HEADER LUMINESCENT PROTEIN 14-NOV-12 3W1C TITLE STRUCTURE OF A PRESSURE SENSITIVE YFP VARIANT YFP-G1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GREEN FLUORESCENT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSSETA2 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PAL7 KEYWDS BETA BARREL, FLUORESCENT PROTEIN, LUMINESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.IMADA,K.YOSHIZAWA,M.KINOSHITA,T.M.WATANABE REVDAT 3 06-DEC-23 3W1C 1 REMARK REVDAT 2 08-NOV-23 3W1C 1 SEQADV LINK REVDAT 1 02-OCT-13 3W1C 0 JRNL AUTH T.M.WATANABE,K.IMADA,K.YOSHIZAWA,M.NISHIYAMA,C.KATO,F.ABE, JRNL AUTH 2 T.J.MORIKAWA,M.KINOSHITA,H.FUJITA,T.YANAGIDA JRNL TITL GLYCINE INSERTION MAKES YELLOW FLUORESCENT PROTEIN SENSITIVE JRNL TITL 2 TO HYDROSTATIC PRESSURE. JRNL REF PLOS ONE V. 8 73212 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 24014139 JRNL DOI 10.1371/JOURNAL.PONE.0073212 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1133833.320 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 54393 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) : 0.196 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2765 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.38 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 8252 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 465 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1832 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13000 REMARK 3 B22 (A**2) : -1.86000 REMARK 3 B33 (A**2) : 1.98000 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) : 0.15 REMARK 3 ESD FROM SIGMAA (A) : 0.10 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) : 0.16 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.10 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.870 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) : 0.980 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.510 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.790 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.630 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.45 REMARK 3 BSOL : 44.39 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_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : CR2_2.PARAM REMARK 3 PARAMETER FILE 4 : CIS_PEPTIDE_MAY11.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : CR2_2.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3W1C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000095761. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 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 : DOUBLE-CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54434 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 17.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.46900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3DQ7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13-15% PEG 8000, 0.1M BIS-TRIS BUFFER, REMARK 280 350-400MM CALCIUM ACETATE , PH 6.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K 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 25.59500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.92000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.38000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.92000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.59500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.38000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 LEU A 232 REMARK 465 GLY A 233 REMARK 465 MET A 234 REMARK 465 ASP A 235 REMARK 465 GLU A 236 REMARK 465 LEU A 237 REMARK 465 TYR A 238 REMARK 465 LYS A 239 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 884 O HOH A 894 