HEADER LUMINESCENT PROTEIN 09-SEP-03 1QY3 TITLE CRYSTAL STRUCTURE OF PRECYCLIZED INTERMEDIATE FOR THE GREEN TITLE 2 FLUORESCENT PROTEIN R96A VARIANT (B) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GREEN-FLUORESCENT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-229; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEQUOREA VICTORIA; SOURCE 3 ORGANISM_TAXID: 6100; SOURCE 4 GENE: GFP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PKEN2 KEYWDS BETA BARREL, TRAPPED INTERMEDIATE, CHROMOPHORE, LUMINESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.P.BARONDEAU,C.D.PUTNAM,C.J.KASSMANN,J.A.TAINER,E.D.GETZOFF REVDAT 5 23-AUG-23 1QY3 1 REMARK REVDAT 4 27-OCT-21 1QY3 1 SEQADV REVDAT 3 24-FEB-09 1QY3 1 VERSN REVDAT 2 14-OCT-03 1QY3 1 JRNL REVDAT 1 23-SEP-03 1QY3 0 JRNL AUTH D.P.BARONDEAU,C.D.PUTNAM,C.J.KASSMANN,J.A.TAINER,E.D.GETZOFF JRNL TITL MECHANISM AND ENERGETICS OF GREEN FLUORESCENT PROTEIN JRNL TITL 2 CHROMOPHORE SYNTHESIS REVEALED BY TRAPPED INTERMEDIATE JRNL TITL 3 STRUCTURES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 12111 2003 JRNL REFN ISSN 0027-8424 JRNL PMID 14523232 JRNL DOI 10.1073/PNAS.2133463100 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 506318.810 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 15381 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) : 0.203 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 749 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2243 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 137 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1791 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 209 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.28000 REMARK 3 B22 (A**2) : -4.14000 REMARK 3 B33 (A**2) : 9.41000 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) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.20 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) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.350 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) : 1.200 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.800 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.930 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.870 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 14.57 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 : PROTEIN.GFP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.GFP.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 1QY3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-SEP-03. REMARK 100 THE DEPOSITION ID IS D_1000020209. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54179 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 16081 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.460 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09900 REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29100 REMARK 200 FOR SHELL : 4.000 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: 1EMA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, MAGNESIUM CHLORIDE, HEPES, REMARK 280 PH 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 25.71650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.48800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.32500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.48800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.71650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.32500 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 1 REMARK 465 SER A 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QXT RELATED DB: PDB REMARK 900 PRECYCLIZATION INTERMEDIATE CRYSTAL STRUCTURE OF R96A GFP VARIANT REMARK 900 RELATED ID: 1QYF RELATED DB: PDB REMARK 900 RELATED ID: 1QYO RELATED DB: PDB REMARK 900 RELATED ID: 1QYQ RELATED DB: PDB DBREF 1QY3 A 1 229 UNP P42212 GFP_AEQVI 1 229 SEQADV 1QY3 LEU A 64 UNP P42212 PHE 64 ENGINEERED MUTATION SEQADV 1QY3 THR A 65 UNP P42212 SER 65 ENGINEERED MUTATION SEQADV 1QY3 ALA A 96 UNP P42212 ARG 96 ENGINEERED MUTATION SEQADV 1QY3 SER A 99 UNP P42212 PHE 99 ENGINEERED MUTATION SEQADV 1QY3 THR A 153 UNP P42212 MET 153 ENGINEERED MUTATION SEQADV 1QY3 ALA A 163 UNP P42212 VAL 163 ENGINEERED MUTATION SEQRES 1 A 229 MET SER LYS GLY GLU GLU LEU PHE THR GLY VAL VAL PRO SEQRES 2 A 229 ILE LEU VAL GLU LEU ASP GLY ASP VAL ASN GLY HIS LYS SEQRES 3 A 229 PHE SER VAL SER GLY GLU GLY GLU GLY ASP ALA THR TYR SEQRES 4 A 229 GLY LYS LEU THR LEU LYS PHE ILE CYS THR THR GLY LYS SEQRES 5 A 229 LEU PRO VAL PRO TRP PRO THR LEU VAL THR THR LEU THR SEQRES 6 A 229 TYR GLY VAL GLN CYS PHE SER ARG TYR PRO ASP HIS MET SEQRES 7 A 229 LYS GLN HIS ASP PHE PHE LYS SER ALA MET PRO GLU GLY SEQRES 8 A 229 TYR VAL GLN GLU ALA THR ILE SER PHE LYS ASP ASP GLY SEQRES 9 A 229 ASN TYR LYS THR ARG ALA GLU VAL LYS PHE GLU GLY ASP SEQRES 10 A 229 THR LEU VAL ASN ARG ILE GLU LEU LYS GLY ILE ASP PHE SEQRES 11 A 229 LYS GLU ASP GLY ASN ILE LEU GLY HIS LYS LEU GLU TYR SEQRES 12 A 229 ASN TYR ASN SER HIS ASN VAL TYR ILE THR ALA ASP LYS SEQRES 13 A 229 GLN LYS ASN GLY ILE LYS ALA ASN PHE LYS ILE ARG HIS SEQRES 14 A 229 ASN ILE GLU ASP GLY SER VAL GLN LEU ALA ASP HIS TYR SEQRES 15 A 229 GLN GLN ASN THR PRO ILE GLY ASP GLY PRO VAL LEU LEU SEQRES 16 A 229 PRO ASP ASN HIS TYR LEU SER THR GLN SER ALA LEU SER SEQRES 17 A 229 LYS ASP PRO ASN GLU LYS ARG ASP HIS MET VAL LEU LEU SEQRES 18 A 229 GLU PHE VAL THR ALA ALA GLY ILE FORMUL 2 HOH *209(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 SHEET 1 A12 VAL A 12 VAL A 22 0 SHEET 2 A12 HIS A 25 ASP A 36 -1 O GLY A 31 N VAL A 16 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 SER A 202 O THR A 225 SHEET 6 A12 HIS A 148 ASP A 155 -1 N HIS A 148 O THR A 203 SHEET 7 A12 GLY A 160 ASN A 170 -1 O LYS A 162 N THR A 153 SHEET 8 A12 VAL A 176 PRO A 187 -1 O HIS A 181 N PHE A 165 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 0.42 CRYST1 51.433 62.650 70.976 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 0.019443 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015962 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014089 0.00000