8C3F | pdb_00008c3f

Double mutant I(L177)H/F(M197)H structure of Photosynthetic Reaction Center From Cereibacter sphaeroides strain RV

PDB DOI: https://doi.org/10.2210/pdb8C3F/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Cereibacter sphaeroides 2.4.1
Expression System: Cereibacter sphaeroides 2.4.1
Mutation(s): Yes
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2022-12-23 Released: 2023-03-08
Deposition Author(s): Gabdulkhakov, A.G., Selikhanov, G.K., Fufina, T.Y., Vasilieva, L.G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.220 (Depositor), 0.194 (DCC)
R-Value Work:
0.194 (Depositor)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Properties and Crystal Structure of the Cereibacter sphaeroides Photosynthetic Reaction Center with Double Amino Acid Substitution I(L177)H + F(M197)H.

Fufina, T.Y., Selikhanov, G.K., Gabdulkhakov, A.G., Vasilieva, L.G.

(2023) Membranes (Basel) 13

PubMed: 36837660 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/membranes13020157
Primary Citation Related Structures:
8C3F

PubMed Abstract:
The photosynthetic reaction center of the purple bacterium Cereibacter sphaeroides with two site-directed mutations Ile-L177-His and M197 Phe-His is of double interest. The substitution I(L177)H results in strong binding of a bacteriochlorophyll molecule with L-subunit. The second mutation F(M197)H introduces a new H-bond between the C2-acetyl carbonyl group of the bacteriochlorophyll P _B and His-M197, which is known to enhance the stability of the complex. Due to this H-bond, π -electron system of P finds itself connected to an extensive H-bonding network on the periplasmic surface of the complex. The crystal structure of the double mutant reaction center obtained with 2.6 Å resolution allows clarifying consequences of the Ile L177 - His substitution. The value of the P/P ⁺ midpoint potential in the double mutant RC was found to be ~20 mV less than the sum of potentials measured in the two RCs with single mutations I(L177)H and F(M197)H. The protein environment of the BChls P _A and B _B were found to be similar to that in the RC with single substitution I(L177)H, whereas an altered pattern of the H-bonding networks was found in the vicinity of bacteriochlorophyll P _B. The data obtained are consistent with our previous assumption on a correlation between the bulk of the H-bonding network connected with the π-electron system of the primary electron donor P and the value of its oxidation potential.

Organizational Affiliation

Federal Research Center Pushchino Scientific Center for Biological Research PSCBR, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya Street 2, 142290 Pushchino, Russia.

