HEADER SIGNALING PROTEIN 03-SEP-15 5DKK TITLE STRUCTURE OF THE DARK-STATE MONOMER 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 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 LOV DNA BINDING PHOTORECEPTOR, SIGNALING PROTEIN, FLAVOPROTEIN, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR U.HEINTZ,I.SCHLICHTING REVDAT 4 10-JAN-24 5DKK 1 REMARK REVDAT 3 27-JUL-16 5DKK 1 JRNL REVDAT 2 20-JAN-16 5DKK 1 JRNL REVDAT 1 13-JAN-16 5DKK 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. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12016 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.010 REMARK 3 FREE R VALUE TEST SET COUNT : 962 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 48.7444 - 4.7814 1.00 1676 146 0.1936 0.2517 REMARK 3 2 4.7814 - 3.7956 1.00 1595 139 0.1699 0.2385 REMARK 3 3 3.7956 - 3.3159 1.00 1577 137 0.2018 0.2355 REMARK 3 4 3.3159 - 3.0128 1.00 1557 135 0.2133 0.2804 REMARK 3 5 3.0128 - 2.7969 1.00 1551 135 0.2170 0.2812 REMARK 3 6 2.7969 - 2.6320 1.00 1554 136 0.2103 0.2607 REMARK 3 7 2.6320 - 2.5002 1.00 1544 134 0.2025 0.2747 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.260 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 2220 REMARK 3 ANGLE : 1.109 3019 REMARK 3 CHIRALITY : 0.050 330 REMARK 3 PLANARITY : 0.007 399 REMARK 3 DIHEDRAL : 12.595 807 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 5DKK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213316. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9780 REMARK 200 MONOCHROMATOR : SI-111 AND SI-113 REFLECTION REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12016 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.50 REMARK 200 R MERGE FOR SHELL (I) : 0.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.500 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: 3UE6, CHAIN A AND RESIDUES 219-317 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% (V/V) ETHYLENE GLYCOL, 0.1 M REMARK 280 SODIUM ACETATE, PH 4.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 -> 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 32.18500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.30000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.60500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.30000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.18500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.60500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A 234 REMARK 465 ALA A 235 REMARK 465 MET A 236 REMARK 465 GLY A 237 REMARK 465 ASP A 238 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 GLY B 234 REMARK 465 ALA B 235 REMARK 465 MET B 236 REMARK 465 GLY B 237 REMARK 465 ASP B 238 REMARK 465 PHE B 239 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 301 NH1 ARG A 304 2.13 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMN B 500 DBREF 5DKK A 234 378 PDB 5DKK 5DKK 234 378 DBREF 5DKK B 234 378 PDB 5DKK 5DKK 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 401 31 HET ACT A 402 4 HET ACT A 403 4 HET EDO A 404 4 HET FMN B 500 31 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN FMN RIBOFLAVIN MONOPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 FMN 2(C17 H21 N4 O9 P) FORMUL 4 ACT 2(C2 H3 O2 1-) FORMUL 6 EDO C2 H6 O2 FORMUL 8 HOH *55(H2 O) HELIX 1 AA1 PHE A 239 ALA A 248 1 10 HELIX 2 AA2 SER A 268 GLY A 276 1 9 HELIX 3 AA3 SER A 278 LEU A 283 1 6 HELIX 4 AA4 ASN A 286 GLN A 291 5 6 HELIX 5 AA5 ASP A 296 GLY A 310 1 15 HELIX 6 AA6 SER A 354 ALA A 372 1 19 HELIX 7 AA7 PHE B 241 ALA B 248 1 8 HELIX 8 AA8 SER B 268 GLY B 276 1 9 HELIX 9 AA9 SER B 278 LEU B 283 1 6 HELIX 10 AB1 ASN B 286 GLN B 291 5 6 HELIX 11 AB2 ASP B 296 GLY B 310 1 15 HELIX 12 AB3 SER B 354 ASN B 374 1 21 SHEET 1 AA1 5 ILE A 264 ALA A 267 0 SHEET 2 AA1 5 ASN A 251 THR A 255 -1 N VAL A 254 O VAL A 265 SHEET 3 AA1 5 VAL A 343 VAL A 353 -1 O GLN A 350 N ASN A 251 SHEET 4 AA1 5 THR A 326 ARG A 337 -1 N LEU A 336 O ASN A 345 SHEET 5 AA1 5 MET A 313 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 LEU B 336 O ASN B 345 SHEET 5 AA2 5 MET B 313 TYR B 320 -1 N LEU B 317 O ASN B 329 SITE 1 AC1 21 VAL A 253 THR A 255 ASN A 262 ASN A 286 SITE 2 AC1 21 CYS A 287 ARG A 288 LEU A 290 GLN A 291 SITE 3 AC1 21 VAL A 300 ILE A 303 ARG A 304 ILE A 307 SITE 4 AC1 21 LEU A 317 ASN A 319 ASN A 329 PHE A 331 SITE 5 AC1 21 PHE A 346 GLY A 348 GLN A 350 HOH A 504 SITE 6 AC1 21 HOH A 514 SITE 1 AC2 1 GLN A 281 SITE 1 AC3 2 VAL A 353 SER A 354 SITE 1 AC4 7 LEU A 318 THR A 326 PHE A 327 TRP A 328 SITE 2 AC4 7 GLU B 301 ARG B 304 LYS B 305 SITE 1 AC5 23 GLU A 294 VAL B 253 THR B 255 ASN B 262 SITE 2 AC5 23 ASN B 286 CYS B 287 ARG B 288 LEU B 290 SITE 3 AC5 23 GLN B 291 VAL B 300 ILE B 303 ARG B 304 SITE 4 AC5 23 ILE B 307 LEU B 317 ASN B 319 ASN B 329 SITE 5 AC5 23 PHE B 331 ILE B 333 PHE B 346 VAL B 347 SITE 6 AC5 23 GLY B 348 GLN B 350 HOH B 601 CRYST1 64.370 69.210 74.600 90.00 90.00 90.00 P 21 21 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 0.015535 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014449 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013405 0.00000