HEADER PHOTOSYNTHESIS 12-JUN-16 5B82 TITLE CRYSTAL STRUCTURE OF THE CYANOBACTERIAL HEME-PROTEIN TLL0287 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TLL0287 PROTEIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOSYNECHOCOCCUS ELONGATUS (STRAIN BP-1); SOURCE 3 ORGANISM_TAXID: 197221; SOURCE 4 STRAIN: BP-1 KEYWDS PAS DOMAIN, HEMEC, PHOTOSYSTEM II, PHOTOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR M.SUGA,T.MOTOMURA,J.R.SHEN REVDAT 3 23-OCT-24 5B82 1 REMARK REVDAT 2 21-JUN-17 5B82 1 JRNL REVDAT 1 03-MAY-17 5B82 0 JRNL AUTH T.MOTOMURA,M.SUGA,R.HIENERWADEL,A.NAKAGAWA,T.L.LAI, JRNL AUTH 2 W.NITSCHKE,T.KUMA,M.SUGIURA,A.BOUSSAC,J.R.SHEN JRNL TITL CRYSTAL STRUCTURE AND REDOX PROPERTIES OF A NOVEL JRNL TITL 2 CYANOBACTERIAL HEME PROTEIN WITH A HIS/CYS HEME AXIAL JRNL TITL 3 LIGATION AND A PER-ARNT-SIM (PAS)-LIKE DOMAIN JRNL REF J. BIOL. CHEM. V. 292 9599 2017 JRNL REFN ESSN 1083-351X JRNL PMID 28428249 JRNL DOI 10.1074/JBC.M116.746263 REMARK 2 REMARK 2 RESOLUTION. 2.00 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 12138 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 612 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 50.6392 - 3.1746 1.00 3047 145 0.1615 0.2228 REMARK 3 2 3.1746 - 2.5198 1.00 2856 160 0.1991 0.2356 REMARK 3 3 2.5198 - 2.2013 1.00 2814 150 0.1865 0.2468 REMARK 3 4 2.2013 - 2.0000 0.99 2809 157 0.2010 0.2653 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.850 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 : 0.007 1381 REMARK 3 ANGLE : 1.030 1888 REMARK 3 CHIRALITY : 0.077 192 REMARK 3 PLANARITY : 0.005 249 REMARK 3 DIHEDRAL : 16.820 504 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): -26.0975 -3.7698 -14.8001 REMARK 3 T TENSOR REMARK 3 T11: 0.2160 T22: 0.1816 REMARK 3 T33: 0.1497 T12: 0.0345 REMARK 3 T13: 0.0415 T23: 0.0204 REMARK 3 L TENSOR REMARK 3 L11: 2.6004 L22: 2.8034 REMARK 3 L33: 2.2765 L12: -1.1626 REMARK 3 L13: -0.8823 L23: 0.7939 REMARK 3 S TENSOR REMARK 3 S11: 0.0828 S12: -0.0336 S13: 0.1593 REMARK 3 S21: -0.0323 S22: 0.0648 S23: 0.2438 REMARK 3 S31: -0.3074 S32: -0.1507 S33: -0.0602 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 5B82 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1300000698. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-14 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 : 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12169 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.623 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.1000 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: SAD REMARK 200 SOFTWARE USED: AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA2HPO4, K2HPO4, (NH4)2HPO4, TRIS, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.62300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.62300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.53800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.62300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.62300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 16.53800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.62300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.62300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 16.53800 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.62300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.62300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 16.53800 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 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 465 VAL A 2 REMARK 465 ARG A 3 REMARK 465 ILE A 4 REMARK 465 PHE A 5 REMARK 465 LEU A 6 REMARK 465 MET A 7 REMARK 465 ALA A 8 REMARK 465 LEU A 9 REMARK 465 LEU A 10 REMARK 465 MET A 11 REMARK 465 ALA A 12 REMARK 465 SER A 13 REMARK 465 LEU A 14 REMARK 465 TRP A 15 REMARK 465 ILE A 16 REMARK 465 GLN A 17 REMARK 465 GLY A 18 REMARK 465 SER A 19 REMARK 465 PRO A 20 REMARK 465 ALA A 21 REMARK 465 PRO A 22 REMARK 465 LEU A 23 REMARK 465 ALA A 24 REMARK 465 SER A 25 REMARK 465 LEU A 187 REMARK 465 GLN A 188 REMARK 465 THR A 189 REMARK 465 SER A 190 REMARK 465 PRO A 191 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 VAL A 67 -57.89 -123.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 68 SG REMARK 620 2 HEC A 501 NA 91.1 REMARK 620 3 HEC A 501 NB 88.6 86.8 REMARK 620 4 HEC A 501 NC 93.5 175.0 91.6 REMARK 620 5 HEC A 501 ND 95.9 91.5 175.3 89.7 REMARK 620 6 HIS A 145 NE2 176.6 90.6 88.7 84.6 86.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEC A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 502 DBREF 5B82 A 1 191 UNP Q8DM36 Q8DM36_THEEB 1 191 SEQRES 1 A 191 MET VAL ARG ILE PHE LEU MET ALA LEU LEU MET ALA SER SEQRES 2 A 191 LEU TRP ILE GLN GLY SER PRO ALA PRO LEU ALA SER ALA SEQRES 3 A 191 ASN PRO GLU GLU LEU GLY LYS VAL VAL THR ALA ILE GLU SEQRES 4 A 191 GLN LEU ASP GLN MET ARG ILE GLY LEU ALA SER THR LEU SEQRES 5 A 191 GLU GLY GLY THR SER GLU PRO THR LEU ASP THR PHE LYS SEQRES 6 A 191 ALA VAL CYS ALA PRO VAL GLY LYS GLN ALA LYS GLU ILE SEQRES 7 A 191 ALA ALA ALA ASN GLY TRP GLN VAL ARG GLN VAL ALA LEU SEQRES 8 A 191 LYS TYR ARG ASN PRO ASN HIS ALA PRO ARG THR ALA LEU SEQRES 9 A 191 ASP VAL GLN ALA LEU ASN GLN PHE ASP ASN ASN HIS HIS SEQRES 10 A 191 LEU GLN ALA PHE TRP GLN THR ASP LYS GLU GLY VAL HIS SEQRES 11 A 191 TYR PHE ARG ARG ILE ASP VAL GLN ALA SER CYS LEU ALA SEQRES 12 A 191 CYS HIS GLY ALA LYS ASN ARG ARG PRO ALA PHE ILE GLN SEQRES 13 A 191 GLU LYS TYR PRO SER ASP ARG ALA TYR GLY PHE ARG VAL SEQRES 14 A 191 GLY ASP LEU ARG GLY MET TYR ALA VAL THR ILE PRO GLN SEQRES 15 A 191 ILE GLN GLN ALA LEU GLN THR SER PRO HET HEC A 501 43 HET CL A 502 1 HETNAM HEC HEME C HETNAM CL CHLORIDE ION FORMUL 2 HEC C34 H34 FE N4 O4 FORMUL 3 CL CL 1- FORMUL 4 HOH *82(H2 O) HELIX 1 AA1 ASN A 27 SER A 50 1 24 HELIX 2 AA2 THR A 60 LYS A 65 5 6 HELIX 3 AA3 CYS A 68 GLY A 83 1 16 HELIX 4 AA4 ASN A 95 ALA A 99 5 5 HELIX 5 AA5 THR A 102 ASN A 115 1 14 HELIX 6 AA6 CYS A 141 GLY A 146 1 6 HELIX 7 AA7 ALA A 147 ARG A 151 5 5 HELIX 8 AA8 PRO A 152 TYR A 159 1 8 SHEET 1 AA1 4 GLN A 85 VAL A 89 0 SHEET 2 AA1 4 LEU A 172 PRO A 181 -1 O MET A 175 N VAL A 89 SHEET 3 AA1 4 GLY A 128 ASP A 136 -1 N VAL A 129 O ILE A 180 SHEET 4 AA1 4 ALA A 120 ASP A 125 -1 N GLN A 123 O HIS A 130 LINK SG CYS A 141 CAB HEC A 501 1555 1555 1.66 LINK SG CYS A 144 CAC HEC A 501 1555 1555 1.83 LINK SG CYS A 68 FE HEC A 501 1555 1555 2.12 LINK NE2 HIS A 145 FE HEC A 501 1555 1555 2.10 SITE 1 AC1 22 ARG A 45 LEU A 52 THR A 63 LYS A 65 SITE 2 AC1 22 VAL A 67 CYS A 68 GLN A 88 TYR A 93 SITE 3 AC1 22 ARG A 94 ASN A 95 HIS A 98 ILE A 135 SITE 4 AC1 22 ASP A 136 GLN A 138 CYS A 141 CYS A 144 SITE 5 AC1 22 HIS A 145 ILE A 155 TYR A 159 ARG A 173 SITE 6 AC1 22 CL A 502 HOH A 613 SITE 1 AC2 4 VAL A 67 CYS A 68 ALA A 69 HEC A 501 CRYST1 101.246 101.246 33.076 90.00 90.00 90.00 P 42 21 2 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 0.009877 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009877 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030233 0.00000