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- PDB-5vcq: A Hyrdrogen Producing Hybrid Streptavidin-Diiron Catalyst -

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Basic information

Entry
Database: PDB / ID: 5vcq
TitleA Hyrdrogen Producing Hybrid Streptavidin-Diiron Catalyst
ComponentsStreptavidin
KeywordsBiotin Binding Protein / Protein-organometallic catalyst / hydrogenase / hybrid protein / 4Fe-4S clusters
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-BN7 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.051 Å
AuthorsSimmons, C.R. / Roy, A. / Vaughn, M.D. / Allen, J.P. / Ghirlanda, G.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0001016 United States
CitationJournal: To Be Published
Title: Enhanced Photocatalytic Hydrogen Production by Hybrid Streptavidin-Diiron Catalysts
Authors: Roy, A. / Vaughn, M.D. / Tomlin, J. / Coffman, G.J. / Kodis, G. / Simmons, C.R. / Allen, J.P. / Ghirlanda, G.
History
DepositionMar 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,6008
Polymers75,3994
Non-polymers1,2024
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9240 Å2
ΔGint-55 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.849, 56.849, 239.611
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Streptavidin


Mass: 18849.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Chemical
ChemComp-BN7 / 2-methylpropyl 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoate


Mass: 300.417 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H24N2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 1.48 Å3/Da / Density % sol: 17.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100mM TRIS pH 8.5, 200mM MgCl2, 20-30% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 54193 / % possible obs: 99.6 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 22.875

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Processing

Software
NameVersionClassification
PHENIX1.9_1692phasing
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.051→49.233 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.49
RfactorNum. reflection% reflection
Rfree0.2184 2002 7.35 %
Rwork0.1648 --
obs0.1689 27231 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.051→49.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3606 0 80 478 4164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073831
X-RAY DIFFRACTIONf_angle_d1.3075248
X-RAY DIFFRACTIONf_dihedral_angle_d13.631282
X-RAY DIFFRACTIONf_chiral_restr0.043586
X-RAY DIFFRACTIONf_plane_restr0.005654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0514-2.10270.2441460.17071791X-RAY DIFFRACTION99
2.1027-2.15950.251400.15881789X-RAY DIFFRACTION100
2.1595-2.22310.21191390.15771772X-RAY DIFFRACTION100
2.2231-2.29480.25151420.16611815X-RAY DIFFRACTION100
2.2948-2.37680.2581440.17131822X-RAY DIFFRACTION100
2.3768-2.4720.22651450.18031806X-RAY DIFFRACTION100
2.472-2.58450.28011390.19011814X-RAY DIFFRACTION100
2.5845-2.72070.2461470.18341786X-RAY DIFFRACTION100
2.7207-2.89120.24531460.18511793X-RAY DIFFRACTION100
2.8912-3.11440.2451450.17671798X-RAY DIFFRACTION100
3.1144-3.42770.20121360.17141809X-RAY DIFFRACTION100
3.4277-3.92350.20081470.14731813X-RAY DIFFRACTION100
3.9235-4.94250.15931450.13311804X-RAY DIFFRACTION100
4.9425-49.24680.19711410.16651817X-RAY DIFFRACTION99

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