HEADER PHOTOSYNTHESIS 06-MAR-19 6JLK TITLE XFEL STRUCTURE OF CYANOBACTERIAL PHOTOSYSTEM II (1F STATE, DATASET1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOTOSYSTEM II PROTEIN D1; COMPND 3 CHAIN: A, a; COMPND 4 SYNONYM: PSII D1 PROTEIN,PHOTOSYSTEM II Q(B) PROTEIN; COMPND 5 EC: 1.10.3.9; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PHOTOSYSTEM II CP47 REACTION CENTER PROTEIN; COMPND 8 CHAIN: B, b; COMPND 9 SYNONYM: PSII 47 KDA PROTEIN,PROTEIN CP-47; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: PHOTOSYSTEM II CP43 REACTION CENTER PROTEIN; COMPND 12 CHAIN: C, c; COMPND 13 SYNONYM: PSII 43 KDA PROTEIN,PROTEIN CP-43; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: PHOTOSYSTEM II D2 PROTEIN; COMPND 16 CHAIN: D, d; COMPND 17 SYNONYM: PSII D2 PROTEIN,PHOTOSYSTEM Q(A) PROTEIN; COMPND 18 EC: 1.10.3.9; COMPND 19 MOL_ID: 5; COMPND 20 MOLECULE: CYTOCHROME B559 SUBUNIT ALPHA; COMPND 21 CHAIN: E, e; COMPND 22 SYNONYM: PSII REACTION CENTER SUBUNIT V; COMPND 23 MOL_ID: 6; COMPND 24 MOLECULE: CYTOCHROME B559 SUBUNIT BETA; COMPND 25 CHAIN: F, f; COMPND 26 SYNONYM: PSII REACTION CENTER SUBUNIT VI; COMPND 27 MOL_ID: 7; COMPND 28 MOLECULE: PHOTOSYSTEM II REACTION CENTER PROTEIN H; COMPND 29 CHAIN: H, h; COMPND 30 SYNONYM: PSII-H; COMPND 31 MOL_ID: 8; COMPND 32 MOLECULE: PHOTOSYSTEM II REACTION CENTER PROTEIN I; COMPND 33 CHAIN: I, i; COMPND 34 SYNONYM: PSII-I,PSII 4.4 KDA PROTEIN; COMPND 35 MOL_ID: 9; COMPND 36 MOLECULE: PHOTOSYSTEM II REACTION CENTER PROTEIN J; COMPND 37 CHAIN: J, j; COMPND 38 SYNONYM: PSII-J; COMPND 39 MOL_ID: 10; COMPND 40 MOLECULE: PHOTOSYSTEM II REACTION CENTER PROTEIN K; COMPND 41 CHAIN: K, k; COMPND 42 SYNONYM: PSII-K; COMPND 43 MOL_ID: 11; COMPND 44 MOLECULE: PHOTOSYSTEM II REACTION CENTER PROTEIN L; COMPND 45 CHAIN: L, l; COMPND 46 SYNONYM: PSII-L; COMPND 47 MOL_ID: 12; COMPND 48 MOLECULE: PHOTOSYSTEM II REACTION CENTER PROTEIN M; COMPND 49 CHAIN: M, m; COMPND 50 SYNONYM: PSII-M; COMPND 51 MOL_ID: 13; COMPND 52 MOLECULE: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE; COMPND 53 CHAIN: O, o; COMPND 54 SYNONYM: MSP; COMPND 55 MOL_ID: 14; COMPND 56 MOLECULE: PHOTOSYSTEM II REACTION CENTER PROTEIN T; COMPND 57 CHAIN: T, t; COMPND 58 SYNONYM: PSII-TC; COMPND 59 MOL_ID: 15; COMPND 60 MOLECULE: PHOTOSYSTEM II 12 KDA EXTRINSIC PROTEIN; COMPND 61 CHAIN: U, u; COMPND 62 SYNONYM: PS II COMPLEX 12 KDA EXTRINSIC PROTEIN,PSII-U; COMPND 63 MOL_ID: 16; COMPND 64 MOLECULE: CYTOCHROME C-550; COMPND 65 CHAIN: V, v; COMPND 66 SYNONYM: CYTOCHROME C550,LOW-POTENTIAL CYTOCHROME C; COMPND 67 MOL_ID: 17; COMPND 68 MOLECULE: PHOTOSYSTEM II REACTION CENTER PROTEIN YCF12; COMPND 69 CHAIN: Y, y; COMPND 70 MOL_ID: 18; COMPND 71 MOLECULE: PHOTOSYSTEM II REACTION CENTER PROTEIN X; COMPND 72 CHAIN: X, x; COMPND 73 MOL_ID: 19; COMPND 74 MOLECULE: PHOTOSYSTEM II REACTION CENTER PROTEIN Z; COMPND 75 CHAIN: Z, z; COMPND 76 SYNONYM: PSII-Z; COMPND 77 MOL_ID: 20; COMPND 78 MOLECULE: PHOTOSYSTEM II PROTEIN Y; COMPND 79 CHAIN: R SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 3 ORGANISM_TAXID: 32053; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 