-0.5212-0.0178-0.0315-0.6453-0.01730.4572-0.02880.1101-0.07950.02190.4794-0.02250.296422.112410.385913.76
62.69190.9519-1.07512.2421-0.28092.9662-0.1136-0.0496-0.18410.0470.0172-0.21560.14930.19760.09110.04910.00510.00830.1191-0.01660.08788.53193.398718.7853
73.7933-2.7506-0.12094.51370.49053.1199-0.0059-0.4141-0.26710.2738-0.0657-0.62290.28490.7441-0.0360.09150.0269-0.02450.41160.01250.281419.09643.276121.5115
83.91242.0961-1.53193.2727-0.99761.49470.1201-0.31730.02470.32870.0274-0.1395-0.15780.3627-0.09070.1295-0.04810.00260.1779-0.03950.08896.845812.827526.027
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2:73 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 74:83 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 84:114 )A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 115:132 )A0
5X-RAY DIFFRACTION5CHAIN A AND (RESID 133:148 )A0
6X-RAY DIFFRACTION6CHAIN A AND (RESID 149:169 )A0
7X-RAY DIFFRACTION7CHAIN A AND (RESID 170:183 )A0
8X-RAY DIFFRACTION8CHAIN A AND (RESID 184:201 )A0

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