HEADER LUMINESCENT PROTEIN 19-JUN-01 1JF0 TITLE THE CRYSTAL STRUCTURE OF OBELIN FROM OBELIA GENICULATA AT 1.82 A TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: OBELIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: OBELIA LONGISSIMA; SOURCE 3 ORGANISM_TAXID: 32570; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21-GOLD; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET19-OG KEYWDS BIOLUMINESCENCE, CALCIUM-REGULATED PHOTOPROTEIN, OBELIN, OBELIA, KEYWDS 2 HYDROID, LUMINESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.DENG,E.VYSOTSKI,Z.-J.LIU,S.MARKOVA,J.LEE,J.ROSE,B.-C.WANG REVDAT 5 16-AUG-23 1JF0 1 REMARK REVDAT 4 04-OCT-17 1JF0 1 REMARK REVDAT 3 19-FEB-14 1JF0 1 JRNL REMARK VERSN REVDAT 2 24-FEB-09 1JF0 1 VERSN REVDAT 1 11-JUL-01 1JF0 0 JRNL AUTH L.DENG,E.VYSOTSKI,Z.-J.LIU,S.MARKOVA,J.LEE,J.ROSE,B.-C.WANG JRNL TITL THE CRYSTAL STRUCTURE OF OBELIN FROM OBELIA GENICULATA AT JRNL TITL 2 1.82 ANGSTROM RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.J.LIU,E.S.VYSOTSKI,C.J.CHEN,J.P.ROSE,J.LEE,B.C.WANG REMARK 1 TITL STRUCTURE OF THE CA2+-REGULATED PHOTOPROTEIN OBELIN AT 1.7 A REMARK 1 TITL 2 RESOLUTION DETERMINED DIRECTLY FROM ITS SULFUR SUBSTRUCTURE. REMARK 1 REF PROTEIN SCI. V. 9 2085 2000 REMARK 1 REFN ISSN 0961-8368 REMARK 1 PMID 11152120 REMARK 1 DOI 10.1110/PS.9.11.2085 REMARK 1 REFERENCE 2 REMARK 1 AUTH E.S.VYSOTSKI,Z.J.LIU,J.ROSE,B.C.WANG,J.LEE REMARK 1 TITL PREPARATION AND PRELIMINARY STUDY OF CRYSTALS OF THE REMARK 1 TITL 2 RECOMBINANT CALCIUM-REGULATED PHOTOPROTEIN OBELIN FROM THE REMARK 1 TITL 3 BIOLUMINESCENT HYDROID OBELIA LONGISSIMA. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 55 1965 1999 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 10531510 REMARK 1 DOI 10.1107/S0907444999011828 REMARK 1 REFERENCE 3 REMARK 1 AUTH E.VYSOTSKI,Z.-J.LIU,L.DENG,J.ROSE,B.-C.WANG,J.LEE REMARK 1 TITL OBELIN CRYSTAL STRUCTURE: IMPLICATIONS FOR THE REMARK 1 TITL 2 BIOLUMINESCENCE MECHANISM REMARK 1 REF BIOLUMINESCENCE AND 2001 REMARK 1 REF 2 CHEMILUMINESCENCE 2000 REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 1.82 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 244092.030 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 14015 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) : 0.212 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1123 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 1.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.93 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2061 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 180 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1528 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.10 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) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.18 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) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 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) : 1.870 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.930 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.270 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.900 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.42 REMARK 3 BSOL : 57.17 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JF0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013693. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-SEP-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14015 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 REMARK 200 RESOLUTION RANGE LOW (A) : 28.