HEADER LUMINESCENT PROTEIN 03-MAY-06 2GW4 TITLE CRYSTAL STRUCTURE OF STONY CORAL FLUORESCENT PROTEIN KAEDE, RED FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: KAEDE; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: KAEDE; COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRACHYPHYLLIA GEOFFROYI; SOURCE 3 ORGANISM_TAXID: 196280; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PRSETB; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: TRACHYPHYLLIA GEOFFROYI; SOURCE 11 ORGANISM_TAXID: 196280; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PRSETB KEYWDS BETA BARREL, LUMINESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.HAYASHI,H.MIZUNO,A.MIYAWAKO,M.IKURA REVDAT 6 15-NOV-23 2GW4 1 COMPND REMARK SEQADV SEQRES REVDAT 6 2 1 HETNAM HETSYN FORMUL LINK REVDAT 6 3 1 ATOM REVDAT 5 13-JUL-11 2GW4 1 VERSN REVDAT 4 07-JUL-09 2GW4 1 SEQADV REVDAT 3 24-FEB-09 2GW4 1 VERSN REVDAT 2 20-NOV-07 2GW4 1 JRNL REVDAT 1 08-MAY-07 2GW4 0 JRNL AUTH I.HAYASHI,H.MIZUNO,K.I.TONG,T.FURUTA,F.TANAKA,M.YOSHIMURA, JRNL AUTH 2 A.MIYAWAKI,M.IKURA JRNL TITL CRYSTALLOGRAPHIC EVIDENCE FOR WATER-ASSISTED PHOTO-INDUCED JRNL TITL 2 PEPTIDE CLEAVAGE IN THE STONY CORAL FLUORESCENT PROTEIN JRNL TITL 3 KAEDE. JRNL REF J.MOL.BIOL. V. 372 918 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17692334 JRNL DOI 10.1016/J.JMB.2007.06.037 REMARK 2 REMARK 2 RESOLUTION. 1.60 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 67774 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 3552 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 437 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 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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 : PROTEIN_KR.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2GW4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000037620. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : MOSFLM REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68143 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR 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 (%): 52.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M LI2SO4, 2MM NICL2, 0.1M TRIS, PH 8, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 66.09850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.58450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 66.09850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.58450 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A TETRAMER. 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 28350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -180.