HEADER FLUORESCENT PROTEIN 14-JUN-24 8ZXO TITLE STRUCTURE OF THE RED FLUORESCENT PROTEIN MSCARLET-H AT PH8.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RED FLUORESCENT PROTEIN MSCARLETH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DISCOSOMA SP.; SOURCE 3 ORGANISM_TAXID: 86600; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RED FLUORESCENT PROTEIN, MSCARLET-H, FLUORESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.LI,M.LI,S.FAN,Q.ZHENG,S.LI,Z.FU REVDAT 2 04-MAR-26 8ZXO 1 JRNL SEQRES REVDAT 1 19-FEB-25 8ZXO 0 JRNL AUTH H.XIONG,Q.CHANG,J.DING,S.WANG,W.ZHANG,Y.LI,Y.WU,P.LIN, JRNL AUTH 2 C.YANG,M.LIU,G.FANG,Y.YANG,J.XIE,D.QI,T.JIANG,W.FU,F.HU, JRNL AUTH 3 Y.CHEN,R.YUE,Y.LI,Y.CUI,M.LI,S.FAN,Y.YANG,Y.XU,D.LI,F.ZHANG, JRNL AUTH 4 H.ZHAO,C.WU,Q.ZHENG,K.D.PIATKEVICH,Z.FU JRNL TITL A HIGHLY STABLE MONOMERIC RED FLUORESCENT PROTEIN FOR JRNL TITL 2 ADVANCED MICROSCOPY. JRNL REF NAT.METHODS V. 22 1288 2025 JRNL REFN ESSN 1548-7105 JRNL PMID 40247125 JRNL DOI 10.1038/S41592-025-02676-5 REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13-2998 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 19451 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3558 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 1.8810 - 1.8160 0.99 0 0 0.2888 0.3352 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) : 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 : 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 8ZXO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 18-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1300048618. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19465 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.816 REMARK 200 RESOLUTION RANGE LOW (A) : 57.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.16700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.13-2998 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM SULFATE,0.1M TRIS8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 42.35750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.67550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.35750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.67550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 A 344 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 465 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 MET A 1 REMARK 465 VAL A 2 REMARK 465 SER A 3 REMARK 465 LYS A 4 REMARK 465 GLY A 5 REMARK 465 GLU A 6 REMARK 465 GLY A 226 REMARK 465 MET A 227 REMARK 465 ASP A 228 REMARK 465 GLU A 229 REMARK 465 LEU A 230 REMARK 465 TYR A 231 REMARK 465 LYS A 232 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 THR A 107 CG2 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 PRO A 56 34.10 -86.05 REMARK 500 PHE A 73 42.20 -107.52 REMARK 500 REMARK 500 REMARK: NULL DBREF 8ZXO A 1 232 PDB 8ZXO 8ZXO 1 232 SEQRES 1 A 230 MET VAL SER LYS GLY GLU ALA VAL ILE LYS GLU PHE MET SEQRES 2 A 230 ARG PHE LYS VAL HIS MET GLU GLY SER MET ASN GLY HIS SEQRES 3 A 230 GLU PHE GLU ILE GLU GLY GLU GLY GLU GLY ARG PRO TYR