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 12.00 REMARK 200 R MERGE (I) : 0.03500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.1900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.21900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1EL4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, POTASSIUM PHOSPHATE, REMARK 280 HEXAMINECOBALTIC CHLORIDE, PH 5.8, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 16.75100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.60450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.91150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.60450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.75100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.91150 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 ALA A 2 REMARK 465 SER A 3 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 TYR A 5 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 8 CG CD CE NZ REMARK 470 GLN A 10 CG CD OE1 NE2 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 ASP A 12 62.52 -159.68 REMARK 500 ASP A 49 -73.15 -118.44 REMARK 500 ASP A 123 64.52 -114.20 REMARK 500 SER A 145 66.01 -151.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CZH A 197 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EL4 RELATED DB: PDB REMARK 900 1EL4 CONTAINS CALCIUM-REGULATED PHOTOPROTEIN OBELIN. REMARK 900 RELATED ID: 1EJ3 RELATED DB: PDB REMARK 900 1EJ3 CONTAINS CALCIUM-REGULATED PHOTOPROTEIN AEQUORIN. DBREF 1JF0 A 1 195 UNP Q27709 OBL_OBELO 1 195 SEQRES 1 A 195 MET ALA SER LYS TYR ALA VAL LYS LEU GLN THR ASP PHE SEQRES 2 A 195 ASP ASN PRO LYS TRP ILE LYS ARG HIS LYS PHE MET PHE SEQRES 3 A 195 ASP TYR LEU ASP ILE ASN GLY ASN GLY GLN ILE THR LEU SEQRES 4 A 195 ASP GLU ILE VAL SER LYS ALA SER ASP ASP ILE CYS LYS SEQRES 5 A 195 ASN LEU GLY ALA THR PRO ALA GLN THR GLN ARG HIS GLN SEQRES 6 A 195 ASP CYS VAL GLU ALA PHE PHE ARG GLY CYS GLY LEU GLU SEQRES 7 A 195 TYR GLY LYS GLU THR LYS PHE PRO GLU PHE LEU GLU GLY SEQRES 8 A 195 TRP LYS ASN LEU ALA ASN ALA ASP LEU ALA LYS TRP ALA SEQRES 9 A 195 ARG ASN GLU PRO THR LEU ILE ARG GLU TRP GLY ASP ALA SEQRES 10 A 195 VAL PHE ASP ILE PHE ASP LYS ASP GLY SER GLY THR ILE SEQRES 11 A 195 THR LEU ASP GLU TRP LYS ALA TYR GLY ARG ILE SER GLY SEQRES 12 A 195 ILE SER PRO SER GLU GLU ASP CYS GLU LYS THR PHE GLN SEQRES 13 A 195 HIS CYS ASP LEU ASP ASN SER GLY GLU LEU ASP VAL ASP SEQRES 14 A 195 GLU MET THR ARG GLN HIS LEU GLY PHE TRP TYR THR LEU SEQRES 15 A 195 ASP PRO GLU ALA ASP GLY LEU TYR GLY ASN GLY VAL PRO HET CZH A 197 34 HETNAM CZH C2-HYDROPEROXY-COELENTERAZINE HETSYN CZH 8-BENZYL-2-HYDROPEROXY-2-(4-HYDROXY-BENZYL)-6-(4- HETSYN 2 CZH HYDROXY-PHENYL)-2H-IMIDAZO[1,2-A]PYRAZIN-3-ONE FORMUL 2 CZH C26 H21 N3 O5 FORMUL 3 HOH *111(H2 O) HELIX 1 1 ASN A 15 ASP A 30 1 16 HELIX 2 2 THR A 38 ASP A 48 1 11 HELIX 3 3 ASP A 49 GLY A 55 1 7 HELIX 4 4 THR A 57 CYS A 75 1 19 HELIX 5 5 LYS A 84 ALA A 104 1 21 HELIX 6 6 THR A 109 PHE A 122 1 14 HELIX 7 7 THR A 131 GLY A 143 1 13 HELIX 8 8 SER A 147 CYS A 158 1 12 HELIX 9 9 VAL A 168 TYR A 180 1 13 HELIX 10 10 ASP A 183 ASP A 187 5 5 SHEET 1 A 2 THR A 129 ILE A 130 0 SHEET 2 A 2 LEU A 166 ASP A 167 -1 O LEU A 166 N ILE A 130 SITE 1 AC1 17 HIS A 22 MET A 25 TYR A 28 LEU A 29 SITE 2 AC1 17 ILE A 42 ILE A 50 PHE A 88 TRP A 92 SITE 3 AC1 17 TRP A 114 GLY A 115 TRP A 135 TYR A 138 SITE 4 AC1 17 MET A 171 HIS A 175 TRP A 179 TYR A 190 SITE 5 AC1 17 HOH A 199 CRYST1 33.502 67.823 69.209 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 0.029849 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014744 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014449 0.00000