HEADER PLANT PROTEIN 26-JUN-19 6S45 TITLE ROOM TEMPERATURE STRUCTURE OF THE DARK STATE OF THE LOV2 DOMAIN OF TITLE 2 PHOTOTROPIN-2 FROM ARABIDOPSIS THALIANA DETERMINED WITH A SERIAL TITLE 3 CRYSTALLOGRAPHY APPROACH COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOTOTROPIN-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEFECTIVE IN CHLOROPLAST AVOIDANCE PROTEIN 1,NON-PHOTOTROPIC COMPND 5 HYPOCOTYL 1-LIKE PROTEIN 1,NPH1-LIKE PROTEIN 1; COMPND 6 EC: 2.7.11.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: THALE CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: PHOT2, CAV1, KIN7, NPL1, AT5G58140, K21L19.6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS LOV DOMAIN, PHOTOACTIVE PROTEIN, FLAVOPROTEIN, TIME-RESOLVED KEYWDS 2 CRYSTALLOGRAPHY, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.AUMONIER,G.SANTONI,G.GOTTHARD,D.VON STETTEN,G.LEONARD,A.ROYANT REVDAT 3 24-JAN-24 6S45 1 REMARK REVDAT 2 05-AUG-20 6S45 1 JRNL REVDAT 1 08-JUL-20 6S45 0 JRNL AUTH S.AUMONIER,G.SANTONI,G.GOTTHARD,D.VON STETTEN,G.A.LEONARD, JRNL AUTH 2 A.ROYANT JRNL TITL MILLISECOND TIME-RESOLVED SERIAL OSCILLATION CRYSTALLOGRAPHY JRNL TITL 2 OF A BLUE-LIGHT PHOTORECEPTOR AT A SYNCHROTRON. JRNL REF IUCRJ V. 7 728 2020 JRNL REFN ESSN 2052-2525 JRNL PMID 32695419 JRNL DOI 10.1107/S2052252520007411 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 6231 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.750 REMARK 3 FREE R VALUE TEST SET COUNT : 296 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 2.2790 - 2.2000 1.00 586 33 0.3329 0.3665 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.100 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 : 0.002 1098 REMARK 3 ANGLE : 0.547 1501 REMARK 3 CHIRALITY : 0.045 156 REMARK 3 PLANARITY : 0.004 198 REMARK 3 DIHEDRAL : 11.215 900 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 6S45 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1292103093. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.968 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6273 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 44.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 87.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 93.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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: 6QQJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12-17 % PEG8000 0.2 M CALCIUM ACETATE REMARK 280 0.1 M MES, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 66.82000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.41250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.41250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 100.23000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.41250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.41250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.41000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.41250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.41250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 100.23000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.41250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.41250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.41000 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 66.82000 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: 