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 242.69699 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 48.91599 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 ALA A -1 REMARK 465 PRO B 221 REMARK 465 ASP B 222 REMARK 465 ASN B 223 REMARK 465 VAL B 224 REMARK 465 LYS B 225 REMARK 465 ALA C -1 REMARK 465 PRO D 221 REMARK 465 ASP D 222 REMARK 465 ASN D 223 REMARK 465 VAL D 224 REMARK 465 LYS D 225 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 MET A 1 C CB REMARK 480 LEU A 3 CD1 CD2 REMARK 480 LYS A 5 CE REMARK 480 GLU A 7 C CD OE1 REMARK 480 LYS A 9 CD CE NZ REMARK 480 LEU A 13 CD1 CD2 REMARK 480 GLU A 15 CG CD REMARK 480 GLY A 16 C REMARK 480 GLN A 22 C CD OE1 NE2 REMARK 480 GLU A 26 CD OE1 OE2 REMARK 480 ASP A 28 CG OD1 OD2 REMARK 480 GLU A 35 CG CD REMARK 480 MET A 40 CE REMARK 480 ASP A 41 CG REMARK 480 LEU A 42 CD1 REMARK 480 GLU A 46 CG CD REMARK 480 ALA A 48 CB REMARK 480 PRO A 49 CA C REMARK 480 PHE A 52 C REMARK 480 NFA A 61 C REMARK 480 LYS B 70 CE NZ REMARK 480 ASP B 73 CG OD1 OD2 REMARK 480 ASP B 77 C CG REMARK 480 SER B 82 C REMARK 480 LYS B 85 C CE NZ REMARK 480 PHE B 87 C REMARK 480 GLU B 96 CD REMARK 480 ASP B 97 CG REMARK 480 ASN B 105 CG REMARK 480 ASP B 106 CG REMARK 480 LYS B 110 CB CG CD CE NZ REMARK 480 GLY B 111 C REMARK 480 ASP B 112 C CG REMARK 480 ARG B 119 CZ NH1 REMARK 480 ASP B 121 CG REMARK 480 VAL B 123 C REMARK 480 ASN B 128 CG REMARK 480 LYS B 134 CE NZ REMARK 480 LYS B 135 CE REMARK 480 LYS B 138 NZ REMARK 480 GLU B 140 C CD REMARK 480 TYR B 147 CZ REMARK 480 LEU B 148 CD2 REMARK 480 ARG B 149 CG CZ REMARK 480 ASP B 150 CG REMARK 480 ASP B 156 CG REMARK 480 LYS B 164 C CD CE NZ REMARK 480 GLY B 165 C REMARK 480 ASP B 166 C CB CG REMARK 480 ASP B 172 CG REMARK 480 ARG B 174 CZ REMARK 480 LYS B 178 CD CE REMARK 480 ARG B 180 C CD CZ REMARK 480 GLU B 182 CD OE1 REMARK 480 LYS B 185 C CE NZ REMARK 480 LEU B 186 CD1 REMARK 480 PRO B 187 CG REMARK 480 TYR B 189 C REMARK 480 HIS B 190 C REMARK 480 ASP B 193 CG REMARK 480 SER B 197 OG REMARK 480 ARG B 200 CZ NH2 REMARK 480 HIS B 201 C REMARK 480 ASP B 202 C CG REMARK 480 LYS B 203 C CG CD CE NZ REMARK 480 ASP B 204 CG OD2 REMARK 480 TYR B 205 C REMARK 480 GLU B 207 CD OE2 REMARK 480 GLU B 212 CD REMARK 480 ALA B 216 C REMARK 480 MET C 1 C CB CE REMARK 480 LEU C 3 CD1 CD2 REMARK 480 LYS C 5 CE REMARK 480 LYS C 9 CD CE NZ REMARK 480 LYS C 11 CD CE NZ REMARK 480 LEU C 13 CD1 CD2 REMARK 480 GLU C 15 CG CD REMARK 480 GLY C 16 C REMARK 480 ASN C 17 C REMARK 480 GLY C 20 C REMARK 480 HIS C 21 NE2 REMARK 480 VAL C 24 C REMARK 480 ASP C 28 CG OD1 OD2 REMARK 480 GLU C 35 CG CD REMARK 480 SER C 39 C REMARK 480 MET