HEADER FLUORESCENT PROTEIN 09-OCT-18 6HUT TITLE GFP8 - A STABILIZED VARIANT OF CYCLE-3 GFP COMPND MOL_ID: 1; COMPND 2 MOLECULE: GREEN 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: GFP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS GREEN FLUORESCENT PROTEIN, CYCLE-3, FLUORESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.PETEK,M.RANGEL PEREIRA REVDAT 2 24-JAN-24 6HUT 1 REMARK REVDAT 1 22-JAN-20 6HUT 0 JRNL AUTH M.PETEK,M.RANGEL PEREIRA JRNL TITL GFP8 - A STABILIZED VARIANT OF CYCLE-3 GFP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1-2575 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) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 58248 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.203 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 1 1.3361 - 1.2900 0.00 0 273 0.3193 0.3342 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 6HUT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-OCT-18. REMARK 100 THE DEPOSITION ID IS D_1200012049. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9282 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58248 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE CCP4 7.0 REMARK 200 STARTING MODEL: 4LQT REMARK 200 REMARK 200 REMARK: LARGE CYLINDER REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM HEPES, 10% V/V ISOPROPANOL, 200 REMARK 280 MM NACL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 26.08000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.60500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.68500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.60500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.08000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.68500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 MET A 1 REMARK 465 HIS A 246 REMARK 465 HIS A 247 REMARK 465 HIS A 248 REMARK 465 HIS A 249 REMARK 465 HIS A 250 REMARK 465 HIS A 251 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 GLU A 6 CB CG CD OE1 OE2 REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 ARG A 122 NE CZ NH1 NH2 REMARK 470 ASP A 133 CB CG OD1 OD2 REMARK 470 LYS A 156 CG CD CE NZ REMARK 470 GLN A 157 CB CG CD OE1 NE2 REMARK 470 LYS A 158 CG CD CE NZ REMARK 470 ASP A 234 OD1 REMARK 470 LYS A 238 CG CD CE NZ REMARK 470 LYS A 239 CE NZ REMARK 470 LEU A 244 CD1 CD2 REMARK 470 GLU A 245 CA C O CB CG CD OE1 REMARK 470 GLU A 245 OE2 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 ASP A 103 -158.38 -153.00 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6HUT A 1 245 UNP A0A059PIQ0_AEQVI DBREF2 6HUT A A0A059PIQ0 1 245 SEQADV 6HUT SER A 2 UNP A0A059PIQ ARG 2 ENGINEERED MUTATION SEQADV 6HUT ARG A 30 UNP A0A059PIQ SER 30 ENGINEERED MUTATION SEQADV 6HUT TYR A 39 UNP A0A059PIQ ASN 39 ENGINEERED MUTATION SEQADV 6HUT CRO A 66 UNP A0A059PIQ THR 65 CHROMOPHORE SEQADV 6HUT CRO A 66 UNP A0A059PIQ TYR 66 CHROMOPHORE SEQADV 6HUT CRO A 66 UNP A0A059PIQ GLY 67 CHROMOPHORE SEQADV 6HUT SER A 72 UNP A0A059PIQ ALA 72 ENGINEERED MUTATION SEQADV 6HUT ARG A 80 UNP A0A059PIQ GLN 80 ENGINEERED MUTATION SEQADV 6HUT TYR A 145 UNP A0A059PIQ PHE 145 ENGINEERED MUTATION SEQADV 6HUT ILE A 171 UNP A0A059PIQ VAL 171 ENGINEERED MUTATION SEQADV 6HUT VAL A 206 UNP A0A059PIQ ALA 206 ENGINEERED MUTATION SEQADV 6HUT LYS