6 ORGANISM_TAXID: 32053; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 9 ORGANISM_TAXID: 32053; SOURCE 10 MOL_ID: 4; SOURCE 11 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 12 ORGANISM_TAXID: 32053; SOURCE 13 MOL_ID: 5; SOURCE 14 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 15 ORGANISM_TAXID: 32053; SOURCE 16 MOL_ID: 6; SOURCE 17 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 18 ORGANISM_COMMON: SYNECHOCOCCUS VULCANUS; SOURCE 19 ORGANISM_TAXID: 32053; SOURCE 20 MOL_ID: 7; SOURCE 21 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 22 ORGANISM_TAXID: 32053; SOURCE 23 MOL_ID: 8; SOURCE 24 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 25 ORGANISM_COMMON: SYNECHOCOCCUS VULCANUS; SOURCE 26 ORGANISM_TAXID: 32053; SOURCE 27 MOL_ID: 9; SOURCE 28 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 29 ORGANISM_COMMON: SYNECHOCOCCUS VULCANUS; SOURCE 30 ORGANISM_TAXID: 32053; SOURCE 31 MOL_ID: 10; SOURCE 32 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 33 ORGANISM_TAXID: 32053; SOURCE 34 MOL_ID: 11; SOURCE 35 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 36 ORGANISM_TAXID: 32053; SOURCE 37 MOL_ID: 12; SOURCE 38 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 39 ORGANISM_COMMON: SYNECHOCOCCUS VULCANUS; SOURCE 40 ORGANISM_TAXID: 32053; SOURCE 41 MOL_ID: 13; SOURCE 42 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 43 ORGANISM_TAXID: 32053; SOURCE 44 MOL_ID: 14; SOURCE 45 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 46 ORGANISM_COMMON: SYNECHOCOCCUS VULCANUS; SOURCE 47 ORGANISM_TAXID: 32053; SOURCE 48 MOL_ID: 15; SOURCE 49 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 50 ORGANISM_TAXID: 32053; SOURCE 51 MOL_ID: 16; SOURCE 52 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 53 ORGANISM_TAXID: 32053; SOURCE 54 MOL_ID: 17; SOURCE 55 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 56 ORGANISM_TAXID: 32053; SOURCE 57 MOL_ID: 18; SOURCE 58 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 59 ORGANISM_TAXID: 32053; SOURCE 60 MOL_ID: 19; SOURCE 61 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 62 ORGANISM_TAXID: 32053; SOURCE 63 MOL_ID: 20; SOURCE 64 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 65 ORGANISM_TAXID: 32053 KEYWDS PHOTOSYSTEM II, PHOTOSYNTHESIS, PSII, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.SUGA,J.R.SHEN REVDAT 5 20-NOV-24 6JLK 1 REMARK REVDAT 4 22-NOV-23 6JLK 1 REMARK HETSYN FORMUL REVDAT 3 29-JUL-20 6JLK 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 30-OCT-19 6JLK 1 JRNL REVDAT 1 16-OCT-19 6JLK 0 JRNL AUTH M.SUGA,F.AKITA,K.YAMASHITA,Y.NAKAJIMA,G.UENO,H.LI,T.YAMANE, JRNL AUTH 2 K.HIRATA,Y.UMENA,S.YONEKURA,L.J.YU,H.MURAKAMI,T.NOMURA, JRNL AUTH 3 T.KIMURA,M.KUBO,S.BABA,T.KUMASAKA,K.TONO,M.YABASHI,H.ISOBE, JRNL AUTH 4 K.YAMAGUCHI,M.YAMAMOTO,H.AGO,J.R.SHEN JRNL TITL AN OXYL/OXO MECHANISM FOR OXYGEN-OXYGEN COUPLING IN PSII JRNL TITL 2 REVEALED BY AN X-RAY FREE-ELECTRON LASER. JRNL REF SCIENCE V. 366 334 2019 JRNL REFN ESSN 1095-9203 JRNL PMID 31624207 JRNL DOI 10.1126/SCIENCE.AAX6998 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 