HEADER LUMINESCENT PROTEIN 26-MAY-06 2H5Q TITLE CRYSTAL STRUCTURE OF MCHERRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: MCHERRY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 FRAGMENT: CORAL; SOURCE 3 ORGANISM_SCIENTIFIC: DISCOSOMA SP.; SOURCE 4 ORGANISM_TAXID: 86600; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA BARREL, LUMINESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.SHU,S.J.REMINGTON REVDAT 4 18-OCT-17 2H5Q 1 REMARK REVDAT 3 07-JUL-09 2H5Q 1 REMARK REVDAT 2 24-FEB-09 2H5Q 1 VERSN REVDAT 1 22-AUG-06 2H5Q 0 JRNL AUTH X.SHU,N.C.SHANER,C.A.YARBROUGH,R.Y.TSIEN,S.J.REMINGTON JRNL TITL NOVEL CHROMOPHORES AND BURIED CHARGES CONTROL COLOR IN JRNL TITL 2 MFRUITS JRNL REF BIOCHEMISTRY V. 45 9639 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16893165 JRNL DOI 10.1021/BI060773L REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.133 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.149 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2482 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 47050 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.140 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.138 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2216 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 42049 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1733 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 378 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2111.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 6 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 19061 REMARK 3 NUMBER OF RESTRAINTS : 22538 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.033 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.068 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.082 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.015 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.049 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.090 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2H5Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000037962. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-05 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 : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 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 : ADSC REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47050 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 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) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NAOAC, 100 MM TRIS PH 8.5, 30% REMARK 280 PEG 4000 , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 21.42750 REMARK 290 SMTRY3 2 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: BIOLOGICAL UNIT: MONOMER REMARK 300 ONE MONOMER PER ASYMMETRIC UNIT 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 -4 REMARK 465 VAL A -3 REMARK 465 SER A -2 REMARK 465 LYS A -1 REMARK 465 GLY A 0 REMARK 465 GLU A 1 REMARK 465 GLU A 2 REMARK 465 ASP A 3 REMARK 465 GLY A 224 REMARK 465 GLY A 225 REMARK 465 MET A 226 REMARK 465 ASP A 227 REMARK 465 GLU A 228 REMARK 465 LEU A 229 REMARK 465 TYR A 230 REMARK 465 LYS A 231 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 MET A 5 CG SD CE REMARK 470 GLU A 19 CG CD OE1 OE2 REMARK 470 GLU A 94 CG CD OE1 OE2 REMARK 470 GLN A 114 CD OE1 NE2 REMARK 470 ARG A 149 CZ NH1 NH2 REMARK 470 ASP A 154 CG OD1 OD2 REMARK 470 LYS A 168 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 125 CD - NE - CZ ANGL. DEV. = 22.4 DEGREES REMARK 500 ARG A 125 NH1 - CZ - NH2 ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG A 125 NE - CZ - NH1 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 125 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES 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 PRO A 55 31.11 -89.38 REMARK 500 TYR A 72 49.29 -107.