HEADER PHOTOSYNTHESIS 10-JAN-15 4XK8 TITLE CRYSTAL STRUCTURE OF PLANT PHOTOSYSTEM I-LHCI SUPER-COMPLEX AT 2.8 TITLE 2 ANGSTROM RESOLUTION CAVEAT 4XK8 CLA A 801 HAS WRONG CHIRALITY AT ATOM CBD CLA A 801 HAS CAVEAT 2 4XK8 WRONG CHIRALITY AT ATOM CBD COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1; COMPND 3 CHAIN: A, a; COMPND 4 SYNONYM: PSI-A,PSAA; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2; COMPND 8 CHAIN: B, b; COMPND 9 SYNONYM: PSI-B,PSAB; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: PHOTOSYSTEM I IRON-SULFUR CENTER; COMPND 13 CHAIN: C, c; COMPND 14 FRAGMENT: UNP RESIDUES 2-81; COMPND 15 SYNONYM: 9 KDA POLYPEPTIDE,PSI-C,PHOTOSYSTEM I SUBUNIT VII,PSAC; COMPND 16 EC: 1.97.1.12; COMPND 17 ENGINEERED: YES; COMPND 18 MOL_ID: 4; COMPND 19 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 20 CHAIN: D, d; COMPND 21 FRAGMENT: UNP RESIDUES 63-203; COMPND 22 ENGINEERED: YES; COMPND 23 MOL_ID: 5; COMPND 24 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 25 CHAIN: E, e; COMPND 26 ENGINEERED: YES; COMPND 27 MOL_ID: 6; COMPND 28 MOLECULE: PHOTOSYSTEM I REACTION CENTER SUBUNIT III, CHLOROPLASTIC; COMPND 29 CHAIN: F, f; COMPND 30 SYNONYM: LIGHT-HARVESTING COMPLEX I 17 KDA PROTEIN,PSI-F; COMPND 31 ENGINEERED: YES; COMPND 32 MOL_ID: 7; COMPND 33 MOLECULE: PHOTOSYSTEM I REACTION CENTER SUBUNIT V, CHLOROPLASTIC; COMPND 34 CHAIN: G, g; COMPND 35 SYNONYM: PSI-G,PHOTOSYSTEM I 9 KDA PROTEIN; COMPND 36 ENGINEERED: YES; COMPND 37 MOL_ID: 8; COMPND 38 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 39 CHAIN: H, h; COMPND 40 ENGINEERED: YES; COMPND 41 MOL_ID: 9; COMPND 42 MOLECULE: PHOTOSYSTEM I REACTION CENTER SUBUNIT VIII; COMPND 43 CHAIN: I, i; COMPND 44 FRAGMENT: UNP RESIDUES 2-31; COMPND 45 SYNONYM: PSI-I; COMPND 46 ENGINEERED: YES; COMPND 47 MOL_ID: 10; COMPND 48 MOLECULE: PHOTOSYSTEM I REACTION CENTER SUBUNIT IX; COMPND 49 CHAIN: J, j; COMPND 50 FRAGMENT: UNP RESIDUES 1-39; COMPND 51 SYNONYM: PSI-J; COMPND 52 ENGINEERED: YES; COMPND 53 MOL_ID: 11; COMPND 54 MOLECULE: PHOTOSYSTEM I REACTION CENTER SUBUNIT X PSAK; COMPND 55 CHAIN: K, k; COMPND 56 ENGINEERED: YES; COMPND 57 MOL_ID: 12; COMPND 58 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 59 CHAIN: L, l; COMPND 60 FRAGMENT: UNP RESIDUES 4-156; COMPND 61 ENGINEERED: YES; COMPND 62 MOL_ID: 13; COMPND 63 MOLECULE: CHLOROPHYLL A-B BINDING PROTEIN 6, CHLOROPLASTIC; COMPND 64 CHAIN: 1, 6; COMPND 65 SYNONYM: LHCI-730,LHCII TYPE III CAB-6,LIGHT-HARVESTING COMPLEX COMPND 66 PROTEIN LHCA1; COMPND 67 ENGINEERED: YES; COMPND 68 MOL_ID: 14; COMPND 69 MOLECULE: TYPE II CHLOROPHYLL A/B BINDING PROTEIN FROM PHOTOSYSTEM I; COMPND 70 CHAIN: 2, 7; COMPND 71 FRAGMENT: UNP RESIDUES 62-267; COMPND 72 ENGINEERED: YES; COMPND 73 MOL_ID: 15; COMPND 74 MOLECULE: CHLOROPHYLL A-B BINDING PROTEIN 3, CHLOROPLASTIC; COMPND 75 CHAIN: 3, 8; COMPND 76 FRAGMENT: UNP RESIDUES 55-272; COMPND 77 SYNONYM: LHCII TYPE III CAB-3; COMPND 78 ENGINEERED: YES; COMPND 79 MOL_ID: 16; COMPND 80 MOLECULE: CHLOROPHYLL A-B BINDING PROTEIN P4, CHLOROPLASTIC; COMPND 81 CHAIN: 4, 