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- PDB-4tqq: Photosynthetic Reaction Center from R. sphaeroides Analyzed at Ro... -

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Basic information

Entry
Database: PDB / ID: 4tqq
TitlePhotosynthetic Reaction Center from R. sphaeroides Analyzed at Room Temperature on an X-ray Transparent Microfluidic Chip
Components(Reaction center protein ...) x 3
KeywordsPHOTOSYNTHESIS / photosynthetic / membrane protein
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / metal ion binding
Similarity search - Function
Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal ...Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / UBIQUINONE-10 / UBIQUINONE-1 / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.499 Å
AuthorsSchieferstein, J.M. / Khvostichenko, D.S. / Pawate, A.S. / Kenis, P.J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM086727 United States
CitationJournal: Cryst.Growth Des. / Year: 2014
Title: X-ray Transparent Microfluidic Chip for Mesophase-Based Crystallization of Membrane Proteins and On-Chip Structure Determination.
Authors: Khvostichenko, D.S. / Schieferstein, J.M. / Pawate, A.S. / Laible, P.D. / Kenis, P.J.
History
DepositionJun 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_nat / pdbx_audit_support ...entity_src_nat / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Reaction center protein H chain
L: Reaction center protein L chain
M: Reaction center protein M chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,83512
Polymers91,2413
Non-polymers6,5949
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30760 Å2
ΔGint-228 kcal/mol
Surface area30310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.484, 102.484, 239.939
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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Reaction center protein ... , 3 types, 3 molecules HLM

#1: Protein Reaction center protein H chain / Photosynthetic reaction center H subunit


Mass: 26022.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: P0C0Y7
#2: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 31346.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: P0C0Y8
#3: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 33871.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: P0C0Y9

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Non-polymers , 6 types, 195 molecules

#4: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#5: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#6: Chemical ChemComp-UQ1 / UBIQUINONE-1


Mass: 250.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18O4
#7: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#8: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 293 K / Method: microfluidic
Details: Protein incorporated into LCP by diffusion, incubated for hours, crystallization induced by addition of Jeffamine M-600 and ammonium sulfate

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Data collection

DiffractionMean temperature: 298 K / Ambient temp details: No cryocooling
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.499→42.814 Å / Num. obs: 45251 / % possible obs: 95.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.165 / Rsym value: 0.165 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 3 / Rsym value: 0.628 / % possible all: 90

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIXrefinement
Cootmodel building
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UWW

2uww


Resolution: 2.499→42.814 Å / FOM work R set: 0.8641 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2134 1915 4.43 %
Rwork0.1622 41332 -
obs0.1645 43247 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.81 Å2 / Biso mean: 35.62 Å2 / Biso min: 13.58 Å2
Refinement stepCycle: final / Resolution: 2.499→42.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6468 0 459 186 7113
Biso mean--31.81 36.76 -
Num. residues----823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017198
X-RAY DIFFRACTIONf_angle_d1.3889889
X-RAY DIFFRACTIONf_chiral_restr0.0541009
X-RAY DIFFRACTIONf_plane_restr0.0081232
X-RAY DIFFRACTIONf_dihedral_angle_d12.9062447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4994-2.56190.25141270.20842688281590
2.5619-2.63120.25021230.19712787291092
2.6312-2.70860.29871290.18542786291593
2.7086-2.7960.24061330.18272843297694
2.796-2.89590.22891300.17482887301795
2.8959-3.01180.23521360.16832915305196
3.0118-3.14880.22451370.16912928306596
3.1488-3.31480.18331350.15712967310297
3.3148-3.52240.19451410.14183015315698
3.5224-3.79420.19441410.14623023316498
3.7942-4.17570.17561420.14313035317799
4.1757-4.77930.18841440.1533076322098
4.7793-6.01870.22361460.16923137328398
6.0187-42.82050.23191510.16243245339697

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