HEADER FLUORESCENT PROTEIN 08-NOV-17 5YR3 TITLE STRUCTURE OF SFYFP66BPA COMPND MOL_ID: 1; COMPND 2 MOLECULE: YELLOW FLUORESCENT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEQUOREA VICTORIA; SOURCE 3 ORGANISM_COMMON: JELLYFISH; SOURCE 4 ORGANISM_TAXID: 6100; SOURCE 5 GENE: YFP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS BIOLUMINESCENCE PROTEIN CHROMOPHORE LINKAGE, FLUORESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.KANG,L.WANG,J.WANG REVDAT 2 22-NOV-23 5YR3 1 REMARK REVDAT 1 30-JAN-19 5YR3 0 JRNL AUTH F.KANG,L.WANG JRNL TITL SFYFP66BPA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 19922 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1993 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 29.4358 - 4.5752 0.92 1328 148 0.2063 0.2426 REMARK 3 2 4.5752 - 3.6336 0.99 1342 149 0.1895 0.2244 REMARK 3 3 3.6336 - 3.1749 0.99 1291 143 0.2306 0.2988 REMARK 3 4 3.1749 - 2.8849 1.00 1292 145 0.2674 0.3112 REMARK 3 5 2.8849 - 2.6783 1.00 1298 144 0.2931 0.3451 REMARK 3 6 2.6783 - 2.5205 1.00 1268 140 0.2868 0.3305 REMARK 3 7 2.5205 - 2.3943 1.00 1292 144 0.2904 0.3292 REMARK 3 8 2.3943 - 2.2901 1.00 1267 141 0.3066 0.3908 REMARK 3 9 2.2901 - 2.2020 1.00 1272 141 0.3108 0.3577 REMARK 3 10 2.2020 - 2.1260 1.00 1258 140 0.3016 0.3194 REMARK 3 11 2.1260 - 2.0596 1.00 1262 140 0.2925 0.3514 REMARK 3 12 2.0596 - 2.0007 1.00 1251 139 0.3071 0.3498 REMARK 3 13 2.0007 - 1.9481 1.00 1263 141 0.2903 0.3364 REMARK 3 14 1.9481 - 1.9005 1.00 1245 138 0.3285 0.3760 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.720 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 : 0.009 1879 REMARK 3 ANGLE : 1.135 2549 REMARK 3 CHIRALITY : 0.057 278 REMARK 3 PLANARITY : 0.005 336 REMARK 3 DIHEDRAL : 16.366 1118 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -0.4003 7.8323 22.8252 REMARK 3 T TENSOR REMARK 3 T11: 0.5236 T22: 0.3154 REMARK 3 T33: 0.4362 T12: 0.0319 REMARK 3 T13: -0.0019 T23: 0.0693 REMARK 3 L TENSOR REMARK 3 L11: 3.4169 L22: 4.1404 REMARK 3 L33: 5.3397 L12: 1.4027 REMARK 3 L13: -1.5638 L23: -1.4496 REMARK 3 S TENSOR REMARK 3 S11: -0.1098 S12: 0.0862 S13: 0.3812 REMARK 3 S21: 0.0883 S22: 0.2584 S23: 0.8882 REMARK 3 S31: -0.1526 S32: -0.7802 S33: -0.1406 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 5YR3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1300005698. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 5.0 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) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19926 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 29.434 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.890 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: 1QYO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 3350, 0.1M MALIC ACID, PH 5.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 89.48850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.85650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.85650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.74425 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.85650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.85650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 134.23275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.85650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.85650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.74425 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.85650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.85650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 134.23275 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 89.48850 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 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 ASN A 23 16.46 52.96 REMARK 500 ASP A 103 -157.61 -158.50 REMARK 500 ASN A 135 -56.68 47.90 REMARK 500 ILE A 136 -74.31 -72.