HEADER PLANT PROTEIN 06-JUN-22 8A2V TITLE ROOM TEMPERATURE STRUCTURE OF THE GROUND STATE OF ATPHOT2LOV2 IN SPACE TITLE 2 GROUP P43212 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, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.ENGILBERGE,N.CARAMELLO,A.ROYANT REVDAT 2 07-FEB-24 8A2V 1 REMARK REVDAT 1 29-MAR-23 8A2V 0 JRNL AUTH S.AUMONIER,S.ENGILBERGE,N.CARAMELLO,D.VON STETTEN, JRNL AUTH 2 G.GOTTHARD,G.A.LEONARD,C.MUELLER-DIECKMANN,A.ROYANT JRNL TITL SLOW PROTEIN DYNAMICS PROBED BY TIME-RESOLVED OSCILLATION JRNL TITL 2 CRYSTALLOGRAPHY AT ROOM TEMPERATURE. JRNL REF IUCRJ V. 9 756 2022 JRNL REFN ESSN 2052-2525 JRNL PMID 36381146 JRNL DOI 10.1107/S2052252522009150 REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 13978 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.73 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 8A2V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1292123515. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 298 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) : 0.9677 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 : 14046 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 34.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 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 : 1.300 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: 6QQK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES PH 6.0, 4 TO 9 % PEG8000, REMARK 280 AND 50 TO 200 MM CALCIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 66.40700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.41450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.41450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 99.61050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.41450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.41450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.20350 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.41450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.41450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 99.61050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.41450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.41450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.20350 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 66.40700 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1187 LIES ON A SPECIAL POSITION. 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 OE2 GLU A 433 O HOH A 1102 2.03 REMARK 500 OE1 GLN A 440 NH1 ARG A 443 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 476 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8A2V A 388 492 UNP P93025 PHOT2_ARATH 388 492 SEQADV 8A2V MET A 387 UNP P93025 INITIATING METHIONINE SEQADV 8A2V GLU A 493 UNP P93025 EXPRESSION TAG SEQADV 8A2V PHE A 494 UNP P93025 EXPRESSION TAG SEQADV 8A2V ILE A 495 UNP P93025 EXPRESSION TAG SEQADV 8A2V PRO A 496 UNP P93025 EXPRESSION TAG SEQADV 8A2V ASN A 497 UNP P93025 EXPRESSION TAG SEQADV 8A2V PRO A 498 UNP P93025 EXPRESSION TAG SEQADV 8A2V LEU A 499 UNP P93025 EXPRESSION TAG SEQADV 8A2V LEU A 500 UNP P93025 EXPRESSION TAG SEQADV 8A2V GLY A 501 UNP P93025 EXPRESSION TAG SEQADV 8A2V LEU A 502 UNP P93025 EXPRESSION TAG SEQADV 8A2V ASP A 503 UNP P93025 EXPRESSION TAG SEQADV 8A2V SER A 504 UNP P93025 EXPRESSION TAG SEQADV 8A2V THR A 505 UNP P93025 EXPRESSION TAG SEQADV 8A2V ARG A 506 UNP P93025 EXPRESSION TAG SEQADV 8A2V THR A 507 UNP P93025 EXPRESSION TAG SEQADV 8A2V GLY A 508 UNP P93025 EXPRESSION TAG SEQADV 8A2V HIS A 509 UNP P93025 EXPRESSION TAG SEQADV 8A2V HIS A 510 UNP P93025 EXPRESSION TAG SEQADV 8A2V HIS A 511 UNP P93025 EXPRESSION TAG SEQADV 8A2V HIS A 512 UNP P93025 EXPRESSION TAG SEQADV 8A2V HIS A 513 UNP P93025 EXPRESSION TAG SEQADV 8A2V 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 HET MES A1002 12 HETNAM FMN FLAVIN MONONUCLEOTIDE HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 3 MES C6 H13 N O4 S FORMUL 4 HOH *90(H2 O) HELIX 1 AA1 SER A 407 GLU A 415 1 9 HELIX 2 AA2 SER A 417 LEU A 422 1 6 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 GLY A 487 N VAL A 392 SHEET 4 AA1 5 LYS A 465 ARG A 476 -1 N LEU A 469 O LEU A 490 SHEET 5 AA1 5 ILE A 452 TYR A 459 -1 N VAL A 454 O PHE A 470 CRYST1 40.829 40.829 132.814 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 0.024492 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024492 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007529 0.00000