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- PDB-2wul: CRYSTAL STRUCTURE OF THE HUMAN GLUTAREDOXIN 5 WITH BOUND GLUTATHI... -

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Basic information

Entry
Database: PDB / ID: 2wul
TitleCRYSTAL STRUCTURE OF THE HUMAN GLUTAREDOXIN 5 WITH BOUND GLUTATHIONE IN AN FES CLUSTER
ComponentsGLUTAREDOXIN RELATED PROTEIN 5
KeywordsOXIDOREDUCTASE / CHROMOSOME 14 OPEN READING FRAME 87 / THIOREDOXIN FAMILY / GLRX5 / PR01238 / FLB4739
Function / homology
Function and homology information


: / : / Mitochondrial iron-sulfur cluster biogenesis / iron-sulfur cluster assembly complex / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / hemopoiesis / cell redox homeostasis / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis ...: / : / Mitochondrial iron-sulfur cluster biogenesis / iron-sulfur cluster assembly complex / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / hemopoiesis / cell redox homeostasis / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis / mitochondrial matrix / neuronal cell body / dendrite / mitochondrion / metal ion binding
Similarity search - Function
Monothiol glutaredoxin-related / Glutaredoxin, PICOT-like / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / GLUTATHIONE / DI(HYDROXYETHYL)ETHER / Glutaredoxin-related protein 5, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsRoos, A.K. / Johansson, C. / Guo, K. / Yue, W.W. / Pike, A.C.W. / Cooper, C.D.O. / Pilka, E.S. / Kavanagh, K.L. / Chaikuad, A. / von Delft, F. ...Roos, A.K. / Johansson, C. / Guo, K. / Yue, W.W. / Pike, A.C.W. / Cooper, C.D.O. / Pilka, E.S. / Kavanagh, K.L. / Chaikuad, A. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
CitationJournal: Biochem.J. / Year: 2011
Title: The Crystal Structure of Human Glrx5: Iron Sulphur Cluster Coordination, Tetrameric Assembly and Monomer Activity.
Authors: Johansson, C. / Roos, A.K. / Montano, S.J. / Sengupta, R. / Filippakopoulos, P. / Guo, K. / von Delft, F. / Holmgren, A. / Oppermann, U. / Kavanagh, K.L.
History
DepositionOct 6, 2009Deposition site: PDBE / Processing site: PDBE
SupersessionOct 20, 2009ID: 2WEM
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 7, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: GLUTAREDOXIN RELATED PROTEIN 5
B: GLUTAREDOXIN RELATED PROTEIN 5
C: GLUTAREDOXIN RELATED PROTEIN 5
D: GLUTAREDOXIN RELATED PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,29115
Polymers51,4624
Non-polymers1,82911
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-99.19 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.995, 68.995, 229.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11D-2001-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSVALVAL2AA51 - 8219 - 50
211LYSLYSVALVAL2CC51 - 8219 - 50
121ALAALAVALVAL2AA86 - 13554 - 103
221ALAALAVALVAL2CC86 - 13554 - 103
131GLUGLULEULEU5AA136 - 148104 - 116
231GLUGLULEULEU5CC136 - 148104 - 116
112LYSLYSVALVAL2BB51 - 8219 - 50
212LYSLYSVALVAL2DD51 - 8219 - 50
122ALAALAVALVAL2BB86 - 13554 - 103
222ALAALAVALVAL2DD86 - 13554 - 103
132GLUGLULEULEU5BB136 - 148104 - 116
232GLUGLULEULEU5DD136 - 148104 - 116

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.989, 0.087, -0.117), (0.093, -0.994, 0.053), (-0.112, -0.063, -0.992)2.75935, -6.3694, 47.68388
2given(-0.992, -0.122, -0.021), (-0.121, 0.993, -0.014), (0.023, -0.011, -1)67.30732, 4.51347, 43.19992
3given(-0.991, 0.033, 0.13), (-0.022, -0.996, 0.087), (0.132, 0.084, 0.988)64.6461, -3.26724, -4.21723

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
GLUTAREDOXIN RELATED PROTEIN 5


Mass: 12865.564 Da / Num. of mol.: 4 / Fragment: RESIDUES 35-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q86SX6

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Non-polymers , 5 types, 104 molecules