Macromolecule Content

Total Structure Weight: 104.12 kDa
Atom Count: 7,413
Modeled Residue Count: 822
Deposited Residue Count: 825
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	A [auth L]	281	Cereibacter sphaeroides 2.4.1	Mutation(s): 2 Gene Names: pufL Membrane Entity: Yes
UniProt
Find proteins for Q3J1A5 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3J1A5 Go to UniProtKB: Q3J1A5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3J1A5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	B [auth M]	303	Cereibacter sphaeroides 2.4.1	Mutation(s): 2 Gene Names: pufM Membrane Entity: Yes
UniProt
Find proteins for Q3J1A6 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3J1A6 Go to UniProtKB: Q3J1A6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3J1A6
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein H chain	C [auth H]	241	Cereibacter sphaeroides 2.4.1	Mutation(s): 0 Gene Names: puhA Membrane Entity: Yes
UniProt
Find proteins for Q3J170 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3J170 Go to UniProtKB: Q3J170
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3J170
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 15 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL (Subject of Investigation/LOI) Query on CDL Download:Ideal Coordinates CCD File SDF format, chain DA [auth M] MOL2 format, chain DA [auth M] mmCIF format, chain DA [auth M]	DA [auth M]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain DA [auth M] Interactions & Density Focus chain DA [auth M]
BCL (Subject of Investigation/LOI) Query on BCL Download:Ideal Coordinates CCD File SDF format, chain H [auth L] SDF format, chain P [auth L] SDF format, chain S [auth M] SDF format, chain V [auth M] MOL2 format, chain H [auth L] MOL2 format, chain P [auth L] MOL2 format, chain S [auth M] MOL2 format, chain V [auth M] mmCIF format, chain H [auth L] mmCIF format, chain P [auth L] mmCIF format, chain S [auth M] mmCIF format, chain V [auth M]	H [auth L], P [auth L], S [auth M], V [auth M]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain H [auth L] Focus chain P [auth L] Focus chain S [auth M] Focus chain V [auth M] Interactions & Density Focus chain H [auth L] Focus chain P [auth L] Focus chain S [auth M] Focus chain V [auth M]
BPB (Subject of Investigation/LOI) Query on BPB Download:Ideal Coordinates CCD File SDF format, chain I [auth L] SDF format, chain W [auth M] MOL2 format, chain I [auth L] MOL2 format, chain W [auth M] mmCIF format, chain I [auth L] mmCIF format, chain W [auth M]	I [auth L], W [auth M]	BACTERIOPHEOPHYTIN B C₅₅ H₇₄ N₄ O₆ SFKCKJXMIAKQMY-GTTFDWDMSA-N		Interactions Focus chain I [auth L] Focus chain W [auth M] Interactions & Density Focus chain I [auth L] Focus chain W [auth M]
U10 (Subject of Investigation/LOI) Query on U10 Download:Ideal Coordinates CCD File SDF format, chain J [auth L] SDF format, chain Y [auth M] MOL2 format, chain J [auth L] MOL2 format, chain Y [auth M] mmCIF format, chain J [auth L] mmCIF format, chain Y [auth M]	J [auth L], Y [auth M]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain J [auth L] Focus chain Y [auth M] Interactions & Density Focus chain J [auth L] Focus chain Y [auth M]
SPN (Subject of Investigation/LOI) Query on SPN Download:Ideal Coordinates CCD File SDF format, chain Z [auth M] MOL2 format, chain Z [auth M] mmCIF format, chain Z [auth M]	Z [auth M]	SPEROIDENONE C₄₁ H₇₀ O₂ GWQAMGYOEYXWJF-YCDPMLDASA-N		Interactions Focus chain Z [auth M] Interactions & Density Focus chain Z [auth M]
LDA Query on LDA Download:Ideal Coordinates CCD File SDF format, chain EA [auth M] SDF format, chain FA [auth M] SDF format, chain GA [auth M] SDF format, chain HA [auth M] SDF format, chain MA [auth H] SDF format, chain N [auth L] SDF format, chain O [auth L] SDF format, chain T [auth M] MOL2 format, chain EA [auth M] MOL2 format, chain FA [auth M] MOL2 format, chain GA [auth M] MOL2 format, chain HA [auth M] MOL2 format, chain MA [auth H] MOL2 format, chain N [auth L] MOL2 format, chain O [auth L] MOL2 format, chain T [auth M] mmCIF format, chain EA [auth M] mmCIF format, chain FA [auth M] mmCIF format, chain GA [auth M] mmCIF format, chain HA [auth M] mmCIF format, chain MA [auth H] mmCIF format, chain N [auth L] mmCIF format, chain O [auth L] mmCIF format, chain T [auth M]	EA [auth M] FA [auth M] GA [auth M] HA [auth M] MA [auth H] EA [auth M], FA [auth M], GA [auth M], HA [auth M], MA [auth H], N [auth L], O [auth L], T [auth M]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain EA [auth M] Focus chain FA [auth M] Focus chain GA [auth M] Focus chain HA [auth M] Focus chain MA [auth H] Focus chain N [auth L] Focus chain O [auth L] Focus chain T [auth M] Interactions & Density Focus chain EA [auth M] Focus chain FA [auth M] Focus chain GA [auth M] Focus chain HA [auth M] Focus chain MA [auth H] Focus chain N [auth L] Focus chain O [auth L] Focus chain T [auth M]
