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- PDB-3ziv: Crystal Structure of Ancestral Thioredoxin Relative to last Archa... -

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Basic information

Entry
Database: PDB / ID: 3ziv
TitleCrystal Structure of Ancestral Thioredoxin Relative to last Archaea- Eukaryotes Common Ancestor (AECA) from the Precambrian Period
ComponentsAECA THIOREDOXIN
KeywordsOXIDOREDUCTASE / ANCESTRAL RECONSTRUCTED
Function / homologyGlutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGavira, J.A. / Ingles-Prieto, A. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.
CitationJournal: Structure / Year: 2013
Title: Conservation of Protein Structure Over Four Billion Years
Authors: Ingles-Prieto, A. / Ibarra-Molero, B. / Delgado-Delgado, A. / Perez-Jimenez, R. / Fernandez, J.M. / Gaucher, E.A. / Sanchez-Ruiz, J.M. / Gavira, J.A.
History
DepositionJan 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AECA THIOREDOXIN
B: AECA THIOREDOXIN
C: AECA THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)36,1023
Polymers36,1023
Non-polymers00
Water1448
1
A: AECA THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)12,0341
Polymers12,0341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AECA THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)12,0341
Polymers12,0341
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: AECA THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)12,0341
Polymers12,0341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.650, 48.850, 91.170
Angle α, β, γ (deg.)90.00, 93.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AECA THIOREDOXIN


Mass: 12034.044 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: thioredoxin-disulfide reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.4 Å3/Da / Density % sol: 49.21 % / Description: NONE
Crystal growTemperature: 277 K / Method: counter-diffusion / pH: 7 / Details: COUNTER DIFFUSION, 25% PEG1500, PH 9.0, 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.65→45.51 Å / Num. obs: 9592 / % possible obs: 97.9 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 59.14 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.21
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.24 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YNX

2ynx


Resolution: 2.65→45.512 Å / SU ML: 0.31 / σ(F): 1.38 / Phase error: 29.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2762 460 4.8 %
Rwork0.1808 --
obs0.1852 9586 97.8 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80 Å2
Refinement stepCycle: LAST / Resolution: 2.65→45.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 0 8 2365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082437
X-RAY DIFFRACTIONf_angle_d1.153324
X-RAY DIFFRACTIONf_dihedral_angle_d14.65855
X-RAY DIFFRACTIONf_chiral_restr0.076390
X-RAY DIFFRACTIONf_plane_restr0.005427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6501-3.03350.35241650.252991X-RAY DIFFRACTION98
3.0335-3.82160.31281550.20443060X-RAY DIFFRACTION98
3.8216-45.51910.23211400.15423075X-RAY DIFFRACTION97
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)
16.1565-0.3992-3.05782.496-2.75045.0485-0.2746-2.10231.76880.6833-0.0458-0.648-2.49051.3878-0.25911.0285-0.3174-0.1370.7232-0.22390.62935.9192.343940.5515
23.3597-0.0648-1.31151.7147-0.38633.06990.49231.05390.7411-0.4677-0.4053-0.07090.0905-0.2815-0.10810.42650.1781-0.03820.45850.05220.48131.8991-8.482329.1953
34.7831-1.86751.11994.9328-5.52387.3656-0.39740.86770.17220.278-0.76191.2125-0.798-1.95011.1570.75480.1230.32151.04-0.05060.4913-8.39371.358737.6971
43.3921-0.8405-1.58433.00962.22296.7579-0.0837-0.52690.42310.52720.1031-0.15770.57451.6569-0.07490.4603-0.0014-0.00680.67070.09180.35595.6541-9.273839.109
54.5085-0.85090.64585.14691.36749.51690.9395-0.46490.17480.5902-0.16830.5719-0.2117-0.2291-1.31290.576-0.28610.01611.03240.06830.6261-9.7813-9.738739.305
62.0706-2.2408-0.9868.39310.47376.9506-0.1503-0.9407-0.40240.1548-0.905-0.77411.50540.5240.96791.20960.09120.09160.58820.1591.0002-9.5434-35.120430.2139
70.64710.36580.33070.67380.51060.39450.39660.2791-1.0861-0.8918-0.31410.13721.43730.68270.13421.05030.41190.0280.6765-0.03990.8162-8.7379-33.67622.2873
84.03680.448-0.17793.337-0.04095.2586-0.4431-0.2782-0.81450.2408-0.18360.2455-0.0429-0.28260.34950.57120.4464-0.01190.4696-0.09380.6297-17.1602-19.270132.8512
95.27273.64893.31832.62832.11972.40110.11230.0424-0.40571.3735-0.08931.58681.4066-0.73580.50070.7549-0.226-0.06660.53120.04620.6105-23.4301-28.383523.5991
102.35431.10410.71154.31894.24895.7044-0.15030.1207-0.9464-0.97960.12040.13060.4512-0.1632-0.05631.11420.2587-0.25640.0464-0.0930.8688-15.6372-34.774721.5808
114.18131.06451.42323.3932-0.70433.3722-0.19120.906-0.6396-0.36590.2676-0.27740.45260.60090.02140.46670.07670.08120.6302-0.03870.4661-11.206-25.860619.1123
123.57370.6624-1.35973.24620.04265.4090.28480.37520.3073-0.7254-0.3519-0.2509-1.6334-1.3537-0.13680.7580.2815-0.05781.15480.18380.67368.5791-5.85958.6028
132.8695-0.51320.44563.8379-0.6790.71830.00061.736-0.3404-0.8323-0.20880.8552-0.3947-1.2096-0.02250.48840.0682-0.06831.23170.08170.57926.7418-14.92567.3808
145.0771-2.35071.5254.4529-2.48934.03020.2349-0.0938-0.42441.2229-0.24921.1101-0.5402-1.5293-0.09230.56030.13680.06971.19880.26370.56581.2751-12.358615.5423
151.5738-0.18910.60413.3268-1.89193.055-0.2113-0.1687-0.41840.0280.54540.7937-0.208-0.3808-0.50970.65080.12510.0411.37410.27691.0523-7.9204-11.640111.7204
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1 THROUGH 20 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 21 THROUGH 46 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 47 THROUGH 51 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 52 THROUGH 93 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 94 THROUGH 105 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 1 THROUGH 9 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 10 THROUGH 26 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 27 THROUGH 31 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 32 THROUGH 46 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 47 THROUGH 57 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 58 THROUGH 105 )
12X-RAY DIFFRACTION12CHAIN C AND (RESID 1 THROUGH 26 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 27 THROUGH 74 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 75 THROUGH 93 )
15X-RAY DIFFRACTION15CHAIN C AND (RESID 94 THROUGH 105 )

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