#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.66 Å3/Da / Density % sol: 53.8 %
Description: INITIAL PHASES BY SE-SAD ALLOWED AN INITIAL MODEL BASED ON 2E7P TO BE PLACED FOR SUBSEQUENT MR INTO THE HIGHER RESOLUTION DATA
Crystal growpH: 6.5
Details: 50% PEG300, 0.2 M MGCL2, 0.1 M CACODYLATE PH 6.5, 0.01 M SPERMINE TETRAHYDROCHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979, 0.9794
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97941
ReflectionResolution: 2.4→69.05 Å / Num. obs: 22752 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 9.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
SHARPphasing
REFMAC5.5.0102refinement
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 2E7P

2e7p


Resolution: 2.4→66.07 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 15.349 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25079 1146 5.1 %RANDOM
Rwork0.19966 ---
obs0.20216 21497 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.087 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2--1.09 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 2.4→66.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3337 0 99 93 3529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223491
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.9984730
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4245432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99925.973149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45315568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.35158
X-RAY DIFFRACTIONr_chiral_restr0.0740.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212624
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.75332159
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.83453459
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.34681332
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.36911267
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A328tight positional0.10.05
12C328tight positional0.10.05
21B328tight positional0.140.05
22D328tight positional0.140.05
11A349medium positional0.240.5
12C349medium positional0.240.5
21B365medium positional0.390.5
22D365medium positional0.390.5
11A42loose positional0.455
12C42loose positional0.455
21B49loose positional0.65
22D49loose positional0.65
11A328tight thermal1.8110
12C328tight thermal1.8110
21B328tight thermal1.6110
22D328tight thermal1.6110
11A349medium thermal2.3620
12C349medium thermal2.3620
21B365medium thermal1.7320
22D365medium thermal1.7320
11A42loose thermal2.7730
12C42loose thermal2.7730
21B49loose thermal3.5130
22D49loose thermal3.5130
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 74 -
Rwork0.285 1560 -
obs--100 %
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)
15.5043-1.1484-0.12831.4497-1.79225.74450.08560.0822-0.0983-0.08910.11020.4424-0.2098-0.9132-0.19580.16470.1405-0.03250.3367-0.01610.229219.4972.01559.9385
25.3944-2.09750.2749.1798-4.03142.9753-0.21490.40460.9423-0.71260.0016-0.5296-0.3407-0.06190.21330.55280.0498-0.06380.3030.07720.196128.977812.84944.6328
34.2432-0.0683-0.16552.0471-1.65666.4297-0.03960.2365-0.04920.02110.06390.2864-0.0135-0.6756-0.02430.1003-0.03170.0130.14980.00070.0719.334-8.845834.5506
43.03070.1632-1.33991.4070.15863.7889-0.11660.03650.3280.22240.0634-0.0791-0.1339-0.07560.05320.1365-0.00820.00050.1386-0.01140.081527.3904-3.36637.4004
514.61316.5468-5.69535.6861-4.184610.05730.13810.0381-1.07770.41660.0554-0.82940.58240.7432-0.19350.24410.1097-0.08180.1322-0.06840.295731.9773-20.49641.0165
65.86380.56410.28914.16641.63543.20920.0928-0.32010.36580.32740.158-0.6127-0.20480.7712-0.25080.205-0.06710.03690.2679-0.08560.211748.92556.689832.424
73.37261.53160.26193.76470.36754.37060.0975-0.62170.41180.61490.02420.1739-0.31470.1028-0.12170.2327-0.06410.04060.2798-0.0810.152540.05467.174138.087
82.5004-0.74760.18282.480.41074.19370.03280.01640.266-0.0648-0.0435-0.3281-0.12420.55590.01070.11310.02920.00360.1415-0.02310.092348.4601-6.01678.8561
92.23610.2712-1.0986.69393.62283.3413-0.03980.01770.121-0.22020.07310.1383-0.1556-0.3196-0.03330.0830.0515-0.00650.19220.03040.036737.6707-7.21436.855
1010.4277-6.3255-6.372312.49691.862215.05090.00590.1533-0.7338-0.0243-0.23961.10780.4153-0.48980.23370.1477-0.05360.03450.1263-0.03180.114238.9163-21.39011.8499
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 116
2X-RAY DIFFRACTION2A117 - 149
3X-RAY DIFFRACTION3B41 - 96
4X-RAY DIFFRACTION4B97 - 128
5X-RAY DIFFRACTION5B129 - 149
6X-RAY DIFFRACTION6C40 - 96
7X-RAY DIFFRACTION7C97 - 148
8X-RAY DIFFRACTION8D41 - 103
9X-RAY DIFFRACTION9D104 - 132
10X-RAY DIFFRACTION10D133 - 149

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