9; COMPND 82 SYNONYM: LHCI TYPE III CAB-P4; COMPND 83 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 4 ORGANISM_COMMON: GARDEN PEA; SOURCE 5 ORGANISM_TAXID: 3888; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 9 ORGANISM_COMMON: GARDEN PEA; SOURCE 10 ORGANISM_TAXID: 3888; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 14 ORGANISM_COMMON: GARDEN PEA; SOURCE 15 ORGANISM_TAXID: 3888; SOURCE 16 MOL_ID: 4; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 19 ORGANISM_COMMON: GARDEN PEA; SOURCE 20 ORGANISM_TAXID: 3888; SOURCE 21 MOL_ID: 5; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 24 ORGANISM_COMMON: GARDEN PEA; SOURCE 25 ORGANISM_TAXID: 3888; SOURCE 26 MOL_ID: 6; SOURCE 27 SYNTHETIC: YES; SOURCE 28 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 29 ORGANISM_COMMON: GARDEN PEA; SOURCE 30 ORGANISM_TAXID: 3888; SOURCE 31 MOL_ID: 7; SOURCE 32 SYNTHETIC: YES; SOURCE 33 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 34 ORGANISM_COMMON: GARDEN PEA; SOURCE 35 ORGANISM_TAXID: 3888; SOURCE 36 MOL_ID: 8; SOURCE 37 SYNTHETIC: YES; SOURCE 38 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 39 ORGANISM_COMMON: GARDEN PEA; SOURCE 40 ORGANISM_TAXID: 3888; SOURCE 41 MOL_ID: 9; SOURCE 42 SYNTHETIC: YES; SOURCE 43 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 44 ORGANISM_COMMON: GARDEN PEA; SOURCE 45 ORGANISM_TAXID: 3888; SOURCE 46 MOL_ID: 10; SOURCE 47 SYNTHETIC: YES; SOURCE 48 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 49 ORGANISM_COMMON: GARDEN PEA; SOURCE 50 ORGANISM_TAXID: 3888; SOURCE 51 MOL_ID: 11; SOURCE 52 SYNTHETIC: YES; SOURCE 53 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 54 ORGANISM_COMMON: GARDEN PEA; SOURCE 55 ORGANISM_TAXID: 3888; SOURCE 56 MOL_ID: 12; SOURCE 57 SYNTHETIC: YES; SOURCE 58 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 59 ORGANISM_COMMON: GARDEN PEA; SOURCE 60 ORGANISM_TAXID: 3888; SOURCE 61 MOL_ID: 13; SOURCE 62 SYNTHETIC: YES; SOURCE 63 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 64 ORGANISM_COMMON: GARDEN PEA; SOURCE 65 ORGANISM_TAXID: 3888; SOURCE 66 MOL_ID: 14; SOURCE 67 SYNTHETIC: YES; SOURCE 68 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 69 ORGANISM_COMMON: GARDEN PEA; SOURCE 70 ORGANISM_TAXID: 3888; SOURCE 71 MOL_ID: 15; SOURCE 72 SYNTHETIC: YES; SOURCE 73 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 74 ORGANISM_COMMON: GARDEN PEA; SOURCE 75 ORGANISM_TAXID: 3888; SOURCE 76 MOL_ID: 16; SOURCE 77 SYNTHETIC: YES; SOURCE 78 ORGANISM_SCIENTIFIC: PISUM SATIVUM; SOURCE 79 ORGANISM_COMMON: GARDEN PEA; SOURCE 80 ORGANISM_TAXID: 3888 KEYWDS PHOTOSYNTHESIS, PHOTOSYSTEM I, PLANT LHCI-PSI SUPERCOMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.SUGA,X.QIN,T.KUANG,J.R.SHEN REVDAT 6 20-NOV-24 4XK8 1 HETSYN FORMUL REVDAT 5 29-JUL-20 4XK8 1 COMPND REMARK HETNAM HETSYN REVDAT 5 2 1 LINK SITE REVDAT 4 04-MAR-20 4XK8 1 COMPND SOURCE REVDAT 3 01-MAY-19 4XK8 1 CAVEAT SOURCE REMARK REVDAT 2 08-JUL-15 4XK8 1 LINK REVDAT 1 10-JUN-15 4XK8 0 JRNL AUTH X.QIN,M.SUGA,T.KUANG,J.R.SHEN JRNL TITL STRUCTURAL BASIS