C 40 CE REMARK 480 LEU C 42 CD1 REMARK 480 LYS C 45 C CE NZ REMARK 480 GLU C 46 CG CD REMARK 480 ALA C 48 C CB REMARK 480 PRO C 49 CA C CD REMARK 480 PHE C 52 C REMARK 480 NFA C 61 C REMARK 480 LYS D 70 CE NZ REMARK 480 ASP D 73 CG OD1 OD2 REMARK 480 ASP D 77 CG REMARK 480 PRO D 84 C CD REMARK 480 LYS D 85 C NZ REMARK 480 PHE D 87 C REMARK 480 SER D 92 C REMARK 480 MET D 94 CG CE REMARK 480 PHE D 95 C REMARK 480 ASN D 105 CG REMARK 480 ASP D 106 C CG REMARK 480 GLY D 111 C REMARK 480 LYS D 117 CG CD CE NZ REMARK 480 ARG D 119 CZ NH1 REMARK 480 ASP D 121 CG REMARK 480 PRO D 127 CG REMARK 480 ASN D 128 CG REMARK 480 GLN D 133 CD REMARK 480 LYS D 134 NZ REMARK 480 LYS D 135 CE REMARK 480 GLU D 140 C CD REMARK 480 GLU D 144 CD REMARK 480 LEU D 148 CD2 REMARK 480 ARG D 149 CG CZ REMARK 480 ASP D 150 CG REMARK 480 LYS D 164 CD CE NZ REMARK 480 GLY D 165 C REMARK 480 ASP D 166 C CB CG REMARK 480 CYS D 171 C REMARK 480 ARG D 174 CZ REMARK 480 LYS D 178 CD CE REMARK 480 ARG D 180 CG CD CZ REMARK 480 GLN D 181 C CD REMARK 480 GLU D 182 CD OE1 REMARK 480 LYS D 185 CE NZ REMARK 480 GLY D 188 C REMARK 480 TYR D 189 C REMARK 480 ASP D 193 CG REMARK 480 SER D 197 OG REMARK 480 ARG D 200 CB CZ REMARK 480 ASP D 202 C CG REMARK 480 LYS D 203 C CG CD CE NZ REMARK 480 ASP D 204 CG OD2 REMARK 480 TYR D 205 C REMARK 480 ASN D 206 CG REMARK 480 GLU D 207 C CD OE2 REMARK 480 LYS D 209 CE NZ REMARK 480 ALA D 214 C REMARK 480 LEU D 220 CA CB CD1 CD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CE MET B 94 CE MET B 94 2756 2.10 REMARK 500 REMARK 500 REMARK: NULL 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 ARG B 66 0.24 -64.76 REMARK 500 SER B 82 27.05 -76.84 REMARK 500 SER D 82 24.97 -75.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI C 440 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 30 NZ REMARK 620 2 HIS A 32 NE2 93.5 REMARK 620 3 HOH A 458 O 80.3 170.6 REMARK 620 4 HOH A 463 O 159.0 102.4 82.1 REMARK 620 5 HOH A 479 O 95.1 90.8 96.8 98.2 REMARK 620 6 HOH C 486 O 90.1 87.1 85.9 77.3 174.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 438 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 484 O REMARK 620 2 HOH A 485 O 90.4 REMARK 620 3 LYS C 30 NZ 101.5 164.9 REMARK 620 4 HIS C 32 NE2 89.5 100.1 89.4 REMARK 620 5 HOH C 459 O 98.8 85.0 84.0 170.3 REMARK 620 6 HOH C 470 O 167.5 79.1 90.0 85.9 87.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 439 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 201 NE2 REMARK 620 2 HOH B 580 O 97.8 REMARK 620 3 HOH B 602 O 147.9 71.