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE THR 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 REMARK 999 AND GLY 67 CONSTITUTE THE CHROMOPHORE BF6 66. DBREF1 5YR3 A 4 230 UNP A0A059PIR9_AEQVI DBREF2 5YR3 A A0A059PIR9 4 230 SEQADV 5YR3 ARG A 30 UNP A0A059PIR SER 30 ENGINEERED MUTATION SEQADV 5YR3 ILE A 39 UNP A0A059PIR ASN 39 ENGINEERED MUTATION SEQADV 5YR3 SER A 48 UNP A0A059PIR CYS 48 ENGINEERED MUTATION SEQADV 5YR3 BF6 A 66 UNP A0A059PIR THR 65 CHROMOPHORE SEQADV 5YR3 BF6 A 66 UNP A0A059PIR TYR 66 CHROMOPHORE SEQADV 5YR3 BF6 A 66 UNP A0A059PIR GLY 67 CHROMOPHORE SEQADV 5YR3 LEU A 68 UNP A0A059PIR VAL 68 ENGINEERED MUTATION SEQADV 5YR3 LYS A 105 UNP A0A059PIR THR 105 ENGINEERED MUTATION SEQADV 5YR3 VAL A 111 UNP A0A059PIR GLU 111 ENGINEERED MUTATION SEQADV 5YR3 THR A 128 UNP A0A059PIR ILE 128 ENGINEERED MUTATION SEQADV 5YR3 GLU A 148 UNP A0A059PIR HIS 148 ENGINEERED MUTATION SEQADV 5YR3 THR A 166 UNP A0A059PIR LYS 166 ENGINEERED MUTATION SEQADV 5YR3 VAL A 167 UNP A0A059PIR ILE 167 ENGINEERED MUTATION SEQADV 5YR3 ASP A 203 UNP A0A059PIR TYR 203 ENGINEERED MUTATION SEQADV 5YR3 THR A 205 UNP A0A059PIR SER 205 ENGINEERED MUTATION SEQADV 5YR3 VAL A 206 UNP A0A059PIR ALA 206 ENGINEERED MUTATION SEQRES 1 A 225 GLY GLU GLU LEU PHE THR GLY VAL VAL PRO ILE LEU VAL SEQRES 2 A 225 GLU LEU ASP GLY ASP VAL ASN GLY HIS LYS PHE SER VAL SEQRES 3 A 225 ARG GLY GLU GLY GLU GLY ASP ALA THR ILE GLY LYS LEU SEQRES 4 A 225 THR LEU LYS PHE ILE SER THR THR GLY LYS LEU PRO VAL SEQRES 5 A 225 PRO TRP PRO THR LEU VAL THR THR LEU BF6 LEU GLN CYS SEQRES 6 A 225 PHE ALA ARG TYR PRO ASP HIS MET LYS GLN HIS ASP PHE SEQRES 7 A 225 PHE LYS SER ALA MET PRO GLU GLY TYR VAL GLN GLU ARG SEQRES 8 A 225 THR ILE SER PHE LYS ASP ASP GLY LYS TYR LYS THR ARG SEQRES 9 A 225 ALA VAL VAL LYS PHE GLU GLY ASP THR LEU VAL ASN ARG SEQRES 10 A 225 ILE GLU LEU LYS GLY THR ASP PHE LYS GLU ASP GLY ASN SEQRES 11 A 225 ILE LEU GLY HIS LYS LEU GLU TYR ASN PHE ASN SER GLU SEQRES 12 A 225 ASN VAL TYR ILE THR ALA ASP LYS GLN LYS ASN GLY ILE SEQRES 13 A 225 LYS ALA ASN PHE THR VAL ARG HIS ASN VAL GLU ASP GLY SEQRES 14 A 225 SER VAL GLN LEU ALA ASP HIS TYR GLN GLN ASN THR PRO SEQRES 15 A 225 ILE GLY ASP GLY PRO VAL LEU LEU PRO ASP ASN HIS TYR SEQRES 16 A 225 LEU SER ASP GLN THR VAL LEU SER LYS ASP PRO ASN GLU SEQRES 17 A 225 LYS ARG ASP HIS MET VAL LEU LEU GLU PHE VAL THR ALA SEQRES 18 A 225 ALA GLY ILE THR HET BF6 A 66 26 HETNAM BF6 [(4Z)-2-(AMINOMETHYL)-4-{[4-(BENZENECARBONYL) HETNAM 2 BF6 PHENYL]METHYLIDENE}-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1- HETNAM 3 BF6 YL]ACETIC ACID HETSYN BF6 PEPTIDE DERIVED CHROMOPHORE FORMUL 1 BF6 C20 H17 N3 O4 FORMUL 2 HOH *72(H2 O) HELIX 1 AA1 GLY A 4 THR A 9 5 6 HELIX 2 AA2 PRO A 56 VAL A 61 5 6 HELIX 3 AA3 LEU A 68 ALA A 72 5 5 HELIX 4 AA4 PRO A 75 HIS A 81 5 7 HELIX 5 AA5 ASP A 82 ALA A 87 1 6 SHEET 1 AA112 VAL A 12 VAL A 22 0 SHEET 2 AA112 HIS A 25 ASP A 36 -1 O VAL A 29 N LEU A 18 SHEET 3 AA112 LYS A 41 SER A 48 -1 O LYS A 41 N ASP A 36 SHEET 4 AA112 HIS A 217 ALA A 227 -1 O MET A 218 N PHE A 46 SHEET 5 AA112 HIS A 199 SER A 208 -1 N SER A 202 O THR A 225 SHEET 6 AA112 ASN A 149 ASP A 155 -1 N ILE A 152 O HIS A 199 SHEET 7 AA112 GLY A 160 ASN A 170 -1 O GLY A 160 N ASP A 155 SHEET 8 AA112 VAL A 176 PRO A 187 -1 O GLN A 177 N HIS A 169 SHEET 9 AA112 TYR A 92 PHE A 100 -1 N SER A 99 O ASP A 180 SHEET 10 AA112 LYS A 105 GLU A 115 -1 O TYR A 106 N ILE A 98 SHEET 11 AA112 THR A 118 THR A 128 -1 O LYS A 126 N LYS A 107 SHEET 12 AA112 VAL A 12 VAL A 22 1 N GLU A 17 O ILE A 123 LINK C LEU A 64 N1 BF6 A 66 1555 1555 1.28 LINK C3 BF6 A 66 N LEU A 68 1555 1555 1.41 CISPEP 1 MET A 88 PRO A 89 0 7.98 CRYST1 51.713 51.713 178.977 90.00 90.00 90.00 P 41 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 0.019337 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019337 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005587 0.00000