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