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI D 441 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 201 NE2 REMARK 620 2 HOH D 587 O 162.8 REMARK 620 3 HOH D 596 O 99.3 68.9 REMARK 620 4 HOH D 597 O 87.9 101.6 167.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 438 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 439 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI C 440 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI D 441 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GW3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STONY CORAL FLUORESCENT PROTEIN KAEDE, GREEN REMARK 900 FORM REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE RESIDUES HIS 62, TYR 63 AND GLY 64 CONSTITUTE THE REMARK 999 CHROMOPHORE CR8 DBREF 2GW4 A 1 61 GB 23503508 BAC20344 1 61 DBREF 2GW4 C 1 61 GB 23503508 BAC20344 1 61 DBREF 2GW4 B 63 224 GB 23503508 BAC20344 62 224 DBREF 2GW4 D 63 224 GB 23503508 BAC20344 62 224 SEQADV 2GW4 ALA A -1 GB 23503508 EXPRESSION TAG SEQADV 2GW4 PRO A 0 GB 23503508 EXPRESSION TAG SEQADV 2GW4 NFA A 61 GB 23503508 PHE 61 MODIFIED RESIDUE SEQADV 2GW4 ALA C -1 GB 23503508 EXPRESSION TAG SEQADV 2GW4 PRO C 0 GB 23503508 EXPRESSION TAG SEQADV 2GW4 NFA C 61 GB 23503508 PHE 61 MODIFIED RESIDUE SEQADV 2GW4 RC7 B 63 GB 23503508 HIS 62 CHROMOPHORE SEQADV 2GW4 RC7 B 63 GB 23503508 TYR 63 CHROMOPHORE SEQADV 2GW4 RC7 B 63 GB 23503508 GLY 64 CHROMOPHORE SEQADV 2GW4 RC7 D 63 GB 23503508 HIS 62 CHROMOPHORE SEQADV 2GW4 RC7 D 63 GB 23503508 TYR 63 CHROMOPHORE SEQADV 2GW4 RC7 D 63 GB 23503508 GLY 64 CHROMOPHORE SEQRES 1 A 63 ALA PRO MET SER LEU ILE LYS PRO GLU MET LYS ILE LYS SEQRES 2 A 63 LEU LEU MET GLU GLY ASN VAL ASN GLY HIS GLN PHE VAL SEQRES 3 A 63 ILE GLU GLY ASP GLY LYS GLY HIS PRO PHE GLU GLY LYS SEQRES 4 A 63 GLN SER MET ASP LEU VAL VAL LYS GLU GLY ALA PRO LEU SEQRES 5 A 63 PRO PHE ALA TYR ASP ILE LEU THR THR ALA NFA SEQRES 1 B 162 RC7 ASN ARG VAL PHE ALA LYS TYR PRO ASP HIS ILE PRO SEQRES 2 B 162 ASP TYR PHE LYS GLN SER PHE PRO LYS GLY PHE SER TRP SEQRES 3 B 162 GLU ARG SER LEU MET PHE GLU ASP GLY GLY VAL CYS ILE SEQRES 4 B 162 ALA THR ASN ASP ILE THR LEU LYS GLY ASP THR PHE PHE SEQRES 5 B 162 ASN LYS VAL ARG PHE ASP GLY VAL ASN PHE PRO PRO ASN SEQRES 6 B 162 GLY PRO VAL MET GLN LYS LYS THR LEU LYS TRP GLU ALA SEQRES 7 B 162 SER THR GLU LYS MET TYR LEU ARG ASP GLY VAL LEU THR SEQRES 8 B 162 GLY ASP ILE THR MET ALA LEU LEU LEU LYS GLY ASP VAL SEQRES 9 B 162 HIS TYR ARG CYS ASP PHE ARG THR THR TYR LYS SER ARG SEQRES 10 B 162 GLN GLU GLY VAL LYS LEU PRO GLY TYR HIS PHE VAL ASP SEQRES 11 B 162 HIS CYS ILE SER ILE LEU ARG HIS ASP LYS ASP TYR ASN SEQRES 12 B 162 GLU VAL LYS LEU TYR GLU HIS ALA VAL ALA HIS SER GLY SEQRES 13 B 162 LEU PRO ASP ASN VAL LYS SEQRES 1 C 63 ALA PRO MET SER LEU ILE LYS PRO GLU MET LYS ILE LYS SEQRES 2 C 63 LEU LEU MET GLU GLY ASN VAL ASN GLY HIS GLN PHE VAL SEQRES 3 C 63 ILE GLU GLY ASP GLY LYS GLY HIS PRO PHE GLU GLY LYS SEQRES 4 C 63 GLN SER MET ASP LEU VAL VAL LYS GLU GLY ALA PRO LEU SEQRES 5 C 63 PRO PHE ALA TYR ASP ILE LEU THR THR ALA NFA SEQRES 1 D 162 RC7 ASN ARG VAL PHE ALA LYS TYR PRO ASP HIS ILE PRO SEQRES 2 D 162 ASP TYR PHE LYS GLN SER PHE PRO LYS GLY PHE SER TRP SEQRES 3 D 162 GLU ARG SER LEU MET PHE GLU ASP GLY GLY VAL CYS ILE SEQRES 4 D 162 ALA THR ASN ASP ILE THR LEU LYS GLY ASP THR PHE PHE SEQRES 5 D 162 ASN LYS VAL ARG PHE ASP GLY VAL ASN PHE PRO PRO ASN SEQRES 6 D 162 GLY PRO VAL MET GLN LYS LYS THR LEU LYS TRP GLU ALA SEQRES 7 D 162 SER THR GLU LYS MET TYR LEU ARG ASP GLY VAL LEU THR SEQRES 8 D 162 GLY ASP ILE THR MET ALA LEU LEU LEU LYS GLY ASP VAL SEQRES 9 D 162 HIS TYR ARG CYS ASP PHE ARG THR THR TYR LYS SER ARG SEQRES 10 D 162 GLN GLU GLY VAL LYS LEU PRO GLY TYR HIS PHE VAL ASP SEQRES 11 D 162 HIS CYS ILE SER ILE LEU ARG HIS ASP LYS ASP TYR ASN SEQRES 12 D 162 GLU VAL LYS LEU TYR GLU HIS ALA VAL ALA HIS SER GLY SEQRES 13 D 162 LEU PRO ASP ASN VAL LYS MODRES 2GW4 NFA A 61 PHE PHENYLALANINE AMIDE MODRES 2GW4 RC7 B 63 HIS MODRES 2GW4 RC7 B 63 TYR MODRES 2GW4 RC7 B 63 GLY MODRES 2GW4 NFA C 61 PHE PHENYLALANINE AMIDE MODRES 2GW4 RC7 D 63 HIS MODRES 2GW4 RC7 D 63 TYR MODRES 2GW4 RC7 D 63 GLY HET NFA A 61 12 HET RC7 B 63 24 HET NFA C 61 12 HET RC7 D 63 24 HET NI A 438 1 HET NI B 439 1 HET NI C 440 1 HET NI D 441 1 HETNAM NFA PHENYLALANINE AMIDE HETNAM RC7 2-[(4Z)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-2-[(E)-2-(1H- HETNAM 2 RC7 IMIDAZOL-4-YL)ETHENYL]-5-OXIDANYLIDENE-IMIDAZOL-1- HETNAM 3 RC7 YL]ETHANOIC ACID HETNAM NI NICKEL (II) ION HETSYN RC7 RED CHROMOPHORE (HIS-TYR-GLY); {(2R)-4-(4- HETSYN 2 RC7 HYDROXYBENZYL)-2-[2-(1H-IMIDAZOL-4-YL)ETHYL]-5-OXO-2, HETSYN 3 RC7 5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID FORMUL 1 NFA 2(C9 H12 N2 O) FORMUL 2 RC7 2(C17 H14 N4 O4) FORMUL 5 NI 4(NI 2+) FORMUL 9 HOH *437(H2 O) HELIX 1 1 ALA A 53 NFA A 61 5 9 HELIX 2 2 ALA C 53 NFA C 61 5 9 SHEET 1 A13 THR B 136 TRP B 139 0 SHEET 2 A13 VAL B 152 LEU B 163 -1 O LEU B 162 N LEU B 137 SHEET 3 A13 VAL B 167 SER B 179 -1 O VAL B 167 N LEU B 163 SHEET 4 A13 PHE B 87 PHE B 95 -1 N SER B 88 O LYS B 178 SHEET 5 A13 VAL B 100 LYS B 110 -1 O CYS B 101 N LEU B 93 SHEET 6 A13 THR B 113 VAL B 123 -1 O PHE B 115 N THR B 108 SHEET 7 A13 MET A 8 VAL A 18 1 N LYS A 11 O PHE B 114 SHEET 8 A13 HIS A 21 HIS A 32 -1 O ILE A 25 N MET A 14 SHEET 9 A13 LYS A 37 GLU A 46 -1 O ASP A 41 N ASP A 28 