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2H5O RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MORANGE REMARK 900 RELATED ID: 2H5P RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MSTRAWBERRY AT PH 9.5 REMARK 900 RELATED ID: 2H5R RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MSTRAWBERRY AT PH 10.5 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE RESIDUES 66, 67, 68 CONSTITUTE THE CHROMOPHORE CH6 66. DBREF 2H5Q A -4 231 PDB 2H5Q 2H5Q -4 231 SEQRES 1 A 234 MET VAL SER LYS GLY GLU GLU ASP ASN MET ALA ILE ILE SEQRES 2 A 234 LYS GLU PHE MET ARG PHE LYS VAL HIS MET GLU GLY SER SEQRES 3 A 234 VAL ASN GLY HIS GLU PHE GLU ILE GLU GLY GLU GLY GLU SEQRES 4 A 234 GLY ARG PRO TYR GLU GLY THR GLN THR ALA LYS LEU LYS SEQRES 5 A 234 VAL THR LYS GLY GLY PRO LEU PRO PHE ALA TRP ASP ILE SEQRES 6 A 234 LEU SER PRO GLN PHE CH6 SER LYS ALA TYR VAL LYS HIS SEQRES 7 A 234 PRO ALA ASP ILE PRO ASP TYR LEU LYS LEU SER PHE PRO SEQRES 8 A 234 GLU GLY PHE LYS TRP GLU ARG VAL MET ASN PHE GLU ASP SEQRES 9 A 234 GLY GLY VAL VAL THR VAL THR GLN ASP SER SER LEU GLN SEQRES 10 A 234 ASP GLY GLU PHE ILE TYR LYS VAL LYS LEU ARG GLY THR SEQRES 11 A 234 ASN PHE PRO SER ASP GLY PRO VAL MET GLN LYS LYS THR SEQRES 12 A 234 MET GLY TRP GLU ALA SER SER GLU ARG MET TYR PRO GLU SEQRES 13 A 234 ASP GLY ALA LEU LYS GLY GLU ILE LYS GLN ARG LEU LYS SEQRES 14 A 234 LEU LYS ASP GLY GLY HIS TYR ASP ALA GLU VAL LYS THR SEQRES 15 A 234 THR TYR LYS ALA LYS LYS PRO VAL GLN LEU PRO GLY ALA SEQRES 16 A 234 TYR ASN VAL ASN ILE LYS LEU ASP ILE THR SER HIS ASN SEQRES 17 A 234 GLU ASP TYR THR ILE VAL GLU GLN TYR GLU ARG ALA GLU SEQRES 18 A 234 GLY ARG HIS SER THR GLY GLY MET ASP GLU LEU TYR LYS MODRES 2H5Q CH6 A 66 MET MODRES 2H5Q CH6 A 66 TYR MODRES 2H5Q CH6 A 66 GLY HET CH6 A 66 23 HETNAM CH6 {(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4- HETNAM 2 CH6 HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H- HETNAM 3 CH6 IMIDAZOL-1-YL}ACETIC ACID HETSYN CH6 CHROMOPHORE (MET-TYR-GLY) FORMUL 1 CH6 C16 H19 N3 O4 S FORMUL 2 HOH *378(H2 O) HELIX 1 1 ALA A 57 PHE A 65 5 9 HELIX 2 2 SER A 69 VAL A 73 5 5 HELIX 3 3 ASP A 81 SER A 86 1 6 SHEET 1 A13 THR A 140 TRP A 143 0 SHEET 2 A13 ALA A 156 LEU A 167 -1 O LYS A 166 N GLY A 142 SHEET 3 A13 HIS A 172 ALA A 183 -1 O TYR A 181 N LEU A 157 SHEET 4 A13 PHE A 91 PHE A 99 -1 N LYS A 92 O LYS A 182 SHEET 5 A13 VAL A 104 GLN A 114 -1 O SER A 111 N PHE A 91 SHEET 6 A13 GLU A 117 THR A 127 -1 O ARG A 125 N THR A 106 SHEET 7 A13 MET A 12 VAL A 22 1 N SER A 21 O GLY A 126 SHEET 8 A13 HIS A 25 ARG A 36 -1 O ILE A 29 N MET A 18 SHEET 9 A13 THR A 41 LYS A 50 -1 O LYS A 45 N GLU A 32 SHEET 10 A13 ILE A 210 HIS A 221 -1 O VAL A 211 N LEU A 46 SHEET 11 A13 TYR A 193 HIS A 204 -1 N ASN A 194 O ARG A 220 SHEET 12 A13 SER A 146 GLU A 153 -1 N MET A 150 O TYR A 193 SHEET 13 A13 ALA A 156 LEU A 167 -1 O LYS A 158 N TYR A 151 LINK C PHE A 65 N1 CH6 A 66 1555 1555 1.18 LINK O PHE A 65 N1 CH6 A 66 1555 1555 1.97 LINK C3 CH6 A 66 N SER A 69 1555 1555 1.32 CISPEP 1 GLY A 52 PRO A 53 0 -6.03 CISPEP 2 PHE A 87 PRO A 88 0 11.77 CRYST1 48.762 42.855 61.057 90.00 112.31 90.00 P 1 21 1 2 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 0.020508 0.000000 0.008415 0.00000 SCALE2 0.000000 0.023334 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017703 0.00000 MASTER 257 0 1 3 13 0 0 6 0 0 0 18 END