FOR ENERGY TRANSFER PATHWAYS IN THE PLANT JRNL TITL 2 PSI-LHCI SUPERCOMPLEX JRNL REF SCIENCE V. 348 989 2015 JRNL REFN ESSN 1095-9203 JRNL PMID 26023133 JRNL DOI 10.1126/SCIENCE.AAB0214 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 268230 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 13498 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 49.1548 - 8.6848 0.99 8636 452 0.2140 0.2307 REMARK 3 2 8.6848 - 6.8995 1.00 8588 461 0.1526 0.1790 REMARK 3 3 6.8995 - 6.0291 1.00 8556 447 0.1800 0.2250 REMARK 3 4 6.0291 - 5.4787 1.00 8560 437 0.1858 0.2118 REMARK 3 5 5.4787 - 5.0864 1.00 8504 456 0.1830 0.2198 REMARK 3 6 5.0864 - 4.7868 1.00 8530 452 0.1806 0.2246 REMARK 3 7 4.7868 - 4.5472 1.00 8557 437 0.1761 0.2117 REMARK 3 8 4.5472 - 4.3494 1.00 8469 445 0.1845 0.2425 REMARK 3 9 4.3494 - 4.1821 1.00 8498 463 0.1876 0.2490 REMARK 3 10 4.1821 - 4.0378 1.00 8537 442 0.1999 0.2457 REMARK 3 11 4.0378 - 3.9116 1.00 8461 455 0.2007 0.2413 REMARK 3 12 3.9116 - 3.7999 1.00 8516 427 0.2066 0.2322 REMARK 3 13 3.7999 - 3.6999 1.00 8504 441 0.2131 0.2672 REMARK 3 14 3.6999 - 3.6096 1.00 8448 451 0.2234 0.2644 REMARK 3 15 3.6096 - 3.5276 1.00 8475 481 0.2207 0.2571 REMARK 3 16 3.5276 - 3.4525 1.00 8509 430 0.2298 0.2597 REMARK 3 17 3.4525 - 3.3835 1.00 8455 473 0.2421 0.2901 REMARK 3 18 3.3835 - 3.3197 1.00 8473 475 0.2514 0.2863 REMARK 3 19 3.3197 - 3.2604 1.00 8461 469 0.2661 0.3066 REMARK 3 20 3.2604 - 3.2051 1.00 8490 417 0.2737 0.3075 REMARK 3 21 3.2051 - 3.1534 1.00 8526 436 0.2761 0.3140 REMARK 3 22 3.1534 - 3.1049 1.00 8462 466 0.2805 0.3153 REMARK 3 23 3.1049 - 3.0593 1.00 8425 473 0.2836 0.3284 REMARK 3 24 3.0593 - 3.0162 1.00 8437 460 0.2906 0.3181 REMARK 3 25 3.0162 - 2.9754 1.00 8527 459 0.3029 0.3476 REMARK 3 26 2.9754 - 2.9368 1.00 8487 440 0.3097 0.3386 REMARK 3 27 2.9368 - 2.9001 1.00 8423 439 0.2983 0.3091 REMARK 3 28 2.9001 - 2.8651 1.00 8515 428 0.3039 0.3270 REMARK 3 29 2.8651 - 2.8318 1.00 8467 451 0.3147 0.3509 REMARK 3 30 2.8318 - 2.8000 0.97 8236 435 0.3514 0.3701 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.530 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 : 0.006 75437 REMARK 3 ANGLE : 1.401 106936 REMARK 3 CHIRALITY : 0.065 8954 REMARK 3 PLANARITY : 0.004 12277 REMARK 3 DIHEDRAL : 21.454 28690 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): -28.0049 -0.0250 145.8210 REMARK 3 T TENSOR REMARK 3 T11: 0.5165 T22: 0.4121 REMARK 3 T33: 0.4781 T12: 0.0309 REMARK 3 T13: 0.1384 T23: 0.0842 REMARK 3 L TENSOR REMARK 3 L11: 0.2538 L22: 0.0518 REMARK 3 L33: 0.2740 L12: 0.0102 REMARK 3 L13: 0.2525 L23: 0.0154 REMARK 3 S TENSOR REMARK 3 S11: -0.0025 S12: -0.0349 S13: -0.0518 REMARK 3 S21: 0.0291 S22: 0.0217 S23: 0.0063 REMARK 3 S31: -0.0381 S32: 0.0350 S33: -0.0157 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 4XK8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000205823. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 268282 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG, VAPOR DIFFUSION, TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM ->