HEADER LUMINESCENT PROTEIN 17-SEP-13 4MRX TITLE CRYSTAL STRUCTURE OF Y138F OBELIN MUTANT FROM OBELIA LONGISSIMA AT TITLE 2 1.72 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: OBELIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OBL; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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: POL-138F KEYWDS LUMINESCENT PROTEIN, CALCIUM BINDING, EF-HAND EXPDTA X-RAY DIFFRACTION AUTHOR P.V.NATASHIN,W.DING,E.V.EREMEEVA,S.V.MARKOVA,J.LEE,E.S.VYSOTSKI, AUTHOR 2 Z.J.LIU REVDAT 3 08-NOV-23 4MRX 1 REMARK REVDAT 2 01-JAN-20 4MRX 1 JRNL SEQADV REVDAT 1 12-MAR-14 4MRX 0 JRNL AUTH P.V.NATASHIN,W.DING,E.V.EREMEEVA,S.V.MARKOVA,J.LEE, JRNL AUTH 2 E.S.VYSOTSKI,Z.J.LIU JRNL TITL STRUCTURES OF THE CA2+-REGULATED PHOTOPROTEIN OBELIN Y138F JRNL TITL 2 MUTANT BEFORE AND AFTER BIOLUMINESCENCE SUPPORT THE JRNL TITL 3 CATALYTIC FUNCTION OF A WATER MOLECULE IN THE REACTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 720 2014 JRNL REFN ESSN 1399-0047 JRNL PMID 24598741 JRNL DOI 10.1107/S1399004713032434 REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 30654 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.520 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 37.3657 - 4.1395 1.00 2104 147 0.1222 0.1348 REMARK 3 2 4.1395 - 3.2863 1.00 2078 142 0.1249 0.1643 REMARK 3 3 3.2863 - 2.8710 1.00 2055 141 0.1549 0.2143 REMARK 3 4 2.8710 - 2.6086 1.00 2055 144 0.1614 0.1609 REMARK 3 5 2.6086 - 2.4217 1.00 2051 146 0.1553 0.1745 REMARK 3 6 2.4217 - 2.2789 1.00 2017 141 0.1312 0.1596 REMARK 3 7 2.2789 - 2.1648 1.00 2042 141 0.1316 0.1602 REMARK 3 8 2.1648 - 2.0706 1.00 2058 145 0.1363 0.1801 REMARK 3 9 2.0706 - 1.9909 1.00 2035 137 0.1391 0.1693 REMARK 3 10 1.9909 - 1.9222 1.00 2029 144 0.1433 0.1877 REMARK 3 11 1.9222 - 1.8621 1.00 2047 143 0.1482 0.1794 REMARK 3 12 1.8621 - 1.8088 1.00 2045 144 0.1695 0.2109 REMARK 3 13 1.8088 - 1.7612 1.00 2027 144 0.1656 0.1909 REMARK 3 14 1.7612 - 1.7183 0.99 1989 139 0.1741 0.2076 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.37 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.018 1688 REMARK 3 ANGLE : 1.735 2299 REMARK 3 CHIRALITY : 0.123 232 REMARK 3 PLANARITY : 0.009 303 REMARK 3 DIHEDRAL : 15.034 633 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 69.6173 24.7600 22.9557 REMARK 3 T TENSOR REMARK 3 T11: 0.1388 T22: 0.0844 REMARK 3 T33: 0.1093 T12: -0.0196 REMARK 3 T13: 0.0213 T23: 0.0037 REMARK 3 L TENSOR REMARK 3 L11: 1.0475 L22: 2.3126 REMARK 3 L33: 1.3847 L12: -0.1271 REMARK 3 L13: -0.0924 L23: -0.1686 REMARK 3 S TENSOR REMARK 3 S11: -0.0340 S12: 0.0430 S13: -0.0131 REMARK 3 S21: -0.0618 S22: 0.1166 S23: 0.1646 REMARK 3 S31: -0.0892 S32: -0.0352 S33: 0.0067 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4MRX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000082290. