HEADER ELECTRON TRANSPORT, PHOTOSYNTHESIS 03-MAR-17 5V2C TITLE RE-REFINEMENT OF CRYSTAL STRUCTURE OF PHOTOSYSTEM II COMPLEX 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 FRAGMENT: RESIDUES 27-163; COMPND 67 SYNONYM: CYTOCHROME C550,LOW-POTENTIAL CYTOCHROME C; COMPND 68 MOL_ID: 17; COMPND 69 MOLECULE: PHOTOSYSTEM II REACTION CENTER PROTEIN YCF12; COMPND 70 CHAIN: Y, y; COMPND 71 MOL_ID: 18; COMPND 72 MOLECULE: PHOTOSYSTEM II REACTION CENTER PROTEIN X; COMPND 73 CHAIN: X, x; COMPND 74 MOL_ID: 19; COMPND 75 MOLECULE: PHOTOSYSTEM II REACTION CENTER PROTEIN Z; COMPND 76 CHAIN: Z, z; COMPND 77 SYNONYM: PSII-Z 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_TAXID: 32053; SOURCE 19 MOL_ID: 7; SOURCE 20 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 21 ORGANISM_TAXID: 32053; SOURCE 22 MOL_ID: 8; SOURCE 23 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 24 ORGANISM_TAXID: 32053; SOURCE 25 MOL_ID: 9; SOURCE 26 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 27 ORGANISM_TAXID: 32053; SOURCE 28 MOL_ID: 10; SOURCE 29 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 30 ORGANISM_TAXID: 32053; SOURCE 31 MOL_ID: 11; SOURCE 32 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 33 ORGANISM_TAXID: 32053; SOURCE 34 MOL_ID: 12; SOURCE 35 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 36 ORGANISM_TAXID: 32053; SOURCE 37 MOL_ID: 13; SOURCE 38 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 39 ORGANISM_TAXID: 32053; SOURCE 40 MOL_ID: 14; SOURCE 41 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 42 ORGANISM_TAXID: 32053; SOURCE 43 MOL_ID: 15; SOURCE 44 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 45 ORGANISM_TAXID: 32053; SOURCE 46 MOL_ID: 16; SOURCE 47 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 48 ORGANISM_TAXID: 32053; SOURCE 49 MOL_ID: 17; SOURCE 50 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 51 ORGANISM_TAXID: 32053; SOURCE 52 MOL_ID: 18; SOURCE 53 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 54 ORGANISM_TAXID: 32053; SOURCE 55 MOL_ID: 19; SOURCE 56 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS VULCANUS; SOURCE 57 ORGANISM_TAXID: 32053 KEYWDS ELECTRON TRANSPORT, PHOTOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR J.WANG,J.M.WIWCZAR,G.W.BRUDVIG REVDAT 5 04-OCT-23 5V2C 1 FORMUL REVDAT 4 10-MAR-21 5V2C 1 COMPND REMARK HET HETNAM REVDAT 4 2 1 HETSYN FORMUL LINK ATOM REVDAT 3 29-JUL-20 5V2C 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 25-OCT-17 5V2C 1 JRNL REVDAT 1 30-AUG-17 5V2C 0 JRNL AUTH J.M.WIWCZAR,A.M.LAFOUNTAIN,J.WANG,H.A.FRANK,G.W.BRUDVIG JRNL TITL CHLOROPHYLL A WITH A FARNESYL TAIL IN THERMOPHILIC JRNL TITL 2 CYANOBACTERIA. JRNL REF PHOTOSYN. RES. V. 134 175 2017 JRNL REFN ISSN 1573-5079 JRNL PMID 28741056 JRNL DOI 10.1007/S11120-017-0425-4 REMARK 0 REMARK 0 THIS ENTRY 5V2C REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL REMARK 0 STRUCTURAL DATA R3ARCSF DETERMINED BY AUTHORS OF THE PDB ENTRY REMARK 0 3ARC: AUTHORS Y. UMENA, K. KAWAKAMI, J.-R. SHEN, N. KAMIYA. THIS REMARK 0 ENTRY 5V2C USES EXPERIMENTAL AMPLITUDES RETRIEVED FROM THE PDB REMARK 0 REPORTED FOR 3ARC AND FOLLOWED BY ANISOTROPY CORRECTION REMARK 0 REFINEMENT. REMARK 0 ORIGINAL DATA REFERENCE 1 REMARK 0 PDB ID: 3ARC REMARK 0 AUTH Y.UMENA,K.KAWAKAMI,J.-R.SHEN,N.KAMIYA REMARK 0 TITL CRYSTAL STRUCTURE OF OXYGEN-EVOLVING PHOTOSYSTEM II AT A REMARK 0 TITL 2 RESOLUTION OF 1.9 A REMARK 0 REF NATURE V. 473 55 2011 REMARK 0 REFN ISSN 0028-0836 REMARK 0 PMID 21499260 REMARK 0 DOI 10.1038/NATURE09913 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 178.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 591655 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.095 REMARK 3 R VALUE (WORKING SET) : 0.092 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 31202 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 43491 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 2261 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 41395 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11954 REMARK 3 SOLVENT ATOMS : 3787 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.50000 REMARK 3 B22 (A**2) : 0.55000 REMARK 3 B33 (A**2) : -1.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.157 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.098 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.077 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.320 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.988 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 55634 ; 0.021 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 55331 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 75230 ; 3.270 ; 2.214 REMARK 3 BOND ANGLES OTHERS (DEGREES):127478 ; 1.138 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 5403 ; 5.840 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 1881 ;33.496 ;23.195 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 6602 ;13.188 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 235 ;16.663 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 7635 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 56209 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 12395 ; 0.013 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 21272 ; 5.070 ; 3.240 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 21271 ; 5.060 ; 3.239 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 26544 ; 6.000 ; 4.854 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 26545 ; 6.000 ; 4.855 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 34362 ; 8.265 ; 4.130 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 34362 ; 8.265 ; 4.130 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 48578 ; 9.515 ; 5.874 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 65934 ; 8.902 ;29.799 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 65935 ; 8.902 ;29.800 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2):110930 ; 3.683 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 852 ;63.088 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2):112031 ;26.094 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5V2C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1000226746. REMARK 200 REMARK 200 AUTHOR USED THE SF DATA FROM ENTRY 3ARC REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% PEG1450, 20MM NACL, 10MM CACL2, REMARK 280 40MM MGSO4, 20MM MES BUFFER, PH 6.1, MICRO-BATCH METHOD UNDER REMARK 280 OIL, TEMPERATURE 285K, EVAPORATION, RECRYSTALLIZATION 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 ->