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- PDB-5v33: R. sphaeroides photosythetic reaction center mutant - Residue L22... -

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Basic information

Entry
Database: PDB / ID: 5v33
TitleR. sphaeroides photosythetic reaction center mutant - Residue L223, Ser to Trp - Room Temperature Structure Solved on X-ray Transparent Microfluidic Chip
Components(Reaction center protein ...) x 3
KeywordsPHOTOSYNTHESIS / reaction center mutant
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / : / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / metal ion binding
Similarity search - Function
Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, H subunit, N-terminal / PRC-barrel domain ...Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / Photosynthetic reaction centre, M subunit / 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 / 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 / molecular replacement / Resolution: 3.487 Å
AuthorsSchieferstein, J.M. / Pawate, A.S. / Sun, C. / Wan, F. / Broecker, J. / Ernst, O.P. / Gennis, R.B. / 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: Biomicrofluidics / Year: 2017
Title: X-ray transparent microfluidic chips for high-throughput screening and optimization of in meso membrane protein crystallization.
Authors: Schieferstein, J.M. / Pawate, A.S. / Sun, C. / Wan, F. / Sheraden, P.N. / Broecker, J. / Ernst, O.P. / Gennis, R.B. / Kenis, P.J.A.
History
DepositionMar 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references / Refinement description
Category: citation / pdbx_audit_support / software
Item: _citation.country / _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)97,68411
Polymers91,3403
Non-polymers6,3448
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30110 Å2
ΔGint-230 kcal/mol
Surface area30790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.332, 102.332, 240.333
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 / Fragment: UNP residues 11-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: puhA / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P0C0Y7
#2: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 31445.521 Da / Num. of mol.: 1 / Mutation: S223W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufL / Production host: 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 genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufM / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: P0C0Y9

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Non-polymers , 4 types, 8 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-FE / FE (III) ION


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


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4

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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: 3.44 Å3/Da / Density % sol: 64.29 %
Crystal growTemperature: 293 K / Method: microfluidic / pH: 7.8
Details: Crystals were grown in microfluidic wells. LCPs were formulated by overlaying ~40 nl of protein solution over ~10 nl of solid monoolein. LCPs formed by diffusion during a 4 hour incubation. ...Details: Crystals were grown in microfluidic wells. LCPs were formulated by overlaying ~40 nl of protein solution over ~10 nl of solid monoolein. LCPs formed by diffusion during a 4 hour incubation. Precipitants were then introduced to the crystallization well, and crystals were observed after 3 days. Crystals were grown at 15-20 mg/mL protein concentration (in 10 mM Tris pH 7.8, 280 mM NaCl, 0.05% LDAO) with a precipitant of 1 M HEPES pH 7.5, 1.15 M (NH4)2(SO4) and 14-15 %w/v Jeffamine M-600.

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Data collection

DiffractionMean temperature: 298 K / Ambient temp details: Room temperature
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 15671 / % possible obs: 92 % / Redundancy: 5.4 % / Biso Wilson estimate: 54.65 Å2 / Rmerge(I) obs: 0.29 / Rpim(I) all: 0.132 / Rrim(I) all: 0.322 / Χ2: 0.926 / Net I/σ(I): 2.9 / Num. measured all: 84779
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.5-3.565.40.727840.6180.3170.7930.82194.6
3.56-3.635.60.6727770.6180.2960.7410.95194.6
3.63-3.695.40.6467930.7530.2840.7120.88894.6
3.69-3.775.40.5957770.7340.2610.6550.90794.6
3.77-3.855.40.5257760.7030.2350.580.9393.5
3.85-3.945.50.4717790.7880.2080.5190.92693.6
3.94-4.045.40.4287700.8550.1910.4730.94993.2
4.04-4.155.40.3897660.8410.1740.4290.9491
4.15-4.275.30.3577800.8560.1660.3970.99591.1
4.27-4.415.60.3257350.8690.1460.360.8990.1
4.41-4.575.30.37630.8840.1380.3340.90390.9
4.57-4.755.70.2967680.9040.1310.3260.92391.2
4.75-4.975.50.2827930.9020.1260.3110.95793
4.97-5.235.60.3097840.8870.1390.3420.9192.6
5.23-5.555.50.3387840.8530.1530.3750.93991.9
5.55-5.985.40.3077840.8910.1410.3410.84991.2
5.98-6.585.30.2777900.9010.1260.3070.87290.5
6.58-7.535.30.1987870.9280.0890.220.85989.9
7.53-9.485.50.1448090.980.060.1570.989.8
9.48-504.80.1488720.960.0810.1721.20788.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000v704xdata collection
HKL-2000v704xdata scaling
PDB_EXTRACT3.22data extraction
HKL-2000v704xdata reduction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TQQ

4tqq


Resolution: 3.487→47.076 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2616 1435 10.06 %Random selection
Rwork0.2205 12825 --
obs0.2246 14260 83.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.41 Å2 / Biso mean: 45.5477 Å2 / Biso min: 24.07 Å2
Refinement stepCycle: final / Resolution: 3.487→47.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6476 0 443 0 6919
Biso mean--42.39 --
Num. residues----823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037190
X-RAY DIFFRACTIONf_angle_d0.7029879
X-RAY DIFFRACTIONf_chiral_restr0.0251009
X-RAY DIFFRACTIONf_plane_restr0.0031232
X-RAY DIFFRACTIONf_dihedral_angle_d13.0532439
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4874-3.6120.28921150.2481034114969
3.612-3.75650.24361370.241188132579
3.7565-3.92740.26191390.23141255139484
3.9274-4.13440.23371420.22311282142485
4.1344-4.39320.2461430.21481293143686
4.3932-4.73210.27341460.20841311145787
4.7321-5.20780.26651520.21831333148587
5.2078-5.96010.31541450.24381331147686
5.9601-7.50420.2641520.22331340149286
7.5042-47.08050.24041640.19331458162287
Refinement TLS params.Method: refined / Origin x: 12.1594 Å / Origin y: -28.4138 Å / Origin z: -33.9378 Å
111213212223313233
T0.2653 Å2-0.0311 Å20.0005 Å2-0.2083 Å20.0012 Å2--0.4608 Å2
L1.1815 °20.3122 °2-0.0791 °2-0.8061 °20.0051 °2--1.4754 °2
S0.0714 Å °0.0021 Å °0.122 Å °0.1151 Å °-0.0523 Å °0.0427 Å °-0.0947 Å °-0.0178 Å °-0.0123 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH11 - 250
2X-RAY DIFFRACTION1allH251
3X-RAY DIFFRACTION1allL1 - 281
4X-RAY DIFFRACTION1allL301 - 303
5X-RAY DIFFRACTION1allM1 - 302
6X-RAY DIFFRACTION1allM402 - 404
7X-RAY DIFFRACTION1allA1

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