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30654 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.718 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 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) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: PHASES REMARK 200 STARTING MODEL: 1QV0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.1M DL-MALIC ACID, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 26.87000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 13.43500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.30500 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 LYS A 4 REMARK 465 TYR A 5 REMARK 465 LYS A 124 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 49 -72.76 -94.90 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 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2F8P RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF OBELIN FOLLOWING CA2+ TRIGGERED REMARK 900 BIOLUMINESCENCE SUGGESTS NEUTRAL COELENTERAMIDE AS THE PRIMARY REMARK 900 EXCITED STATE REMARK 900 RELATED ID: 1QV0 RELATED DB: PDB REMARK 900 ATOMIC RESOLUTION STRUCTURE OF OBELIN FROM OBELIA LONGISSIMA REMARK 900 RELATED ID: 1JF2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF W92F OBELIN MUTANT FROM OBELIA LONGISSIMA AT REMARK 900 1.72 ANGSTROM RESOLUTION REMARK 900 RELATED ID: 1S36 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A CA2+-DISCHARGED PHOTOPROTEIN: IMPLICATIONS REMARK 900 FOR THE MECHANISMS OF THE CALCIUM TRIGGER AND THE BIOLUMINESCENCE REMARK 900 RELATED ID: 1SL7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CALCIUM-LOADED APO-OBELIN FROM OBELIA REMARK 900 LONGISSIMA REMARK 900 RELATED ID: 1EJ3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AEQUORIN REMARK 900 RELATED ID: 4MRY RELATED DB: PDB DBREF 4MRX A 1 195 UNP Q27709 OBL_OBELO 1 195 SEQADV 4MRX ALA A 2 UNP Q27709 SER 2 ENGINEERED MUTATION SEQADV 4MRX PHE A 138 UNP Q27709 TYR 138 ENGINEERED MUTATION SEQRES 1 A 195 MET ALA SER LYS TYR ALA VAL LYS LEU LYS THR ASP PHE SEQRES 2 A 195 ASP ASN PRO ARG TRP ILE LYS ARG HIS LYS HIS MET PHE SEQRES 3 A 195 ASP PHE LEU ASP ILE ASN GLY ASN GLY LYS ILE THR LEU SEQRES 4 A 195 ASP GLU ILE VAL SER LYS ALA SER ASP ASP ILE CYS ALA SEQRES 5 A 195 LYS LEU GLU ALA THR PRO GLU GLN THR LYS ARG HIS GLN SEQRES 6 A 195 VAL CYS VAL GLU ALA PHE PHE ARG GLY CYS GLY MET GLU SEQRES 7 A 195 TYR GLY LYS GLU ILE ALA PHE PRO GLN PHE LEU ASP GLY SEQRES 8 A 195 TRP LYS GLN LEU ALA THR SER GLU LEU LYS 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 PHE GLY LYS ILE SER GLY SEQRES 12 A 195 ILE SER PRO SER GLN GLU ASP CYS GLU ALA THR PHE ARG SEQRES 13 A 195 HIS CYS ASP LEU ASP ASN SER GLY ASP 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 201 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 *298(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 LEU A 54 1 6 HELIX 4 4 THR A 57 CYS A 75 1 19 HELIX 5 5 PHE A 85 ARG A 105 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 LYS A 36 ILE A 37 0 SHEET 2 A 2 ILE A 83 ALA A 84 -1 O ILE A 83 N ILE A 37 SHEET 1 B 2 THR A 129 ILE A 130 0 SHEET 2 B 2 LEU A 166 ASP A 167 -1 O LEU A 166 N ILE A 130 CISPEP 1 GLY A 126 SER A 127 0 -11.93 SITE 1 AC1 16 HIS A 22 MET A 25 ILE A 42 ILE A 50 SITE 2 AC1 16 PHE A 88 TRP A 92 TRP A 114 GLY A 115 SITE 3 AC1 16 PHE A 119 PHE A 138 ILE A 144 MET A 171 SITE 4 AC1 16 HIS A 175 TRP A 179 TYR A 190 HOH A 301 CRYST1 73.491 73.491 53.740 90.00 90.00 90.00 P 41 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 0.013607 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013607 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018608 0.00000