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- PDB-5cax: CRYSTAL STRUCTURE OF METHANOSARCINA ACETIVORANS METHANOREDOXIN -

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Basic information

Entry
Database: PDB / ID: 5cax
TitleCRYSTAL STRUCTURE OF METHANOSARCINA ACETIVORANS METHANOREDOXIN
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / METHANOGENESIS / OXIDATIVE STRESS / COENZYME M
Function / homology
Function and homology information


protein-disulfide reductase activity / cell redox homeostasis / electron transfer activity
Similarity search - Function
Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / : / Glutaredoxin
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.451 Å
AuthorsYennawar, N.H. / Yennawar, H.P. / Ferry, G.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-95ER20198 MOD16 United States
CitationJournal: Biochemistry / Year: 2016
Title: Structural and Biochemical Characterizations of Methanoredoxin from Methanosarcina acetivorans, a Glutaredoxin-Like Enzyme with Coenzyme M-Dependent Protein Disulfide Reductase Activity.
Authors: Yenugudhati, D. / Prakash, D. / Kumar, A.K. / Kumar, R.S. / Yennawar, N.H. / Yennawar, H.P. / Ferry, J.G.
History
DepositionJun 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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
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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutaredoxin
B: Glutaredoxin
C: Glutaredoxin
D: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,71022
Polymers45,9294
Non-polymers1,78118
Water1,72996
1
A: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8805
Polymers11,4821
Non-polymers3974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9165
Polymers11,4821
Non-polymers4334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8194
Polymers11,4821
Non-polymers3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0968
Polymers11,4821
Non-polymers6137
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.154, 59.154, 172.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Glutaredoxin


Mass: 11482.263 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A) (archaea)
Strain: ATCC 35395 / DSM 2834 / JCM 12185 / C2A / Gene: MA_1658 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TQ93
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES buffer, pH 7.5, 0.05 M cadmium sulfate and 1M sodium acetate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 15, 2013
RadiationMonochromator: Varimax optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 21962 / % possible obs: 94.7 % / Redundancy: 2.8 % / Net I/σ(I): 11.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NZN