2.03 REMARK 500 OD2 ASP A 102 O HOH A 910 2.10 REMARK 500 OE1 GLU A 132 O HOH A 501 2.13 REMARK 500 O HOH A 822 O HOH A 884 2.14 REMARK 500 O HOH A 677 O HOH A 884 2.14 REMARK 500 O GLN A 69 O HOH A 712 2.16 REMARK 500 O SER A 86 O HOH A 855 2.17 REMARK 500 O HOH A 666 O HOH A 804 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3W1D RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE SER 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 REMARK 999 AND GLY 67 CONSTITUTE THE CHROMOPHORE CR2 66. DBREF 3W1C A 2 239 UNP P42212 GFP_AEQVI 2 238 SEQADV 3W1C VAL A 1 UNP P42212 EXPRESSION TAG SEQADV 3W1C CR2 A 66 UNP P42212 SER 65 CHROMOPHORE SEQADV 3W1C CR2 A 66 UNP P42212 TYR 66 CHROMOPHORE SEQADV 3W1C CR2 A 66 UNP P42212 GLY 67 CHROMOPHORE SEQADV 3W1C LEU A 68 UNP P42212 VAL 68 ENGINEERED MUTATION SEQADV 3W1C ALA A 72 UNP P42212 SER 72 ENGINEERED MUTATION SEQADV 3W1C GLY A 145 UNP P42212 INSERTION SEQADV 3W1C TYR A 204 UNP P42212 THR 203 ENGINEERED MUTATION SEQADV 3W1C LEU A 232 UNP P42212 HIS 231 ENGINEERED MUTATION SEQRES 1 A 237 VAL SER LYS GLY GLU GLU LEU PHE THR GLY VAL VAL PRO SEQRES 2 A 237 ILE LEU VAL GLU LEU ASP GLY ASP VAL ASN GLY HIS LYS SEQRES 3 A 237 PHE SER VAL SER GLY GLU GLY GLU GLY ASP ALA THR TYR SEQRES 4 A 237 GLY LYS LEU THR LEU LYS PHE ILE CYS THR THR GLY LYS SEQRES 5 A 237 LEU PRO VAL PRO TRP PRO THR LEU VAL THR THR PHE CR2 SEQRES 6 A 237 LEU GLN CYS PHE ALA ARG TYR PRO ASP HIS MET LYS GLN SEQRES 7 A 237 HIS ASP PHE PHE LYS SER ALA MET PRO GLU GLY TYR VAL SEQRES 8 A 237 GLN GLU ARG THR ILE PHE PHE LYS ASP ASP GLY ASN TYR SEQRES 9 A 237 LYS THR ARG ALA GLU VAL LYS PHE GLU GLY ASP THR LEU SEQRES 10 A 237 VAL ASN ARG ILE GLU LEU LYS GLY ILE ASP PHE LYS GLU SEQRES 11 A 237 ASP GLY ASN ILE LEU GLY HIS LYS LEU GLU TYR ASN GLY SEQRES 12 A 237 TYR ASN SER HIS ASN VAL TYR ILE MET ALA ASP LYS GLN SEQRES 13 A 237 LYS ASN GLY ILE LYS VAL ASN PHE LYS ILE ARG HIS ASN SEQRES 14 A 237 ILE GLU ASP GLY SER VAL GLN LEU ALA ASP HIS TYR GLN SEQRES 15 A 237 GLN ASN THR PRO ILE GLY ASP GLY PRO VAL LEU LEU PRO SEQRES 16 A 237 ASP ASN HIS TYR LEU SER TYR GLN SER ALA LEU SER LYS SEQRES 17 A 237 ASP PRO ASN GLU LYS ARG ASP HIS MET VAL LEU LEU GLU SEQRES 18 A 237 PHE VAL THR ALA ALA GLY ILE THR LEU GLY MET ASP GLU SEQRES 19 A 237 LEU TYR LYS MODRES 3W1C CR2 A 66 GLY MODRES 3W1C CR2 A 66 TYR MODRES 3W1C CR2 A 66 GLY HET CR2 A 66 19 HETNAM CR2 {(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]- HETNAM 2 CR2 5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID HETSYN CR2 CHROMOPHORE (GLY-TYR-GLY) FORMUL 1 CR2 C13 H13 N3 O4 FORMUL 2 HOH *410(H2 O) HELIX 1 1 SER A 2 LEU A 7 1 6 HELIX 2 2 ALA A 37 TYR A 39 5 3 HELIX 3 3 PRO A 56 VAL A 61 5 6 HELIX 4 4 LEU A 68 ALA 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 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 218 ALA A 228 -1 O MET A 219 N PHE A 46 SHEET 5 A12 HIS A 200 SER A 209 -1 N SER A 203 O THR A 226 SHEET 6 A12 VAL A 151 ASP A 156 -1 N ILE A 153 O HIS A 200 SHEET 7 A12 GLY A 161 ASN A 171 -1 O LYS A 163 N MET A 154 SHEET 8 A12 VAL A 177 PRO A 188 -1 O GLN A 184 N VAL A 164 SHEET 9 A12 TYR A 92 PHE A 100 -1 N GLU A 95 O GLN A 185 SHEET 10 A12 ASN A 105 GLU A 115 -1 O TYR A 106 N ILE A 98 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 LINK C PHE A 64 N1 CR2 A 66 1555 1555 1.34 LINK C3 CR2 A 66 N LEU A 68 1555 1555 1.33 CISPEP 1 MET A 88 PRO A 89 0 2.01 CRYST1 51.190 62.760 69.840 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 0.019535 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015934 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014318 0.00000