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- PDB-5vju: De Novo Photosynthetic Reaction Center Protein Variant Equipped w... -

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Basic information

Entry
Database: PDB / ID: 5vju
TitleDe Novo Photosynthetic Reaction Center Protein Variant Equipped with His-Tyr H-bond, Heme B, and Cd(II) ions
ComponentsReaction Center Maquette Leu71His variant
KeywordsDE NOVO PROTEIN / maquette / protein design / charge separation / artificial photosynthesis
Function / homology: / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / MAD / Resolution: 2.08 Å
AuthorsEnnist, N.M. / Stayrook, S.E. / Dutton, P.L. / 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 1.1Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Mar 16, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / 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_audit_support.funding_organization / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_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.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
Revision 1.3Aug 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 1.4May 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 Leu71His variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9599
Polymers22,5551
Non-polymers1,4038
Water1,58588
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)44.485, 25.876, 73.708
Angle α, β, γ (deg.)90.000, 103.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Reaction Center Maquette Leu71His variant


Mass: 22555.418 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)
#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-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1.83 Å3/Da / Density % sol: 32.7 % / Description: parallelepiped
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 24% w/v PEG 1500, 70 mM CdCl2, 100 mM Na acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 7, 2015 / Details: Osmic VariMax mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.02→71.63 Å / Num. obs: 10744 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 6.705 % / Biso Wilson estimate: 25.547 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.055 / Χ2: 0.995 / Net I/σ(I): 25.98
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.02-2.073.3470.1019.465620.9830.1271
2.07-2.135.7380.09314.457480.9930.10292.5
2.13-2.196.7570.08418.467560.9950.091100
2.19-2.267.1110.08219.557270.9960.08899.5
2.26-2.337.170.0820.157350.9960.086100
2.33-2.427.1450.07322.076820.9970.079100
2.42-2.517.1910.064256710.9970.06999.6
2.51-2.617.0680.06524.786730.9970.07100
2.61-2.737.0230.06625.66130.9970.07199.7
2.73-2.867.1040.06127.036030.9970.06699.7
2.86-3.017.0450.05629.415540.9980.06100
3.01-3.26.9960.05330.825560.9980.05899.8
3.2-3.427.0260.04932.614990.9980.053100
3.42-3.697.060.04137.074870.9990.04499.8
3.69-4.046.8830.04238.344290.9990.04599.8
4.04-4.526.8960.04138.864030.9990.044100
4.52-5.226.7030.04138.143600.9990.04599.7
5.22-6.396.5890.04736.973090.9980.051100
6.39-9.046.4790.03938.792360.9990.04299.6
9.04-71.635.830.03938.111410.9990.04296.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XSCALEVERSION Oct 15, 2015 BUILT=20151015data scaling
MOLREP11.4.03phasing
PDB_EXTRACT3.22data extraction
XDSVERSION Oct 15, 2015data reduction
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→71.63 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.898 / SU B: 5.176 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.312 / ESU R Free: 0.219
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 527 5.2 %RANDOM
Rwork0.1834 ---
obs0.1869 9587 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 73.21 Å2 / Biso mean: 31.833 Å2 / Biso min: 4.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å2-0.27 Å2
2--0.94 Å2-0 Å2
3----1.2 Å2
Refinement stepCycle: final / Resolution: 2.08→71.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1587 0 49 88 1724
Biso mean--27.87 33.16 -
Num. residues----197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191651
X-RAY DIFFRACTIONr_bond_other_d0.0030.021643
X-RAY DIFFRACTIONr_angle_refined_deg1.7822.0222221
X-RAY DIFFRACTIONr_angle_other_deg1.02733782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3225195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.43227.36391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3915347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.954157
X-RAY DIFFRACTIONr_chiral_restr0.1040.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021926
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02373
LS refinement shellResolution: 2.076→2.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 25 -
Rwork0.17 643 -
all-668 -
obs--86.75 %

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