HTO Query on HTO Download:Ideal Coordinates CCD File SDF format, chain G [auth L] SDF format, chain R [auth M] MOL2 format, chain G [auth L] MOL2 format, chain R [auth M] mmCIF format, chain G [auth L] mmCIF format, chain R [auth M]	G [auth L], R [auth M]	HEPTANE-1,2,3-TRIOL C₇ H₁₆ O₃ HXYCHJFUBNTKQR-RNFRBKRXSA-N		Interactions Focus chain G [auth L] Focus chain R [auth M] Interactions & Density Focus chain G [auth L] Focus chain R [auth M]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain LA [auth H] MOL2 format, chain LA [auth H] mmCIF format, chain LA [auth H]	LA [auth H]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain LA [auth H] Interactions & Density Focus chain LA [auth H]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain CA [auth M] SDF format, chain K [auth L] SDF format, chain L MOL2 format, chain CA [auth M] MOL2 format, chain K [auth L] MOL2 format, chain L mmCIF format, chain CA [auth M] mmCIF format, chain K [auth L] mmCIF format, chain L	CA [auth M], K [auth L], L	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth M] Focus chain K [auth L] Focus chain L Interactions & Density Focus chain CA [auth M] Focus chain K [auth L] Focus chain L
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth L] MOL2 format, chain M [auth L] mmCIF format, chain M [auth L]	M [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth L] Interactions & Density Focus chain M [auth L]
DIO Query on DIO Download:Ideal Coordinates CCD File SDF format, chain F [auth L] MOL2 format, chain F [auth L] mmCIF format, chain F [auth L]	F [auth L]	1,4-DIETHYLENE DIOXIDE C₄ H₈ O₂ RYHBNJHYFVUHQT-UHFFFAOYSA-N		Interactions Focus chain F [auth L] Interactions & Density Focus chain F [auth L]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth L] SDF format, chain E [auth L] SDF format, chain IA [auth M] SDF format, chain JA [auth H] SDF format, chain KA [auth H] SDF format, chain Q [auth M] SDF format, chain U [auth M] MOL2 format, chain D [auth L] MOL2 format, chain E [auth L] MOL2 format, chain IA [auth M] MOL2 format, chain JA [auth H] MOL2 format, chain KA [auth H] MOL2 format, chain Q [auth M] MOL2 format, chain U [auth M] mmCIF format, chain D [auth L] mmCIF format, chain E [auth L] mmCIF format, chain IA [auth M] mmCIF format, chain JA [auth H] mmCIF format, chain KA [auth H] mmCIF format, chain Q [auth M] mmCIF format, chain U [auth M]	D [auth L] E [auth L] IA [auth M] JA [auth H] KA [auth H] D [auth L], E [auth L], IA [auth M], JA [auth H], KA [auth H], Q [auth M], U [auth M]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth L] Focus chain E [auth L] Focus chain IA [auth M] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain Q [auth M] Focus chain U [auth M] Interactions & Density Focus chain D [auth L] Focus chain E [auth L] Focus chain IA [auth M] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain Q [auth M] Focus chain U [auth M]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain X [auth M] MOL2 format, chain X [auth M] mmCIF format, chain X [auth M]	X [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain X [auth M] Interactions & Density Focus chain X [auth M]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain AA [auth M] SDF format, chain NA [auth H] MOL2 format, chain AA [auth M] MOL2 format, chain NA [auth H] mmCIF format, chain AA [auth M] mmCIF format, chain NA [auth H]	AA [auth M], NA [auth H]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth M] Focus chain NA [auth H] Interactions & Density Focus chain AA [auth M] Focus chain NA [auth H]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain BA [auth M] MOL2 format, chain BA [auth M] mmCIF format, chain BA [auth M]	BA [auth M]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth M] Interactions & Density Focus chain BA [auth M]