407701 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 21624 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.9854 - 6.6020 1.00 14300 773 0.1523 0.1715 REMARK 3 2 6.6020 - 5.2719 1.00 13920 755 0.1387 0.1854 REMARK 3 3 5.2719 - 4.6149 1.00 13895 711 0.1182 0.1527 REMARK 3 4 4.6149 - 4.1972 1.00 13729 760 0.1156 0.1503 REMARK 3 5 4.1972 - 3.8987 1.00 13766 710 0.1227 0.1628 REMARK 3 6 3.8987 - 3.6704 1.00 13727 741 0.1213 0.1665 REMARK 3 7 3.6704 - 3.4876 1.00 13732 690 0.1252 0.1653 REMARK 3 8 3.4876 - 3.3365 1.00 13723 724 0.1253 0.1716 REMARK 3 9 3.3365 - 3.2086 1.00 13629 773 0.1255 0.1810 REMARK 3 10 3.2086 - 3.0983 1.00 13682 731 0.1334 0.1879 REMARK 3 11 3.0983 - 3.0017 1.00 13678 705 0.1293 0.1825 REMARK 3 12 3.0017 - 2.9162 1.00 13634 705 0.1335 0.1935 REMARK 3 13 2.9162 - 2.8396 1.00 13613 738 0.1339 0.1864 REMARK 3 14 2.8396 - 2.7705 1.00 13676 702 0.1411 0.2155 REMARK 3 15 2.7705 - 2.7077 1.00 13625 710 0.1428 0.2022 REMARK 3 16 2.7077 - 2.6502 1.00 13603 743 0.1510 0.2147 REMARK 3 17 2.6502 - 2.5973 1.00 13581 717 0.1629 0.2178 REMARK 3 18 2.5973 - 2.5484 1.00 13666 735 0.1726 0.2253 REMARK 3 19 2.5484 - 2.5030 1.00 13626 729 0.1854 0.2406 REMARK 3 20 2.5030 - 2.4606 1.00 13536 723 0.1953 0.2419 REMARK 3 21 2.4606 - 2.4210 1.00 13642 703 0.2088 0.2744 REMARK 3 22 2.4210 - 2.3838 1.00 13594 691 0.2181 0.2691 REMARK 3 23 2.3838 - 2.3488 1.00 13623 693 0.2216 0.2727 REMARK 3 24 2.3488 - 2.3158 1.00 13532 770 0.2310 0.2775 REMARK 3 25 2.3158 - 2.2845 1.00 13661 678 0.2496 0.2914 REMARK 3 26 2.2845 - 2.2549 1.00 13504 732 0.2581 0.3080 REMARK 3 27 2.2549 - 2.2267 1.00 13648 674 0.2643 0.3043 REMARK 3 28 2.2267 - 2.2000 1.00 13618 702 0.2705 0.3104 REMARK 3 29 2.2000 - 2.1744 1.00 13570 705 0.2816 0.3244 REMARK 3 30 2.1744 - 2.1500 1.00 13568 701 0.2873 0.3304 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 55090 REMARK 3 ANGLE : 1.372 75315 REMARK 3 CHIRALITY : 0.051 7557 REMARK 3 PLANARITY : 0.006 8883 REMARK 3 DIHEDRAL : 23.013 21656 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 13.0781 -13.7806 -25.4096 REMARK 3 T TENSOR REMARK 3 T11: 0.2969 T22: 0.2469 REMARK 3 T33: 0.2407 T12: -0.0535 REMARK 3 T13: -0.0363 T23: 0.0488 REMARK 3 L TENSOR REMARK 3 L11: 0.1936 L22: 0.3997 REMARK 3 L33: 0.4537 L12: -0.0705 REMARK 3 L13: -0.0216 L23: 0.1257 REMARK 3 S TENSOR REMARK 3 S11: -0.0055 S12: -0.0225 S13: -0.0303 REMARK 3 S21: 0.0499 S22: 0.0358 S23: -0.0066 REMARK 3 S31: -0.0108 S32: 0.0058 S33: -0.0305 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6JLK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1300011282. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : BL3 REMARK 200 X-RAY GENERATOR MODEL : SACLA BEAMLINE BL3 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2398 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 407701 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 1269. REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6JLJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, MAGNESIUM SULFATE, BATCH MODE, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM ->