HEADER SIGNALING PROTEIN 03-SEP-15 5DKL TITLE STRUCTURE OF THE LIGHT-STATE DIMER OF THE BLUE LIGHT PHOTORECEPTOR TITLE 2 AUREOCHROME 1A LOV FROM P. TRICORNUTUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOV DOMAIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 234-378; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHAEODACTYLUM TRICORNUTUM; SOURCE 3 ORGANISM_TAXID: 2850; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PETM-11 KEYWDS LIGHT OXYGEN VOLTAGE DNA BINDING PHOTORECEPTOR BLUE LIGHT, SIGNALING KEYWDS 2 PROTEIN, FLAVOPROTEIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR U.HEINTZ,I.SCHLICHTING REVDAT 5 06-NOV-24 5DKL 1 REMARK REVDAT 4 10-JAN-24 5DKL 1 LINK REVDAT 3 27-JUL-16 5DKL 1 JRNL REVDAT 2 20-JAN-16 5DKL 1 JRNL REVDAT 1 13-JAN-16 5DKL 0 JRNL AUTH U.HEINTZ,I.SCHLICHTING JRNL TITL BLUE LIGHT-INDUCED LOV DOMAIN DIMERIZATION ENHANCES THE JRNL TITL 2 AFFINITY OF AUREOCHROME 1A FOR ITS TARGET DNA SEQUENCE. JRNL REF ELIFE V. 5 11860 2016 JRNL REFN ESSN 2050-084X JRNL PMID 26754770 JRNL DOI 10.7554/ELIFE.11860 REMARK 2 REMARK 2 RESOLUTION. 2.70 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 19785 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 990 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 45.7307 - 5.1630 1.00 2828 149 0.1944 0.2308 REMARK 3 2 5.1630 - 4.0989 1.00 2737 145 0.1725 0.1965 REMARK 3 3 4.0989 - 3.5810 0.99 2673 140 0.1948 0.2256 REMARK 3 4 3.5810 - 3.2537 0.99 2672 141 0.2111 0.2466 REMARK 3 5 3.2537 - 3.0205 0.98 2620 138 0.2695 0.3286 REMARK 3 6 3.0205 - 2.8425 0.98 2621 138 0.3046 0.3336 REMARK 3 7 2.8425 - 2.7001 0.98 2644 139 0.3491 0.4318 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) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.160 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 : 0.009 2206 REMARK 3 ANGLE : 1.090 3000 REMARK 3 CHIRALITY : 0.041 326 REMARK 3 PLANARITY : 0.007 394 REMARK 3 DIHEDRAL : 15.145 796 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 5DKL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213317. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19785 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.460 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5DKK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5 M SODIUM FORMATE, 0.1 M HEXAMINE REMARK 280 COBALT (III) CHLORIDE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.77333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.88667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 34.88667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 69.77333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLU A 367 REMARK 465 GLU A 368 REMARK 465 GLU A 369 REMARK 465 GLU A 370 REMARK 465 ALA A 371 REMARK 465 ALA A 372 REMARK 465 ALA A 373 REMARK 465 ASN A 374 REMARK 465 ASP A 375 REMARK 465 ASP A 376 REMARK 465 GLU A 377 REMARK 465 ASP A 378 REMARK 465 ALA B 371 REMARK 465 ALA B 372 REMARK 465 ALA B 373 REMARK 465 ASN B 374 REMARK 465 ASP B 375 REMARK 465 ASP B 376 REMARK 465 GLU B 377 REMARK 465 ASP B 378 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 ASP A 238 57.77 -98.57 REMARK 500 ILE A 282 -70.10 -109.54 REMARK 500 GLU B 366 -58.35 70.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMN A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide FMN B 500 and CYS B REMARK 800 287 DBREF 5DKL A 234 378 PDB 5DKL 5DKL 234 378 DBREF 5DKL B 234 378 PDB 5DKL 5DKL 234 378 SEQRES 1 A 145 GLY ALA MET GLY ASP PHE SER PHE ILE LYS ALA LEU GLN SEQRES 2 A 145 THR ALA GLN GLN ASN PHE VAL VAL THR ASP PRO SER LEU SEQRES 3 A 145 PRO ASP ASN PRO ILE VAL TYR ALA SER GLN GLY PHE LEU SEQRES 4 A 145 ASN LEU THR GLY TYR SER LEU ASP GLN ILE LEU GLY ARG SEQRES 5 A 145 ASN CYS ARG PHE LEU GLN GLY PRO GLU THR ASP PRO LYS SEQRES 6 A 145 ALA VAL GLU ARG ILE ARG LYS ALA ILE GLU GLN GLY ASN SEQRES 7 A 145 ASP MET SER VAL CYS LEU LEU ASN TYR ARG VAL ASP GLY SEQRES 8 A 145 THR THR PHE TRP ASN GLN PHE PHE ILE ALA ALA LEU ARG SEQRES 9 A 145 ASP ALA GLY GLY ASN VAL THR ASN PHE VAL GLY VAL GLN SEQRES 10 A 145 CYS LYS VAL SER ASP GLN TYR ALA ALA THR VAL THR LYS SEQRES 11 A 145 GLN GLN GLU GLU GLU GLU GLU ALA ALA ALA ASN ASP ASP SEQRES 12 A 145 GLU ASP SEQRES 1 B 145 GLY ALA MET GLY ASP PHE SER PHE ILE LYS ALA LEU GLN SEQRES 2 B 145 THR ALA GLN GLN ASN PHE VAL VAL THR ASP PRO SER LEU SEQRES 3 B 145 PRO ASP ASN PRO ILE VAL TYR ALA SER GLN GLY PHE LEU SEQRES 4 B 145 ASN LEU THR GLY TYR SER LEU ASP GLN ILE LEU GLY ARG SEQRES 5 B 145 ASN CYS ARG PHE LEU GLN GLY PRO GLU THR ASP PRO LYS SEQRES 6 B 145 ALA VAL GLU ARG ILE ARG LYS ALA ILE GLU GLN GLY ASN SEQRES 7 B 145 ASP MET SER VAL CYS LEU LEU ASN TYR ARG VAL ASP GLY SEQRES 8 B 145 THR THR PHE TRP ASN GLN PHE PHE ILE ALA ALA LEU ARG SEQRES 9 B 145 ASP ALA GLY GLY ASN VAL THR ASN PHE VAL GLY VAL GLN SEQRES 10 B 145 CYS LYS VAL SER ASP GLN TYR ALA ALA THR VAL THR LYS SEQRES 11 B 145 GLN GLN GLU GLU GLU GLU GLU ALA ALA ALA ASN ASP ASP SEQRES 12 B 145 GLU ASP HET FMN A 500 31 HET FMN B 500 31 HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 3 FMN 2(C17 H21 N4 O9 P) FORMUL 5 HOH *2(H2 O) HELIX 1 AA1 SER A 240 GLN A 249 1 10 HELIX 2 AA2 SER A 268 GLY A 276 1 9 HELIX 3 AA3 SER A 278 ILE A 282 5 5 HELIX 4 AA4 ASN A 286 GLN A 291 5 6 HELIX 5 AA5 ASP A 296 GLN A 309 1 14 HELIX 6 AA6 SER A 354 GLN A 364 1 11 HELIX 7 AA7 ASP B 238 ALA B 248 1 11 HELIX 8 AA8 SER B 268 GLY B 276 1 9 HELIX 9 AA9 ASN B 286 GLN B 291 5 6 HELIX 10 AB1 ASP B 296 GLY B 310 1 15 HELIX 11 AB2 SER B 354 GLU B 368 1 15 SHEET 1 AA1 5 ILE A 264 ALA A 267 0 SHEET 2 AA1 5 PHE A 252 THR A 255 -1 N VAL A 254 O VAL A 265 SHEET 3 AA1 5 VAL A 343 VAL A 353 -1 O PHE A 346 N THR A 255 SHEET 4 AA1 5 THR A 326 ARG A 337 -1 N LEU A 336 O ASN A 345 SHEET 5 AA1 5 SER A 314 TYR A 320 -1 N VAL A 315 O PHE A 331 SHEET 1 AA2 5 ILE B 264 ALA B 267 0 SHEET 2 AA2 5 ASN B 251 THR B 255 -1 N VAL B 254 O VAL B 265 SHEET 3 AA2 5 VAL B 343 VAL B 353 -1 O GLN B 350 N ASN B 251 SHEET 4 AA2 5 THR B 326 ARG B 337 -1 N ALA B 334 O VAL B 347 SHEET 5 AA2 5 MET B 313 TYR B 320 -1 N LEU B 317 O ASN B 329 LINK SG CYS A 287 C4A FMN A 500 1555 1555 2.03 LINK SG CYS B 287 C4A FMN B 500 1555 1555 2.01 SITE 1 AC1 17 ASN A 262 ASN A 286 CYS A 287 ARG A 288 SITE 2 AC1 17 GLN A 291 VAL A 300 ARG A 304 ILE A 307 SITE 3 AC1 17 LEU A 317 ASN A 319 ASN A 329 PHE A 331 SITE 4 AC1 17 ILE A 333 VAL A 347 GLY A 348 GLN A 350 SITE 5 AC1 17 HOH A 601 SITE 1 AC2 23 THR B 255 ASN B 262 ILE B 264 ARG B 285 SITE 2 AC2 23 ASN B 286 ARG B 288 PHE B 289 LEU B 290 SITE 3 AC2 23 GLN B 291 VAL B 300 ILE B 303 ARG B 304 SITE 4 AC2 23 ILE B 307 LEU B 317 ASN B 319 ASN B 329 SITE 5 AC2 23 PHE B 331 ILE B 333 PHE B 346 VAL B 347 SITE 6 AC2 23 GLY B 348 GLN B 350 HOH B 601 CRYST1 108.560 108.560 104.660 90.00 90.00 120.00 P 32 2 1 12 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 0.009211 0.005318 0.000000 0.00000 SCALE2 0.000000 0.010637 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009555 0.00000