870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 ASP A 503 REMARK 465 SER A 504 REMARK 465 THR A 505 REMARK 465 ARG A 506 REMARK 465 THR A 507 REMARK 465 GLY A 508 REMARK 465 HIS A 509 REMARK 465 HIS A 510 REMARK 465 HIS A 511 REMARK 465 HIS A 512 REMARK 465 HIS A 513 REMARK 465 HIS A 514 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 NH2 ARG A 397 O GLN A 483 2.07 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 1001 DBREF 6S45 A 388 492 UNP P93025 PHOT2_ARATH 388 492 SEQADV 6S45 MET A 387 UNP P93025 INITIATING METHIONINE SEQADV 6S45 GLU A 493 UNP P93025 EXPRESSION TAG SEQADV 6S45 PHE A 494 UNP P93025 EXPRESSION TAG SEQADV 6S45 ILE A 495 UNP P93025 EXPRESSION TAG SEQADV 6S45 PRO A 496 UNP P93025 EXPRESSION TAG SEQADV 6S45 ASN A 497 UNP P93025 EXPRESSION TAG SEQADV 6S45 PRO A 498 UNP P93025 EXPRESSION TAG SEQADV 6S45 LEU A 499 UNP P93025 EXPRESSION TAG SEQADV 6S45 LEU A 500 UNP P93025 EXPRESSION TAG SEQADV 6S45 GLY A 501 UNP P93025 EXPRESSION TAG SEQADV 6S45 LEU A 502 UNP P93025 EXPRESSION TAG SEQADV 6S45 ASP A 503 UNP P93025 EXPRESSION TAG SEQADV 6S45 SER A 504 UNP P93025 EXPRESSION TAG SEQADV 6S45 THR A 505 UNP P93025 EXPRESSION TAG SEQADV 6S45 ARG A 506 UNP P93025 EXPRESSION TAG SEQADV 6S45 THR A 507 UNP P93025 EXPRESSION TAG SEQADV 6S45 GLY A 508 UNP P93025 EXPRESSION TAG SEQADV 6S45 HIS A 509 UNP P93025 EXPRESSION TAG SEQADV 6S45 HIS A 510 UNP P93025 EXPRESSION TAG SEQADV 6S45 HIS A 511 UNP P93025 EXPRESSION TAG SEQADV 6S45 HIS A 512 UNP P93025 EXPRESSION TAG SEQADV 6S45 HIS A 513 UNP P93025 EXPRESSION TAG SEQADV 6S45 HIS A 514 UNP P93025 EXPRESSION TAG SEQRES 1 A 128 MET GLU LYS ASN PHE VAL ILE SER ASP PRO ARG LEU PRO SEQRES 2 A 128 ASP ASN PRO ILE ILE PHE ALA SER ASP SER PHE LEU GLU SEQRES 3 A 128 LEU THR GLU TYR SER ARG GLU GLU ILE LEU GLY ARG ASN SEQRES 4 A 128 CYS ARG PHE LEU GLN GLY PRO GLU THR ASP GLN ALA THR SEQRES 5 A 128 VAL GLN LYS ILE ARG ASP ALA ILE ARG ASP GLN ARG GLU SEQRES 6 A 128 ILE THR VAL GLN LEU ILE ASN TYR THR LYS SER GLY LYS SEQRES 7 A 128 LYS PHE TRP ASN LEU PHE HIS LEU GLN PRO MET ARG ASP SEQRES 8 A 128 GLN LYS GLY GLU LEU GLN TYR PHE ILE GLY VAL GLN LEU SEQRES 9 A 128 ASP GLY GLU PHE ILE PRO ASN PRO LEU LEU GLY LEU ASP SEQRES 10 A 128 SER THR ARG THR GLY HIS HIS HIS HIS HIS HIS HET FMN A1001 31 HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 3 HOH *42(H2 O) HELIX 1 AA1 SER A 407 GLU A 415 1 9 HELIX 2 AA2 SER A 417 ILE A 421 5 5 HELIX 3 AA3 ASN A 425 GLN A 430 5 6 HELIX 4 AA4 ASP A 435 GLN A 449 1 15 HELIX 5 AA5 PRO A 496 GLY A 501 1 6 SHEET 1 AA1 5 ILE A 403 ALA A 406 0 SHEET 2 AA1 5 ASN A 390 SER A 394 -1 N ILE A 393 O ILE A 404 SHEET 3 AA1 5 LEU A 482 ASP A 491 -1 O PHE A 485 N SER A 394 SHEET 4 AA1 5 LYS A 465 ARG A 476 -1 N MET A 475 O GLN A 483 SHEET 5 AA1 5 ILE A 452 TYR A 459 -1 N VAL A 454 O PHE A 470 SITE 1 AC1 22 VAL A 392 SER A 394 ASN A 425 CYS A 426 SITE 2 AC1 22 ARG A 427 LEU A 429 GLN A 430 VAL A 439 SITE 3 AC1 22 ARG A 443 ILE A 446 LEU A 456 ASN A 458 SITE 4 AC1 22 ASN A 468 PHE A 470 LEU A 472 PHE A 485 SITE 5 AC1 22 GLY A 487 GLN A 489 HOH A1102 HOH A1105 SITE 6 AC1 22 HOH A1117 HOH A1129 CRYST1 40.825 40.825 133.640 90.00 90.00 90.00 P 43 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 0.024495 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024495 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007483 0.00000