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- PDB-3zyy: Reductive activator for corrinoid,iron-sulfur protein -

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Basic information

Entry
Database: PDB / ID: 3zyy
TitleReductive activator for corrinoid,iron-sulfur protein
ComponentsIRON-SULFUR CLUSTER BINDING PROTEIN
KeywordsIRON-SULFUR-BINDING PROTEIN / ASHKA FAMILY / ATPASE
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
Ubiquitin-like (UB roll) - #880 / Domain of unknown function (DUF4445) / RACo, C-terminal / RACo linker region / RACo, middle region / RACo, middle domain superfamily / C-terminal domain of RACo the ASKHA domain / RACo linker region / RACo middle region / Beta-grasp domain ...Ubiquitin-like (UB roll) - #880 / Domain of unknown function (DUF4445) / RACo, C-terminal / RACo linker region / RACo, middle region / RACo, middle domain superfamily / C-terminal domain of RACo the ASKHA domain / RACo linker region / RACo middle region / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / ATPase, nucleotide binding domain / Ubiquitin-like (UB roll) / Nucleotidyltransferase; domain 5 / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
(R,R)-2,3-BUTANEDIOL / FE2/S2 (INORGANIC) CLUSTER / PHOSPHATE ION / Iron-sulfur cluster binding protein
Similarity search - Component
Biological speciesCARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å
AuthorsHennig, S.E. / Jeoung, J.-H. / Goetzl, S. / Dobbek, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Redox-Dependent Complex Formation by an ATP-Dependent Activator of the Corrinoid/Iron-Sulfur Protein.
Authors: Hennig, S.E. / Jeoung, J.H. / Goetzl, S. / Dobbek, H.
History
DepositionAug 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Other
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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
X: IRON-SULFUR CLUSTER BINDING PROTEIN
Y: IRON-SULFUR CLUSTER BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,08919
Polymers137,5392
Non-polymers1,54917
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-182.2 kcal/mol
Surface area45330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.527, 91.191, 252.887
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN X AND (RESSEQ 108:425 OR RESSEQ 429:629 )
211CHAIN Y AND (RESSEQ 108:425 OR RESSEQ 429:629 )

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Components

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Protein , 1 types, 2 molecules XY

#1: Protein IRON-SULFUR CLUSTER BINDING PROTEIN / ATP-DEPENDENT REDUCTIVE ACTIVATOR


Mass: 68769.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CARBOXYDOTHERMUS HYDROGENOFORMANS (bacteria)
Strain: Z-2091 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3ACS2

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Non-polymers , 6 types, 413 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.26 Å3/Da / Density % sol: 45.7 % / Description: NONE
Crystal growDetails: 0.15 M MG-FORMATE, 15% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 339176 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 13.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7_650)refinement
AutoSolphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.2→19.936 Å / SU ML: 0.29 / σ(F): 1.99 / Phase error: 27.76 / Stereochemistry target values: ML
Details: RESIDUES FROM 3 TO 107 IN CHAIN WERE NOT MODELED BECAUSE OF NO OBSERVABLE ELECTRON DENSITY. RESIDUES CYS38 TO CYS44 IN CHAIN X WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflection
Rfree0.258 4174 5 %
Rwork0.22 --
obs0.222 83461 99.8 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.258 Å2 / ksol: 0.366 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.8817 Å20 Å20 Å2
2---7.5969 Å20 Å2
3----9.2848 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8781 0 79 396 9256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079378
X-RAY DIFFRACTIONf_angle_d1.83612321
X-RAY DIFFRACTIONf_dihedral_angle_d16.4763382
X-RAY DIFFRACTIONf_chiral_restr0.0521435
X-RAY DIFFRACTIONf_plane_restr0.0031580
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11X3897X-RAY DIFFRACTIONPOSITIONAL
12Y3897X-RAY DIFFRACTIONPOSITIONAL0.083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.36421390.31332627X-RAY DIFFRACTION100
2.225-2.25110.36451340.30052567X-RAY DIFFRACTION100
2.2511-2.27850.31911410.2992670X-RAY DIFFRACTION100
2.2785-2.30730.31061340.27642551X-RAY DIFFRACTION100
2.3073-2.33760.32491390.27122633X-RAY DIFFRACTION100
2.3376-2.36960.32971370.25982597X-RAY DIFFRACTION100
2.3696-2.40340.28921390.26762644X-RAY DIFFRACTION100
2.4034-2.43920.31061360.26622590X-RAY DIFFRACTION100
2.4392-2.47730.3511390.27112633X-RAY DIFFRACTION100
2.4773-2.51780.37721370.28312617X-RAY DIFFRACTION100
2.5178-2.56110.30551370.27812595X-RAY DIFFRACTION100
2.5611-2.60760.34051390.26092641X-RAY DIFFRACTION100
2.6076-2.65770.30581360.25672590X-RAY DIFFRACTION100
2.6577-2.71180.27231410.25152660X-RAY DIFFRACTION100
2.7118-2.77060.30081360.24782587X-RAY DIFFRACTION100
2.7706-2.83490.30081390.25112649X-RAY DIFFRACTION100
2.8349-2.90550.28061370.2552607X-RAY DIFFRACTION100
2.9055-2.98390.27551390.24452641X-RAY DIFFRACTION100
2.9839-3.07140.26931390.24222640X-RAY DIFFRACTION100
3.0714-3.17010.2611400.24442653X-RAY DIFFRACTION100
3.1701-3.28290.27621380.23162634X-RAY DIFFRACTION100
3.2829-3.41380.28961400.22522654X-RAY DIFFRACTION100
3.4138-3.56830.27751390.21792640X-RAY DIFFRACTION100
3.5683-3.75520.25571410.20042672X-RAY DIFFRACTION100
3.7552-3.98880.22451400.19532662X-RAY DIFFRACTION100
3.9888-4.29390.20531390.1772651X-RAY DIFFRACTION100
4.2939-4.72080.21251420.16462695X-RAY DIFFRACTION100
4.7208-5.39210.22971420.19022702X-RAY DIFFRACTION100
5.3921-6.74940.24591450.21642747X-RAY DIFFRACTION100
6.7494-19.93710.18011500.18412838X-RAY DIFFRACTION99

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