SHEET 10 A13 GLU B 207 HIS B 217 -1 O VAL B 208 N LEU A 42 SHEET 11 A13 HIS B 190 HIS B 201 -1 N ASP B 193 O VAL B 215 SHEET 12 A13 SER B 142 ARG B 149 -1 N SER B 142 O HIS B 194 SHEET 13 A13 VAL B 152 LEU B 163 -1 O THR B 154 N TYR B 147 SHEET 1 B13 THR D 136 TRP D 139 0 SHEET 2 B13 VAL D 152 LEU D 163 -1 O LEU D 162 N LEU D 137 SHEET 3 B13 VAL D 167 SER D 179 -1 O VAL D 167 N LEU D 163 SHEET 4 B13 PHE D 87 PHE D 95 -1 N SER D 88 O LYS D 178 SHEET 5 B13 VAL D 100 LYS D 110 -1 O CYS D 101 N LEU D 93 SHEET 6 B13 THR D 113 VAL D 123 -1 O ASP D 121 N ILE D 102 SHEET 7 B13 MET C 8 VAL C 18 1 N LYS C 11 O PHE D 114 SHEET 8 B13 HIS C 21 HIS C 32 -1 O ILE C 25 N MET C 14 SHEET 9 B13 LYS C 37 GLU C 46 -1 O LYS C 37 N HIS C 32 SHEET 10 B13 GLU D 207 HIS D 217 -1 O VAL D 208 N LEU C 42 SHEET 11 B13 HIS D 190 HIS D 201 -1 N ASP D 193 O VAL D 215 SHEET 12 B13 SER D 142 ARG D 149 -1 N GLU D 144 O VAL D 192 SHEET 13 B13 VAL D 152 LEU D 163 -1 O THR D 154 N TYR D 147 LINK C ALA A 60 N NFA A 61 1555 1555 1.33 LINK C3 RC7 B 63 N ASN B 65 1555 1555 1.33 LINK C ALA C 60 N NFA C 61 1555 1555 1.33 LINK C3 RC7 D 63 N ASN D 65 1555 1555 1.33 LINK NZ LYS A 30 NI NI C 440 4645 1555 2.16 LINK NE2 HIS A 32 NI NI C 440 4645 1555 2.14 LINK NI NI A 438 O HOH A 484 1555 1555 2.07 LINK NI NI A 438 O HOH A 485 1555 1555 2.22 LINK NI NI A 438 NZ LYS C 30 1555 4656 2.25 LINK NI NI A 438 NE2 HIS C 32 1555 4656 2.16 LINK NI NI A 438 O HOH C 459 1555 4656 2.24 LINK NI NI A 438 O HOH C 470 1555 4656 2.07 LINK O HOH A 458 NI NI C 440 4645 1555 2.23 LINK O HOH A 463 NI NI C 440 4645 1555 2.23 LINK O HOH A 479 NI NI C 440 4645 1555 2.19 LINK NE2 HIS B 201 NI NI B 439 1555 1555 2.22 LINK NI NI B 439 O HOH B 580 1555 1555 2.39 LINK NI NI B 439 O HOH B 602 1555 1555 2.60 LINK NI NI C 440 O HOH C 486 1555 1555 2.05 LINK NE2 HIS D 201 NI NI D 441 1555 1555 2.26 LINK NI NI D 441 O HOH D 587 1555 1555 2.49 LINK NI NI D 441 O HOH D 596 1555 1555 2.64 LINK NI NI D 441 O HOH D 597 1555 1555 2.62 CISPEP 1 ALA A 48 PRO A 49 0 -0.21 CISPEP 2 PHE B 83 PRO B 84 0 0.55 CISPEP 3 ALA C 48 PRO C 49 0 -0.22 CISPEP 4 PHE D 83 PRO D 84 0 0.33 SITE 1 AC1 6 HOH A 484 HOH A 485 LYS C 30 HIS C 32 SITE 2 AC1 6 HOH C 459 HOH C 470 SITE 1 AC2 4 HIS B 201 HOH B 580 HOH B 581 HOH B 602 SITE 1 AC3 6 LYS A 30 HIS A 32 HOH A 458 HOH A 463 SITE 2 AC3 6 HOH A 479 HOH C 486 SITE 1 AC4 4 HIS D 201 HOH D 587 HOH D 596 HOH D 597 CRYST1 132.197 81.169 53.512 90.00 113.92 90.00 C 1 2 1 8 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 0.007564 0.000000 0.003355 0.00000 SCALE2 0.000000 0.012320 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020443 0.00000