HEADER PLANT PROTEIN 10-JUN-22 8A4E TITLE ROOM TEMPERATURE STRUCTURE OF ATPHOT2LOV2 IN A PHOTOSTATIONARY TITLE 2 EQUILIBRIUM 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 8A4E 1 REMARK REVDAT 1 29-MAR-23 8A4E 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. 1.96 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.7 REMARK 3 NUMBER OF REFLECTIONS : 7756 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.560 REMARK 3 FREE R VALUE TEST SET COUNT : 354 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 35.2300 - 2.8200 1.00 3014 151 0.1645 0.2025 REMARK 3 2 2.8200 - 2.2400 1.00 2847 118 0.2346 0.2790 REMARK 3 3 2.2400 - 1.9600 0.56 1541 85 0.2595 0.2940 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.39 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 8A4E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1292123624. 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) : 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) : 0.9677 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 : 7757 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 39.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 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 : 1.500 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: 6QQK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 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 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 66.42500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.77750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.77750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 99.63750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.77750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.77750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.21250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.77750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.77750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 99.63750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.77750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.77750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.21250 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 66.42500 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 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 387 REMARK 465 GLU A 388 REMARK 465 PRO A 496 REMARK 465 ASN A 497 REMARK 465 PRO A 498 REMARK 465 LEU A 499 REMARK 465 LEU A 500 REMARK 465 GLY A 501 REMARK 465 LEU A 502 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 701 2.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 412 N GLU A 412 CA 0.145 REMARK 500 MET A 475 N MET A 475 CA 0.151 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 746 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A 747 DISTANCE = 6.80 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 FMA A 601 DBREF 8A4E A 388 492 UNP P93025 PHOT2_ARATH 388 492 SEQADV 8A4E MET A 387 UNP P93025 INITIATING METHIONINE SEQADV 8A4E GLU A 493 UNP P93025 EXPRESSION TAG SEQADV 8A4E PHE A 494 UNP P93025 EXPRESSION TAG SEQADV 8A4E ILE A 495 UNP P93025 EXPRESSION TAG SEQADV 8A4E PRO A 496 UNP P93025 EXPRESSION TAG SEQADV 8A4E ASN A 497 UNP P93025 EXPRESSION TAG SEQADV 8A4E PRO A 498 UNP P93025 EXPRESSION TAG SEQADV 8A4E LEU A 499 UNP P93025 EXPRESSION TAG SEQADV 8A4E LEU A 500 UNP P93025 EXPRESSION TAG SEQADV 8A4E GLY A 501 UNP P93025 EXPRESSION TAG SEQADV 8A4E LEU A 502 UNP P93025 EXPRESSION TAG SEQADV 8A4E ASP A 503 UNP P93025 EXPRESSION TAG SEQADV 8A4E SER A 504 UNP P93025 EXPRESSION TAG SEQADV 8A4E THR A 505 UNP P93025 EXPRESSION TAG SEQADV 8A4E ARG A 506 UNP P93025 EXPRESSION TAG SEQADV 8A4E THR A 507 UNP P93025 EXPRESSION TAG SEQADV 8A4E GLY A 508 UNP P93025 EXPRESSION TAG SEQADV 8A4E HIS A 509 UNP P93025 EXPRESSION TAG SEQADV 8A4E HIS A 510 UNP P93025 EXPRESSION TAG SEQADV 8A4E HIS A 511 UNP P93025 EXPRESSION TAG SEQADV 8A4E HIS A 512 UNP P93025 EXPRESSION TAG SEQADV 8A4E HIS A 513 UNP P93025 EXPRESSION TAG SEQADV 8A4E 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 FMA A 601 31 HET FMN A 602 31 HETNAM FMA 6-(3-TETRADECANOIC ACID) FLAVINE MONONUCLEOTIDE HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 FMA C31 H47 N4 O11 P FORMUL 3 FMN C17 H21 N4 O9 P FORMUL 4 HOH *47(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 SHEET 1 AA1 5 ILE A 403 ALA A 406 0 SHEET 2 AA1 5 PHE A 391 SER A 394 -1 N ILE A 393 O ILE A 404 SHEET 3 AA1 5 LEU A 482 GLN A 489 -1 O GLY A 487 N VAL A 392 SHEET 4 AA1 5 LYS A 465 ARG A 476 -1 N MET A 475 O TYR A 484 SHEET 5 AA1 5 ILE A 452 TYR A 459 -1 N ILE A 452 O LEU A 472 LINK SG ACYS A 426 C4AAFMA A 601 1555 1555 1.77 CRYST1 41.555 41.555 132.850 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 0.024064 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024064 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007527 0.00000