HEADER PHOTOSYNTHESIS 13-DEC-23 8XF1 TITLE CRYSTAL STRUCTURE OF THE DISSOCIATED C-PHYCOCYANIN BETA-CHAIN FROM TITLE 2 THERMOLEPTOLYNGBYA SP. O-77 COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-PHYCOCYANIN BETA CHAIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEPTOLYNGBYA SP. O-77; SOURCE 3 ORGANISM_TAXID: 1080068 KEYWDS DISSOCIATED SUBUNIT, C-PHYCOCYANIN, PHOTOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR H.K.NGUYEN,T.TERAMOTO,Y.KAKUTA,K.S.YOON REVDAT 1 22-MAY-24 8XF1 0 JRNL AUTH H.K.NGUYEN,T.MINATO,T.TERAMOTO,S.OGO,Y.KAKUTA,K.S.YOON JRNL TITL DISASSEMBLY AND REASSEMBLY OF THE NON-CONVENTIONAL JRNL TITL 2 THERMOPHILIC C-PHYCOCYANIN. JRNL REF J.BIOSCI.BIOENG. V. 137 179 2024 JRNL REFN ISSN 1389-1723 JRNL PMID 38238241 JRNL DOI 10.1016/J.JBIOSC.2023.12.015 REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 26538 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2672 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 48.8700 - 5.1700 1.00 1274 140 0.1730 0.1789 REMARK 3 2 5.1700 - 4.1000 1.00 1270 136 0.1464 0.1911 REMARK 3 3 4.1000 - 3.5900 1.00 1250 141 0.1505 0.2041 REMARK 3 4 3.5800 - 3.2600 1.00 1251 144 0.1684 0.2216 REMARK 3 5 3.2600 - 3.0200 1.00 1261 139 0.1808 0.2068 REMARK 3 6 3.0200 - 2.8500 1.00 1258 144 0.1941 0.2595 REMARK 3 7 2.8400 - 2.7000 1.00 1247 142 0.1926 0.2563 REMARK 3 8 2.7000 - 2.5900 1.00 1260 137 0.2066 0.2423 REMARK 3 9 2.5900 - 2.4900 1.00 1258 146 0.2160 0.2924 REMARK 3 10 2.4900 - 2.4000 1.00 1257 142 0.2100 0.2484 REMARK 3 11 2.4000 - 2.3300 1.00 1244 143 0.2259 0.2472 REMARK 3 12 2.3300 - 2.2600 1.00 1253 140 0.2228 0.2679 REMARK 3 13 2.2600 - 2.2000 1.00 1277 146 0.2520 0.3040 REMARK 3 14 2.2000 - 2.1500 1.00 1232 135 0.2740 0.2665 REMARK 3 15 2.1500 - 2.1000 1.00 1294 140 0.3008 0.4351 REMARK 3 16 2.1000 - 2.0500 1.00 1235 137 0.3088 0.3647 REMARK 3 17 2.0500 - 2.0100 0.99 1244 143 0.3283 0.3794 REMARK 3 18 2.0100 - 1.9700 1.00 1248 140 0.3499 0.3829 REMARK 3 19 1.9700 - 1.9400 0.98 1253 137 0.3751 0.4607 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.080 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 : 0.008 1383 REMARK 3 ANGLE : 1.547 1885 REMARK 3 CHIRALITY : 0.051 211 REMARK 3 PLANARITY : 0.010 245 REMARK 3 DIHEDRAL : 11.965 223 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 8XF1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1300043318. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL45XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26569 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 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 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG3350, 0.2 M MG(CH3COO)2 REMARK 280 4H2O, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.06450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.06450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 19.24550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 72.52950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 19.24550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 72.52950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.06450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 19.24550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 72.52950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 33.06450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 19.24550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 72.52950 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -87.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 145.05900 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 66.12900 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 75 149.95 75.07 REMARK 500 REMARK 500 REMARK: NULL DBREF 8XF1 A 1 172 PDB 8XF1 8XF1 1 172 SEQRES 1 A 172 MET LEU ASP ALA PHE ALA LYS VAL VAL SER GLN ALA ASP SEQRES 2 A 172 THR LYS GLY GLU PHE LEU SER SER ALA GLN LEU ASP ALA SEQRES 3 A 172 LEU SER ASN VAL VAL LYS ASP GLY SER LYS ARG LEU ASP SEQRES 4 A 172 ALA VAL ASN ARG MET THR SER ASN ALA SER THR ILE VAL SEQRES 5 A 172 ALA ASN ALA ALA ARG SER LEU PHE GLU GLU GLN PRO GLN SEQRES 6 A 172 LEU ILE GLN PRO GLY GLY MEN ALA TYR THR ASN ARG ARG SEQRES 7 A 172 MET ALA ALA CYS LEU ARG ASP MET GLU ILE ILE LEU ARG SEQRES 8 A 172 TYR VAL THR TYR ALA THR LEU ALA GLY ASP SER SER VAL SEQRES 9 A 172 LEU ASP ASP ARG CYS LEU ASN GLY LEU ARG GLU THR TYR SEQRES 10 A 172 GLN ALA LEU GLY VAL PRO GLY GLY SER VAL ALA ALA GLY SEQRES 11 A 172 VAL ALA LYS MET LYS ASP ALA ALA ILE ALA ILE VAL ASN SEQRES 12 A 172 ASP PRO ASN GLY ILE THR LYS GLY ASP CYS SER ALA LEU SEQRES 13 A 172 VAL SER GLU ILE ALA SER TYR PHE ASP ARG ALA ALA ALA SEQRES 14 A 172 ALA VAL ALA HET MEN A 72 15 HET CYC A 201 43 HET CYC A 202 43 HETNAM MEN N-METHYL ASPARAGINE HETNAM CYC PHYCOCYANOBILIN FORMUL 1 MEN C5 H10 N2 O3 FORMUL 2 CYC 2(C33 H40 N4 O6) FORMUL 4 HOH *97(H2 O) HELIX 1 AA1 LEU A 2 GLY A 16 1 15 HELIX 2 AA2 SER A 20 ASN A 47 1 28 HELIX 3 AA3 ASN A 47 GLN A 63 1 17 HELIX 4 AA4 PRO A 64 GLN A 68 5 5 HELIX 5 AA5 THR A 75 GLY A 100 1 26 HELIX 6 AA6 SER A 102 CYS A 109 1 8 HELIX 7 AA7 GLY A 112 GLY A 121 1 10 HELIX 8 AA8 PRO A 123 ASN A 143 1 21 HELIX 9 AA9 CYS A 153 ALA A 172 1 20 LINK C GLY A 71 N MEN A 72 1555 1555 1.33 LINK C MEN A 72 N ALA A 73 1555 1555 1.33 LINK SG CYS A 82 CAC CYC A 201 1555 1555 1.77 LINK SG CYS A 153 CAC CYC A 202 1555 1555 1.77 CRYST1 38.491 145.059 66.129 90.00 90.00 90.00 C 2 2 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.025980 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006894 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015122 0.00000