PDB Short entry for 1OXF HEADER LUMINESCENT PROTEIN 02-APR-03 1OXF TITLE EXPANSION OF THE GENETIC CODE ENABLES DESIGN OF A NOVEL "GOLD" CLASS TITLE 2 OF GREEN FLUORESCENT PROTEINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYAN FLUORESCENT PROTEIN CFP; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CFP MARKER PLASMID PWM1009; SOURCE 3 ORGANISM_TAXID: 141850; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GREEN FLUORESCENT PROTEIN, CHROMOPHORE, AMINO ACID INCORPORATION, KEYWDS 2 TRYPTOPHAN, GENETIC CODE, LUMINESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.HYUN BAE,M.RUBINI,G.JUNG,G.WIEGAND,M.H.SEIFERT,M.K.AZIM,J.S.KIM, AUTHOR 2 A.ZUMBUSCH,T.A.HOLAK,L.MORODER,R.HUBER,N.BUDISA REVDAT 6 15-NOV-23 1OXF 1 LINK ATOM REVDAT 5 21-DEC-22 1OXF 1 SEQADV LINK REVDAT 4 31-JAN-18 1OXF 1 REMARK REVDAT 3 12-MAY-09 1OXF 1 REMARK SEQADV REVDAT 2 24-FEB-09 1OXF 1 VERSN REVDAT 1 02-DEC-03 1OXF 0 JRNL AUTH J.HYUN BAE,M.RUBINI,G.JUNG,G.WIEGAND,M.H.SEIFERT,M.K.AZIM, JRNL AUTH 2 J.S.KIM,A.ZUMBUSCH,T.A.HOLAK,L.MORODER,R.HUBER,N.BUDISA JRNL TITL EXPANSION OF THE GENETIC CODE ENABLES DESIGN OF A NOVEL JRNL TITL 2 "GOLD" CLASS OF GREEN FLUORESCENT PROTEINS JRNL REF J.MOL.BIOL. V. 328 1071 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12729742 JRNL DOI 10.1016/S0022-2836(03)00364-4 REMARK 2 REMARK 2 RESOLUTION. 1.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.6 REMARK 3 NUMBER OF REFLECTIONS : 23827 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2346 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.69 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3199 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 345 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1751 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 94 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.40000 REMARK 3 B22 (A**2) : 0.98000 REMARK 3 B33 (A**2) : 1.42000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 3.920 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.51 REMARK 3 BSOL : 64.01 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PRO_4CRO_4IND.PAR REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PRO_4CRO_4IND.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OXF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000018771. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MPG/DESY, HAMBURG REMARK 200 BEAMLINE : BW6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.05 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24503 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 7.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.9 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 <I/SIGMA(I)> 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: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1000, PH 7.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 25K, TEMPERATURE 298.0K 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 25.79550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.50000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.41200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.50000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.79550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.41200 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 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 SER A 2 OG REMARK 470 LYS A 3 CG CD CE NZ REMARK 470 GLU A 5 CG CD OE1 OE2 REMARK 470 GLU A 6 CG CD OE1 OE2 REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 LYS A 79 CG CD CE NZ REMARK 470 GLN A 80 CG CD OE1 NE2 REMARK 470 GLU A 132 CG CD OE1 OE2 REMARK 470 LYS A 156 CG CD CE NZ REMARK 470 GLN A 157 CG CD OE1 NE2 REMARK 470 LYS A 158 CG CD CE NZ REMARK 470 GLU A 172 CG CD OE1 OE2 REMARK 470 ASP A 190 CG OD1 OD2 REMARK 470 GLN A 204 CG CD OE1 NE2 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 21 111.17 -160.16 REMARK 500 ASN A 144 -169.36 -161.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EMB RELATED DB: PDB REMARK 900 GFP VARIANT REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 65THR, 66TRP AND 67GLY ARE REMARK 999 MODIFIED TO MAKE THE CHROMOPHORE 5ZA66 DBREF 1OXF A 2 228 GB 11321072 AAG34040 2 228 SEQADV 1OXF 5ZA A 66 GB 11321072 THR 65 CHROMOPHORE SEQADV 1OXF 5ZA A 66 GB 11321072 TRP 66 CHROMOPHORE SEQADV 1OXF 5ZA A 66 GB 11321072 GLY 67 CHROMOPHORE SEQRES 1 A 225 SER LYS GLY GLU GLU LEU PHE THR GLY VAL VAL PRO ILE SEQRES 2 A 225 LEU VAL GLU LEU ASP GLY ASP VAL ASN GLY HIS LYS PHE SEQRES 3 A 225 SER VAL SER GLY GLU GLY GLU GLY ASP ALA THR TYR GLY SEQRES 4 A 225 LYS LEU THR LEU LYS PHE ILE CYS THR THR GLY LYS LEU SEQRES 5 A 225 PRO VAL PRO 4IN PRO THR LEU VAL THR THR LEU 5ZA VAL SEQRES 6 A 225 GLN CYS PHE SER ARG TYR PRO ASP HIS MET LYS GLN HIS SEQRES 7 A 225 ASP PHE PHE LYS SER ALA MET PRO GLU GLY TYR VAL GLN SEQRES 8 A 225 GLU ARG THR ILE PHE PHE LYS ASP ASP GLY ASN TYR LYS SEQRES 9 A 225 THR ARG ALA GLU VAL LYS PHE GLU GLY ASP THR LEU VAL SEQRES 10 A 225 ASN ARG ILE GLU LEU LYS GLY ILE ASP PHE LYS GLU ASP SEQRES 11 A 225 GLY ASN ILE LEU GLY HIS LYS LEU GLU TYR ASN TYR ILE SEQRES 12 A 225 SER HIS ASN VAL TYR ILE THR ALA ASP LYS GLN LYS ASN SEQRES 13 A 225 GLY ILE LYS ALA ASN PHE LYS ILE ARG HIS ASN ILE GLU SEQRES 14 A 225 ASP GLY SER VAL GLN LEU ALA ASP HIS TYR GLN GLN ASN SEQRES 15 A 225 THR PRO ILE GLY ASP GLY PRO VAL LEU LEU PRO ASP ASN SEQRES 16 A 225 HIS TYR LEU SER THR GLN SER ALA LEU SER LYS ASP PRO SEQRES 17 A 225 ASN GLU LYS ARG ASP HIS MET VAL LEU LEU GLU PHE VAL SEQRES 18 A 225 THR ALA ALA GLY MODRES 1OXF 4IN A 57 TRP 4-AMINO-L-TRYPTOPHAN MODRES 1OXF 5ZA A 66 THR MODRES 1OXF 5ZA A 66 TRP MODRES 1OXF 5ZA A 66 GLY HET 4IN A 57 15 HET 5ZA A 66 25 HETNAM 4IN 4-AMINO-L-TRYPTOPHAN HETNAM 5ZA (5Z)-2-[(1S,2R)-1-AMINO-2-HYDROXYPROPYL]-5-[(4-AMINO- HETNAM 2 5ZA 1H-INDOL-3-YL)METHYLENE]-3-(2-HYDROXYETHYL)-3,5- HETNAM 3 5ZA DIHYDRO-4H-IMIDAZOL-4-ONE HETSYN 4IN 2-AMINO-3-(4-AMINO-1H-INDOL-3-YL)PROPANOIC ACID FORMUL 1 4IN C11 H13 N3 O2 FORMUL 1 5ZA C17 H19 N5 O4 FORMUL 2 HOH *94(H2 O) HELIX 1 1 GLY A 4 THR A 9 5 6 HELIX 2 2 PRO A 56 VAL A 61 5 6 HELIX 3 3 VAL A 68 SER A 72 5 5 HELIX 4 4 PRO A 75 HIS A 81 5 7 HELIX 5 5 ASP A 82 ALA A 87 1 6 HELIX 6 6 LYS A 156 ASN A 159 5 4 SHEET 1 A12 VAL A 12 VAL A 22 0 SHEET 2 A12 HIS A 25 ASP A 36 -1 O PHE A 27 N GLY A 20 SHEET 3 A12 LYS A 41 CYS A 48 -1 O ILE A 47 N SER A 30 SHEET 4 A12 HIS A 217 ALA A 227 -1 O LEU A 220 N LEU A 44 SHEET 5 A12 HIS A 199 SER A 208 -1 N GLN A 204 O PHE A 223 SHEET 6 A12 ASN A 149 ASP A 155 -1 N ILE A 152 O HIS A 199 SHEET 7 A12 GLY A 160 ASN A 170 -1 O GLY A 160 N ASP A 155 SHEET 8 A12 VAL A 176 PRO A 187 -1 O GLN A 183 N ALA A 163 SHEET 9 A12 TYR A 92 PHE A 100 -1 N VAL A 93 O THR A 186 SHEET 10 A12 ASN A 105 GLU A 115 -1 O VAL A 112 N TYR A 92 SHEET 11 A12 THR A 118 ILE A 128 -1 O VAL A 120 N LYS A 113 SHEET 12 A12 VAL A 12 VAL A 22 1 N GLU A 17 O ILE A 123 LINK C PRO A 56 N 4IN A 57 1555 1555 1.33 LINK C 4IN A 57 N PRO A 58 1555 1555 1.35 LINK C LEU A 64 N1 5ZA A 66 1555 1555 1.53 LINK C3 5ZA A 66 N VAL A 68 1555 1555 1.55 CISPEP 1 MET A 88 PRO A 89 0 0.31 CRYST1 51.591 62.824 65.000 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 0.019383 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015917 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015385 0.00000