SEQRES 4 A 230 GLU GLY THR GLN THR ALA LYS LEU LYS VAL THR LYS GLY SEQRES 5 A 230 GLY PRO LEU PRO PHE SER TRP ASP ILE LEU SER PRO GLN SEQRES 6 A 230 PHE NRQ SER ARG ALA PHE THR LYS HIS PRO ALA ASP ILE SEQRES 7 A 230 PRO ASP TYR TYR LYS GLN SER PHE PRO GLU GLY PHE LYS SEQRES 8 A 230 TRP GLU ARG VAL MET ASN PHE GLU ASP GLY GLY ALA VAL SEQRES 9 A 230 THR VAL THR GLN ASP THR SER LEU GLU ASP GLY THR LEU SEQRES 10 A 230 ILE TYR LYS VAL LYS LEU ARG GLY THR ASN PHE PRO PRO SEQRES 11 A 230 ASP GLY PRO VAL MET GLN LYS LYS THR MET GLY TRP GLU SEQRES 12 A 230 ALA SER THR GLU ARG LEU TYR PRO GLU ASP GLY VAL LEU SEQRES 13 A 230 LYS GLY ASP ILE LYS HIS ALA LEU ARG LEU LYS ASP GLY SEQRES 14 A 230 GLY ARG TYR LEU ALA ASP PHE LYS THR THR TYR LYS ALA SEQRES 15 A 230 LYS LYS PRO VAL GLN MET PRO GLY ALA TYR ASN VAL ASP SEQRES 16 A 230 ARG LYS LEU ASP ILE THR SER HIS ASN GLU ASP TYR THR SEQRES 17 A 230 VAL VAL GLU GLN TYR GLU ARG SER GLU GLY ARG HIS SER SEQRES 18 A 230 THR GLY GLY MET ASP GLU LEU TYR LYS HET NRQ A 67 23 HETNAM NRQ {(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO) HETNAM 2 NRQ PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1- HETNAM 3 NRQ YL}ACETIC ACID HETSYN NRQ CHROMOPHORE (MET-TYR-GLY) FORMUL 1 NRQ C16 H17 N3 O4 S FORMUL 2 HOH *173(H2 O) HELIX 1 AA1 SER A 58 PHE A 66 5 9 HELIX 2 AA2 SER A 70 THR A 74 5 5 HELIX 3 AA3 ASP A 82 SER A 87 1 6 SHEET 1 AA113 THR A 141 TRP A 144 0 SHEET 2 AA113 VAL A 157 LEU A 168 -1 O ARG A 167 N GLY A 143 SHEET 3 AA113 ARG A 173 ALA A 184 -1 O ALA A 176 N HIS A 164 SHEET 4 AA113 PHE A 92 PHE A 100 -1 N LYS A 93 O LYS A 183 SHEET 5 AA113 ALA A 105 GLU A 115 -1 O VAL A 108 N ARG A 96 SHEET 6 AA113 THR A 118 THR A 128 -1 O ILE A 120 N SER A 113 SHEET 7 AA113 MET A 13 MET A 23 1 N SER A 22 O GLY A 127 SHEET 8 AA113 HIS A 26 ARG A 37 -1 O ILE A 30 N MET A 19 SHEET 9 AA113 THR A 42 LYS A 51 -1 O LYS A 46 N GLU A 33 SHEET 10 AA113 VAL A 211 ARG A 221 -1 O VAL A 212 N LEU A 47 SHEET 11 AA113 TYR A 194 HIS A 205 -1 N ASN A 195 O ARG A 221 SHEET 12 AA113 SER A 147 GLU A 154 -1 N LEU A 151 O TYR A 194 SHEET 13 AA113 VAL A 157 LEU A 168 -1 O ASP A 161 N ARG A 150 LINK C PHE A 66 N1 NRQ A 67 1555 1555 1.43 LINK C3 NRQ A 67 N SER A 70 1555 1555 1.43 CISPEP 1 GLY A 53 PRO A 54 0 -6.66 CISPEP 2 PHE A 88 PRO A 89 0 8.09 CRYST1 84.715 45.351 58.658 90.00 102.10 90.00 C 1 2 1 4 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 0.011804 0.000000 0.002530 0.00000 SCALE2 0.000000 0.022050 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017435 0.00000 CONECT 471 480 CONECT 480 471 485 CONECT 481 482 CONECT 482 481 483 CONECT 483 482 484 CONECT 484 483 485 CONECT 485 480 484 486 CONECT 486 485 487 499 CONECT 487 486 496 CONECT 488 491 CONECT 489 490 494 CONECT 490 489 491 CONECT 491 488 490 492 CONECT 492 491 493 CONECT 493 492 494 CONECT 494 489 493 495 CONECT 495 494 496 CONECT 496 487 495 497 CONECT 497 496 498 499 CONECT 498 497 CONECT 499 486 497 500 CONECT 500 499 501 CONECT 501 500 502 503 CONECT 502 501 CONECT 503 501 MASTER 242 0 1 3 13 0 0 6 1925 1 25 18 END