HEADER LUMINESCENT PROTEIN 08-JAN-05 1YHI TITLE UNCYCLIZED PRECURSOR STRUCTURE OF S65A Y66S R96A GFP VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: GREEN FLUORESCENT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: S65A, Y66S, R96A, F99S, M153T, V163A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEQUOREA VICTORIA; SOURCE 3 ORGANISM_TAXID: 6100; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RIL; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS CHROMOPHORE, UNCYCLIZED, LUMINESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.P.BARONDEAU,C.J.KASSMANN,J.A.TAINER,E.D.GETZOFF REVDAT 5 14-FEB-24 1YHI 1 REMARK REVDAT 4 20-OCT-21 1YHI 1 SEQADV REVDAT 3 11-OCT-17 1YHI 1 REMARK REVDAT 2 24-FEB-09 1YHI 1 VERSN REVDAT 1 15-FEB-05 1YHI 0 JRNL AUTH D.P.BARONDEAU,C.J.KASSMANN,J.A.TAINER,E.D.GETZOFF JRNL TITL UNDERSTANDING GFP CHROMOPHORE BIOSYNTHESIS: CONTROLLING JRNL TITL 2 BACKBONE CYCLIZATION AND MODIFYING POST-TRANSLATIONAL JRNL TITL 3 CHEMISTRY(,). JRNL REF BIOCHEMISTRY V. 44 1960 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15697221 JRNL DOI 10.1021/BI0479205 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.P.BARONDEAU,C.D.PUTNAM,C.J.KASSMANN,J.A.TAINER,E.D.GETZOFF REMARK 1 TITL MECHANISM AND ENERGETICS OF GREEN FLUORESCENT PROTEIN REMARK 1 TITL 2 CHROMOPHORE SYNTHESIS REVEALED BY TRAPPED INTERMEDIATE REMARK 1 TITL 3 STRUCTURES REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 100 12111 2003 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 18337 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 935 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1783 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 125 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.87400 REMARK 3 B22 (A**2) : 4.30900 REMARK 3 B33 (A**2) : -8.18300 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YHI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031516. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.984 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19956 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.31400 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, 50 MM MGCL2, 50 MM HEPES, PH REMARK 280 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 27.26450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.23600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.12800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.23600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.26450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.12800 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 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 0 REMARK 465 ALA A 1 REMARK 465 ILE A 229 REMARK 465 THR A 230 REMARK 465 HIS A 231 REMARK 465 GLY A 232 REMARK 465 MET A 233 REMARK 465 ASP A 234 REMARK 465 GLU A 235 REMARK 465 LEU A 236 REMARK 465 TYR A 237 REMARK 465 LYS A 238 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YHG RELATED DB: PDB REMARK 900 UNCYCLIZED PRECURSOR STRUCTURE OF S65G Y66S V68G VARIANT REMARK 900 RELATED ID: 1YHH RELATED DB: PDB REMARK 900 UNCYCLIZED PRECURSOR STRUCTURE OF S65A Y66S G67A VARIANT REMARK 900 RELATED ID: 1YJ2 RELATED DB: PDB REMARK 900 RELATED ID: 1YJF RELATED DB: PDB DBREF 1YHI A 2 238 UNP P42212 GFP_AEQVI 2 238 SEQADV 1YHI MET A 0 UNP P42212 INITIATING METHIONINE SEQADV 1YHI ALA A 1 UNP P42212 INSERTION SEQADV 1YHI ALA A 65 UNP P42212 SER 65 ENGINEERED MUTATION SEQADV 1YHI SER A 66 UNP P42212 TYR 66 ENGINEERED MUTATION SEQADV 1YHI ALA A 96 UNP P42212 ARG 96 ENGINEERED MUTATION SEQADV 1YHI SER A 99 UNP P42212 PHE 99 ENGINEERED MUTATION SEQADV 1YHI THR A 153 UNP P42212 MET 153 ENGINEERED MUTATION SEQADV 1YHI ALA A 163 UNP P42212 VAL 163 ENGINEERED MUTATION SEQRES 1 A 239 MET ALA SER LYS GLY GLU GLU LEU PHE THR GLY VAL VAL SEQRES 2 A 239 PRO ILE LEU VAL GLU LEU ASP GLY ASP VAL ASN GLY HIS SEQRES 3 A 239 LYS PHE SER VAL SER GLY GLU GLY GLU GLY ASP ALA THR SEQRES 4 A 239 TYR GLY LYS LEU THR LEU LYS PHE ILE CYS THR THR GLY SEQRES 5 A 239 LYS LEU PRO VAL PRO TRP PRO THR LEU VAL THR THR PHE SEQRES 6 A 239 ALA SER GLY VAL GLN CYS PHE SER ARG TYR PRO ASP HIS SEQRES 7 A 239 MET LYS GLN HIS ASP PHE PHE LYS SER ALA MET PRO GLU SEQRES 8 A 239 GLY TYR VAL GLN GLU ALA THR ILE SER PHE LYS ASP ASP SEQRES 9 A 239 GLY ASN TYR LYS THR ARG ALA GLU VAL LYS PHE GLU GLY SEQRES 10 A 239 ASP THR LEU VAL ASN ARG ILE GLU LEU LYS GLY ILE ASP SEQRES 11 A 239 PHE LYS GLU ASP GLY ASN ILE LEU GLY HIS LYS LEU GLU SEQRES 12 A 239 TYR ASN TYR ASN SER HIS ASN VAL TYR ILE THR ALA ASP SEQRES 13 A 239 LYS GLN LYS ASN GLY ILE LYS ALA ASN PHE LYS ILE ARG SEQRES 14 A 239 HIS ASN ILE GLU ASP GLY SER VAL GLN LEU ALA ASP HIS SEQRES 15 A 239 TYR GLN GLN ASN THR PRO ILE GLY ASP GLY PRO VAL LEU SEQRES 16 A 239 LEU PRO ASP ASN HIS TYR LEU SER THR GLN SER ALA LEU SEQRES 17 A 239 SER LYS ASP PRO ASN GLU LYS ARG ASP HIS MET VAL LEU SEQRES 18 A 239 LEU GLU PHE VAL THR ALA ALA GLY ILE THR HIS GLY MET SEQRES 19 A 239 ASP GLU LEU TYR LYS FORMUL 2 HOH *125(H2 O) HELIX 1 1 LYS A 3 THR A 9 5 7 HELIX 2 2 PRO A 56 THR A 59 5 4 HELIX 3 3 LEU A 60 GLY A 67 1 8 HELIX 4 4 VAL A 68 SER A 72 5 5 HELIX 5 5 PRO A 75 HIS A 81 5 7 HELIX 6 6 ASP A 82 ALA A 87 1 6 HELIX 7 7 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 MET A 218 N PHE A 46 SHEET 5 A12 HIS A 199 SER A 208 -1 N SER A 202 O THR A 225 SHEET 6 A12 HIS A 148 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 ALA A 179 N ILE A 167 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 ALA A 110 N GLN A 94 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 ASP A 21 O GLY A 127 CISPEP 1 MET A 88 PRO A 89 0 0.06 CRYST1 54.529 64.256 70.472 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 0.018339 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015563 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014190 0.00000