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- PDB-2jiy: PHOTOSYNTHETIC REACTION CENTER MUTANT WITH ALA M149 REPLACED WITH... -

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Basic information

Entry
Database: PDB / ID: 2jiy
TitlePHOTOSYNTHETIC REACTION CENTER MUTANT WITH ALA M149 REPLACED WITH TRP (CHAIN M, AM149W)
Components(REACTION CENTER PROTEIN ...) x 3
KeywordsPHOTOSYNTHESIS / MEMBRANE PROTEIN / ELECTRON TRANSPORT / BACTERIOCHLOROPHYLL / CHLOROPHYLL / METAL-BINDING / TRANSPORT / CHROMOPHORE
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 / CARDIOLIPIN / DODECANE / : / PHOSPHATE ION / SPEROIDENONE / 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 / Resolution: 2.2 Å
AuthorsFyfe, P.K. / Potter, J.A. / Cheng, J. / Williams, C.M. / Watson, A.J. / Jones, M.R.
Citation
Journal: Biochemistry / Year: 2007
Title: Structural Responses to Cavity-Creating Mutations in an Integral Membrane Protein.
Authors: Fyfe, P.K. / Potter, J.A. / Cheng, J. / Williams, C.M. / Watson, A.J. / Jones, M.R.
#1: Journal: Photosyn. Res. / Year: 2005
Title: On the Role of Basic Residues in Adapting the Purple Bacterial Reaction Centre-Lh1 Photosystem for Growth at Elevated Temperature
Authors: Watson, A.J. / Hughes, A.V. / Fyfe, P.K. / Wakeham, M.C. / Holden-Dye, K. / Heathcote, P. / Jones, M.R.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structural Details of an Interaction between Cardiolipin and an Integral Membrane Protein.
Authors: Mcauley, K.E. / Fyfe, P.K. / Ridge, J.P. / Isaacs, N.W. / Cogdell, R.J. / Jones, M.R.
History
DepositionJul 3, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_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.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)103,19418
Polymers94,0583
Non-polymers9,13615
Water6,900383
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34710 Å2
ΔGint-242.8 kcal/mol
Surface area28980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.785, 139.785, 185.454
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: 28066.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Strain: NCIB 8253 / Plasmid: PRKEH10D / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): AM149W / 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 genetically manipulated source
Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Strain: NCIB 8253 / Plasmid: PRKEH10D / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): AM149W / References: UniProt: P0C0Y8
#3: Protein REACTION CENTER PROTEIN M CHAIN / PHOTOSYNTHETIC REACTION CENTER M SUBUNIT


Mass: 34644.867 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Strain: NCIB 8253 / Plasmid: PRKEH10D / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): AM149W / References: UniProt: P0C0Y9

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Non-polymers , 11 types, 398 molecules

#4: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#6: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H76N4O6
#7: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#8: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#9: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#10: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#11: Chemical ChemComp-SPN / SPEROIDENONE


Mass: 594.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H70O2
#12: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#13: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN M, ALA 149 TO TRP

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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: 5.5 Å3/Da / Density % sol: 76 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 0.977
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.2→15.9 Å / Num. obs: 106556 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.6
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.7 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD-TYPE RHODOBACTER SPHAEROIDES COORDINATES UNPUBLISHED DATA

Resolution: 2.2→15.97 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.663 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 5200 5 %RANDOM
Rwork0.181 ---
obs0.183 99574 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20.62 Å20 Å2
2--1.24 Å20 Å2
3----1.86 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6473 0 571 383 7427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227497
X-RAY DIFFRACTIONr_bond_other_d0.0010.025011
X-RAY DIFFRACTIONr_angle_refined_deg1.362.03710292
X-RAY DIFFRACTIONr_angle_other_deg0.932312148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9935845
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44722.578287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37115998
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2741534
X-RAY DIFFRACTIONr_chiral_restr0.1390.21035
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021601
X-RAY DIFFRACTIONr_nbd_refined0.2070.21562
X-RAY DIFFRACTIONr_nbd_other0.1880.25082
X-RAY DIFFRACTIONr_nbtor_refined0.1860.23636
X-RAY DIFFRACTIONr_nbtor_other0.0840.23277
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2385
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0310.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2960.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5691.54436
X-RAY DIFFRACTIONr_mcbond_other0.1121.51707
X-RAY DIFFRACTIONr_mcangle_it0.85526635
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.23333997
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8164.53643
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 347 -
Rwork0.221 7217 -
obs--98.34 %
Refinement TLS params.Method: refined / Origin x: -58.785 Å / Origin y: -18.667 Å / Origin z: 34.691 Å
111213212223313233
T-0.0384 Å20.028 Å20.0301 Å2--0.2267 Å2-0.0261 Å2---0.0953 Å2
L1.3492 °2-0.3575 °2-0.4669 °2-0.6154 °20.2185 °2--0.8125 °2
S0.0058 Å °0.0949 Å °-0.0384 Å °-0.0394 Å °0.0138 Å °-0.0539 Å °-0.0312 Å °0.0193 Å °-0.0196 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1M2 - 302
2X-RAY DIFFRACTION1H11 - 250
3X-RAY DIFFRACTION1L1282 - 1284
4X-RAY DIFFRACTION1M - L1303
5X-RAY DIFFRACTION1L1285
6X-RAY DIFFRACTION1M1306
7X-RAY DIFFRACTION1L1 - 281
8X-RAY DIFFRACTION1M1309
9X-RAY DIFFRACTION1M1304
10X-RAY DIFFRACTION1H1251
11X-RAY DIFFRACTION1M1307
12X-RAY DIFFRACTION1M1314
13X-RAY DIFFRACTION1M1310
14X-RAY DIFFRACTION1L1286
15X-RAY DIFFRACTION1M1305
16X-RAY DIFFRACTION1M1311

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