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- PDB-5vjs: De Novo Photosynthetic Reaction Center Protein Equipped with Heme... -

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Basic information

Entry
Database: PDB / ID: 5vjs
TitleDe Novo Photosynthetic Reaction Center Protein Equipped with Heme B, a synthetic Zn porphyrin, and Zn(II) cations
ComponentsReaction Center Maquette
KeywordsDE NOVO PROTEIN / maquette / protein design / charge separation / artificial photosynthesis
Function / homologyChem-9D7 / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsEnnist, N.M. / Dutton, P.L. / Stayrook, S.E. / Moser, C.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DESC0001035 United States
CitationJournal: Nat Commun / Year: 2022
Title: De novo protein design of photochemical reaction centers.
Authors: Ennist, N.M. / Zhao, Z. / Stayrook, S.E. / Discher, B.M. / Dutton, P.L. / Moser, C.C.
History
DepositionApr 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Author supporting evidence / Data collection / Database references
Category: database_2 / diffrn_radiation_wavelength / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _pdbx_audit_support.funding_organization
Revision 1.2Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Reaction Center Maquette
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9548
Polymers22,5301
Non-polymers1,4247
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.749, 43.749, 245.737
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Reaction Center Maquette


Mass: 22530.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: de novo designed protein / Source: (gene. exp.) synthetic construct (others) / Gene: designed / Plasmid: pJ414 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Non-polymers , 5 types, 46 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-9D7 / [4-(15-phenylporphyrin-5-yl-kappa~4~N~21~,N~22~,N~23~,N~24~)benzoato(2-)]zinc


Mass: 569.946 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H20N4O2Zn
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.61 Å3/Da / Density % sol: 52.86 % / Description: octahedron
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.4 / Details: 3.4 M NaCl, 100 mM Na acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781, 1.2824, 1.2831
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 20, 2013 / Details: Oxford Danfysik toroidal focusing mirror
RadiationMonochromator: channel cut monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.07811
21.28241
31.28311
ReflectionResolution: 2→61.43 Å / Num. obs: 17105 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.603 % / Biso Wilson estimate: 37.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.091 / Χ2: 1.014 / Net I/σ(I): 16.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.057.4090.972.5211940.8881.04198.8
2.05-2.117.8130.7413.4411960.9060.793100
2.11-2.177.8110.624.1911860.940.663100
2.17-2.247.7860.5025.1511360.970.537100
2.24-2.317.8150.4545.6511300.9710.486100
2.31-2.397.7990.35710670.9810.37599.8
2.39-2.487.7870.298.3210290.9820.3199.8
2.48-2.587.7210.21110.3510340.990.22699.9
2.58-2.77.830.19211.439390.9920.20699.8
2.7-2.837.6730.16113.169240.9940.17299.9
2.83-2.987.7670.10817.738790.9970.11699.7
2.98-3.167.6460.08821.098560.9980.09599.3
3.16-3.387.5720.06727.217920.9990.07299.2
3.38-3.657.5250.04735.837490.9990.05199.1
3.65-47.3630.03941.456810.9990.04299
4-4.477.3150.03444.56350.9990.03698.6
4.47-5.167.210.0344.645630.9990.03298.4
5.16-6.337.0160.03739.774880.9990.0497.6
6.33-8.946.8020.02747.6938810.02996
8.94-61.435.770.02749.6123910.0395.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSVERSION March 30, 2013data reduction
XSCALEVERSION July 4, 2012 BUILT=20130706data scaling
AutoSolphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MAD / Resolution: 2→61.43 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.099 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.185
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 830 4.9 %RANDOM
Rwork0.2345 ---
obs0.2366 16280 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.99 Å2 / Biso mean: 40.772 Å2 / Biso min: 20.17 Å2
Baniso -1Baniso -2Baniso -3
1-2.38 Å2-0 Å2-0 Å2
2--2.38 Å2-0 Å2
3----4.76 Å2
Refinement stepCycle: final / Resolution: 2→61.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1585 0 88 39 1712
Biso mean--37.31 39.72 -
Num. residues----196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191728
X-RAY DIFFRACTIONr_bond_other_d0.0060.021687
X-RAY DIFFRACTIONr_angle_refined_deg1.8292.0612332
X-RAY DIFFRACTIONr_angle_other_deg1.09533881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9475201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.58527.592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18515354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.471157
X-RAY DIFFRACTIONr_chiral_restr0.1140.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022004
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02391
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 52 -
Rwork0.337 1131 -
all-1183 -
obs--98.09 %

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