3nzn


Resolution: 2.451→19.492 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2719 1717 10.04 %
Rwork0.2149 --
obs0.2207 17106 78.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.451→19.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 0 38 96 3170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113103
X-RAY DIFFRACTIONf_angle_d1.5494157
X-RAY DIFFRACTIONf_dihedral_angle_d13.1211168
X-RAY DIFFRACTIONf_chiral_restr0.067470
X-RAY DIFFRACTIONf_plane_restr0.006521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4508-2.52270.34031370.2931323X-RAY DIFFRACTION83
2.5227-2.6040.32281380.29171204X-RAY DIFFRACTION74
2.604-2.69680.34551440.2771306X-RAY DIFFRACTION79
2.6968-2.80450.33391460.26161280X-RAY DIFFRACTION80
2.8045-2.93170.33331390.25751251X-RAY DIFFRACTION78
2.9317-3.08570.33021600.25421369X-RAY DIFFRACTION84
3.0857-3.27820.30561570.2191380X-RAY DIFFRACTION85
3.2782-3.530.26731600.19631364X-RAY DIFFRACTION85
3.53-3.88270.24281570.191390X-RAY DIFFRACTION86
3.8827-4.43870.22491430.17431278X-RAY DIFFRACTION78
4.4387-5.57060.22231270.18721170X-RAY DIFFRACTION71
5.5706-19.49240.26651090.21661074X-RAY DIFFRACTION65
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)
15.9538-1.9698-4.16826.34522.53483.81030.4849-0.91060.1343-0.61421.3080.50621.0626-0.1762-1.00940.8161-0.196-0.43890.50180.36550.584515.560340.1466-8.764
28.6702-3.22870.86743.9269-1.21892.1714-0.20130.0634-0.59520.0969-0.04180.31160.44530.08530.31560.735-0.06950.020.4530.01590.55412.837634.25-0.8917
36.1132-0.5883-1.55248.67930.24326.6389-0.1616-0.33980.5460.6356-0.3729-0.4729-0.33091.04870.52650.5957-0.0259-0.18550.50680.15410.504921.158942.54150.6222
45.3533-3.5587-1.52495.0678-2.16364.260.0927-2.135-0.84210.67831.33292.73351.0767-0.7042-1.40640.6669-0.06630.10120.72880.22941.00824.928636.10337.4326
56.70630.65393.00742.52832.48063.4990.02130.3781-0.06560.2555-0.07160.16930.63180.52420.09860.73480.0296-0.04540.42910.04860.5019.02549.4516-12.1713
64.38713.68773.2763.65971.09576.2255-0.44160.30480.2726-0.26320.2315-0.1138-0.8504-0.46380.16560.52890.0547-0.0370.4741-0.01860.56562.109559.8321-16.7659
78.0511.0480.87556.4280.36328.42080.1755-0.186-0.6324-0.096-0.01831.3288-0.1303-1.3445-0.06440.3820.0625-0.03760.60560.04190.6444-2.520448.0724-17.0337
84.9013-0.31390.21156.0766-0.27117.00920.0964-0.18850.48870.25730.44130.0801-1.0829-0.4907-0.40120.59880.15290.11160.5344-0.11030.5916-1.360757.9356-6.8339
95.11053.41061.52533.65540.68163.9957-0.3526-0.82810.90340.7302-1.1560.4943-0.1201-1.5440.35760.6963-0.3342-0.10851.60610.15640.176611.193746.5393-23.6858
107.7634-7.0863-1.41279.87131.87542.6308-0.71730.6255-0.74430.6440.4581.14960.24430.13660.12940.4906-0.05790.06450.5399-0.03840.48338.085542.3154-30.7402
114.4008-0.03881.33852.1589-1.48633.75720.17410.4698-0.00710.0528-0.01320.47480.2741-0.1226-0.23020.42350.0001-0.0610.59230.0110.50323.652645.9169-31.32
125.29712.093-0.51064.5607-2.28662.1015-0.490.01751.66480.19550.1315-0.3612-2.5292-0.01030.61351.25070.1086-0.42250.7680.16080.996116.180157.2351-30.5456
134.1264-3.28441.4356.402-4.05257.50640.12860.57160.0392-0.6099-0.4266-0.37520.20450.06930.27820.4984-0.01280.01280.7574-0.00740.458611.406742.652-39.6553
143.91281.0466-1.96324.86694.02025.573-1.98390.54880.7934-0.540.32981.5026-0.2283-1.58211.28450.53250.1322-0.0830.8519-0.02060.476112.795632.7892-17.2004
152.890.613-0.01870.98461.20372.120.9836-0.33610.13630.8993-0.1017-1.2079-0.37010.5672-0.41540.73880.4379-0.27311.0662-0.43131.297422.390542.0638-17.5461
165.0284-0.42380.64528.5513-7.10299.68620.17920.2001-0.42720.7116-0.3597-0.1628-0.71920.63680.07490.5088-0.04880.10220.44550.02430.457824.842633.6637-20.8874
176.1682-1.14130.05119.2843-2.7197.2911-0.221-0.9903-0.00630.9930.3635-0.7827-0.03370.5545-0.15710.43270.06-0.05160.5949-0.03470.387727.60833.0401-16.0165
182.9253-1.64661.11646.20623.32593.2904-0.20220.0528-1.77360.2636-0.68390.6376-1.5051-1.26921.1120.83240.0345-0.08930.60390.04430.997815.332722.1094-18.1122
195.3683-1.15483.82696.53570.30448.10210.56770.3395-0.9874-0.1748-0.4880.50950.93130.1020.09560.80550.0560.12970.516-0.05580.64625.688125.5831-25.4142
203.0604-1.74471.59653.9317-4.16224.4808-0.64690.9199-1.88390.2597-0.858-1.4218-0.5512-0.38231.30040.4932-0.05110.22660.7214-0.05470.913534.38733.973-29.4323
211.99881.99551.9981.99912.00024.89832.1214-1.90891.8967-0.2845-0.8049-4.2771-1.81290.7432-1.42041.204-0.84690.04190.71480.25190.510433.837440.5622-29.6696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 47 )
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 91 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 101 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 21 )
6X-RAY DIFFRACTION6chain 'B' and (resid 22 through 43 )
7X-RAY DIFFRACTION7chain 'B' and (resid 44 through 70 )
8X-RAY DIFFRACTION8chain 'B' and (resid 71 through 100 )
9X-RAY DIFFRACTION9chain 'C' and (resid 7 through 13 )
10X-RAY DIFFRACTION10chain 'C' and (resid 14 through 30 )
11X-RAY DIFFRACTION11chain 'C' and (resid 31 through 56 )
12X-RAY DIFFRACTION12chain 'C' and (resid 57 through 68 )
13X-RAY DIFFRACTION13chain 'C' and (resid 69 through 101 )
14X-RAY DIFFRACTION14chain 'D' and (resid 6 through 10 )
15X-RAY DIFFRACTION15chain 'D' and (resid 11 through 15 )
16X-RAY DIFFRACTION16chain 'D' and (resid 16 through 30 )
17X-RAY DIFFRACTION17chain 'D' and (resid 31 through 56 )
18X-RAY DIFFRACTION18chain 'D' and (resid 57 through 70 )
19X-RAY DIFFRACTION19chain 'D' and (resid 71 through 91 )
20X-RAY DIFFRACTION20chain 'D' and (resid 92 through 100 )
21X-RAY DIFFRACTION21chain 'D' and (resid 101 through 101 )

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