A 239 UNP A0A059PIQ ARG 239 ENGINEERED MUTATION SEQADV 6HUT LEU A 240 UNP A0A059PIQ PRO 240 ENGINEERED MUTATION SEQADV 6HUT ALA A 243 UNP A0A059PIQ ASN 243 ENGINEERED MUTATION SEQADV 6HUT LEU A 244 UNP A0A059PIQ ASP 244 ENGINEERED MUTATION SEQADV 6HUT HIS A 246 UNP A0A059PIQ EXPRESSION TAG SEQADV 6HUT HIS A 247 UNP A0A059PIQ EXPRESSION TAG SEQADV 6HUT HIS A 248 UNP A0A059PIQ EXPRESSION TAG SEQADV 6HUT HIS A 249 UNP A0A059PIQ EXPRESSION TAG SEQADV 6HUT HIS A 250 UNP A0A059PIQ EXPRESSION TAG SEQADV 6HUT HIS A 251 UNP A0A059PIQ EXPRESSION TAG SEQRES 1 A 249 MET SER LYS GLY GLU GLU LEU PHE THR GLY VAL VAL PRO SEQRES 2 A 249 ILE LEU VAL GLU LEU ASP GLY ASP VAL ASN GLY HIS LYS SEQRES 3 A 249 PHE SER VAL ARG GLY GLU GLY GLU GLY ASP ALA THR TYR SEQRES 4 A 249 GLY LYS LEU THR LEU LYS PHE ILE CYS THR THR GLY LYS SEQRES 5 A 249 LEU PRO VAL PRO TRP PRO THR LEU VAL THR THR LEU CRO SEQRES 6 A 249 VAL GLN CYS PHE SER ARG TYR PRO ASP HIS MET LYS ARG SEQRES 7 A 249 HIS ASP PHE PHE LYS SER ALA MET PRO GLU GLY TYR VAL SEQRES 8 A 249 GLN GLU ARG THR ILE SER PHE LYS ASP ASP GLY THR TYR SEQRES 9 A 249 LYS THR ARG ALA GLU VAL LYS PHE GLU GLY ASP THR LEU SEQRES 10 A 249 VAL ASN ARG ILE GLU LEU LYS GLY ILE ASP PHE LYS GLU SEQRES 11 A 249 ASP GLY ASN ILE LEU GLY HIS LYS LEU GLU TYR ASN TYR SEQRES 12 A 249 ASN SER HIS ASN VAL TYR ILE THR ALA ASP LYS GLN LYS SEQRES 13 A 249 ASN GLY ILE LYS ALA ASN PHE LYS ILE ARG HIS ASN ILE SEQRES 14 A 249 GLU ASP GLY SER VAL GLN LEU ALA ASP HIS TYR GLN GLN SEQRES 15 A 249 ASN THR PRO ILE GLY ASP GLY PRO VAL LEU LEU PRO ASP SEQRES 16 A 249 ASN HIS TYR LEU SER THR GLN SER VAL LEU SER LYS ASP SEQRES 17 A 249 PRO ASN GLU LYS ARG ASP HIS MET VAL LEU LEU GLU PHE SEQRES 18 A 249 VAL THR ALA ALA GLY ILE THR HIS GLY MET ASP GLU LEU SEQRES 19 A 249 TYR LYS LYS LEU ALA ALA ALA LEU GLU HIS HIS HIS HIS SEQRES 20 A 249 HIS HIS MODRES 6HUT CRO A 66 GLY CHROMOPHORE HET CRO A 66 35 HETNAM CRO {2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4- HETNAM 2 CRO HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1- HETNAM 3 CRO YL}ACETIC ACID HETSYN CRO PEPTIDE DERIVED CHROMOPHORE FORMUL 1 CRO C15 H17 N3 O5 FORMUL 2 HOH *211(H2 O) HELIX 1 AA1 LYS A 3 THR A 9 5 7 HELIX 2 AA2 PRO A 56 VAL A 61 5 6 HELIX 3 AA3 VAL A 68 SER 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 HELIX 6 AA6 LYS A 156 ASN A 159 5 4 HELIX 7 AA7 MET A 233 LEU A 244 1 12 SHEET 1 AA112 VAL A 12 VAL A 22 0 SHEET 2 AA112 HIS A 25 ASP A 36 -1 O PHE A 27 N GLY A 20 SHEET 3 AA112 LYS A 41 CYS A 48 -1 O ILE A 47 N ARG A 30 SHEET 4 AA112 HIS A 217 ALA A 227 -1 O LEU A 220 N LEU A 44 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 HIS A 181 N PHE A 165 SHEET 9 AA112 TYR A 92 PHE A 100 -1 N VAL A 93 O THR A 186 SHEET 10 AA112 THR A 105 GLU A 115 -1 O TYR A 106 N ILE A 98 SHEET 11 AA112 THR A 118 ILE A 128 -1 O VAL A 120 N LYS A 113 SHEET 12 AA112 VAL A 12 VAL A 22 1 N ASP A 21 O GLY A 127 LINK C LEU A 64 N1 CRO A 66 1555 1555 1.36 LINK C3 CRO A 66 N VAL A 68 1555 1555 1.49 CISPEP 1 MET A 88 PRO A 89 0 6.87 CRYST1 52.160 63.370 69.210 90.00 90.00 90.00 P 21 21 21 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 0.019172 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015780 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014449 0.00000