HEADER FLUORESCENT PROTEIN, HYDROLASE 17-NOV-09 3KPX TITLE CRYSTAL STRUCTURE ANALYSIS OF PHOTOPROTEIN CLYTIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOPHOTOPROTEIN CLYTIN-3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CLYTIN, APOPHOTOPROTEIN CLYTIN-5, APOPHOTOPROTEIN CLYTIN-6; COMPND 5 EC: 1.13.12.5; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLYTIA GREGARIA; SOURCE 3 ORGANISM_COMMON: PHIALIDIUM GREGARIUM; SOURCE 4 ORGANISM_TAXID: 27801 KEYWDS PHOTOPROTEIN CLYTIN, FLUORESCENT PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.S.TITUSHIN,Y.LI,G.A.STEPANYUK,B.-C.WANG,J.LEE,E.S.VYSOTSKI,Z.-J.LIU REVDAT 3 01-NOV-23 3KPX 1 REMARK REVDAT 2 29-DEC-10 3KPX 1 JRNL REVDAT 1 06-OCT-10 3KPX 0 JRNL AUTH M.S.TITUSHIN,Y.FENG,G.A.STEPANYUK,Y.LI,S.V.MARKOVA,S.GOLZ, JRNL AUTH 2 B.-C.WANG,J.LEE,J.WANG,E.S.VYSOTSKI,Z.-J.LIU JRNL TITL NMR DERIVED TOPOLOGY OF A GFP-PHOTOPROTEIN ENERGY TRANSFER JRNL TITL 2 COMPLEX JRNL REF J.BIOL.CHEM. V. 285 40891 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20926380 JRNL DOI 10.1074/JBC.M110.133843 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 13990 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 696 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 20.3073 - 3.2435 1.00 2806 125 0.1634 0.1812 REMARK 3 2 3.2435 - 2.5761 1.00 2641 155 0.1639 0.2443 REMARK 3 3 2.5761 - 2.2509 1.00 2654 135 0.1545 0.2120 REMARK 3 4 2.2509 - 2.0454 1.00 2604 147 0.1636 0.2208 REMARK 3 5 2.0454 - 1.8989 0.98 2589 134 0.2235 0.2805 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 : 0.42 REMARK 3 B_SOL : 47.84 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.65100 REMARK 3 B22 (A**2) : 0.55500 REMARK 3 B33 (A**2) : -1.20600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.011 1592 REMARK 3 ANGLE : 1.186 2152 REMARK 3 CHIRALITY : 0.082 216 REMARK 3 PLANARITY : 0.011 278 REMARK 3 DIHEDRAL : 17.516 587 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3KPX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1000056299. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14018 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.899 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 (%) : 99.5 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2F8P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 57.67400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.67400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 21.69600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.46600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 21.69600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.46600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 57.67400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 21.69600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 34.46600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.67400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 21.69600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 34.46600 REMARK 290 SMTRY3 8 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 254 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 283 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 284 LIES ON A SPECIAL POSITION. 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 THR A 2 REMARK 465 ASP A 3 REMARK 465 THR A 4 REMARK 465 ALA A 5 REMARK 465 SER A 6 REMARK 465 LYS A 7 REMARK 465 TYR A 8 REMARK 465 ALA A 9 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 ASN A 15 57.66 -143.22 REMARK 500 ASP A 52 -71.67 -105.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 CZH A 201 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 CA A 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 33 OD1 REMARK 620 2 ASN A 35 OD1 80.6 REMARK 620 3 ASN A 37 OD1 87.9 82.0 REMARK 620 4 LYS A 39 O 98.3 167.0 85.0 REMARK 620 5 HOH A 223 O 170.5 96.5 82.7 82.4 REMARK 620 N 1 2 3 4 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 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 202 DBREF 3KPX A 1 198 UNP 3KPX D7PM14_CLYGR 1 198 SEQRES 1 A 198 MET THR ASP THR ALA SER LYS TYR ALA VAL LYS LEU LYS SEQRES 2 A 198 THR ASN PHE GLU ASP PRO LYS TRP VAL ASN ARG HIS LYS SEQRES 3 A 198 PHE MET PHE ASN PHE LEU ASP ILE ASN GLY ASN GLY LYS SEQRES 4 A 198 ILE THR LEU ASP GLU ILE VAL SER LYS ALA SER ASP ASP SEQRES 5 A 198 ILE CYS ALA LYS LEU GLY ALA THR PRO ALA GLN THR GLN SEQRES 6 A 198 ARG HIS GLN GLU ALA VAL GLU ALA PHE PHE LYS LYS ILE SEQRES 7 A 198 GLY LEU ASP TYR GLY LYS GLU VAL GLU PHE PRO ALA PHE SEQRES 8 A 198 VAL ASN GLY TRP LYS GLU LEU ALA LYS HIS ASP LEU LYS SEQRES 9 A 198 LEU TRP SER GLN ASN LYS LYS SER LEU ILE ARG ASN TRP SEQRES 10 A 198 GLY GLU ALA VAL PHE ASP ILE PHE ASP LYS ASP GLY SER SEQRES 11 A 198 GLY SER ILE SER LEU ASP GLU TRP LYS THR TYR GLY GLY SEQRES 12 A 198 ILE SER GLY ILE CYS PRO SER ASP GLU ASP ALA GLU LYS SEQRES 13 A 198 THR PHE LYS HIS CYS ASP LEU ASP ASN SER GLY LYS LEU SEQRES 14 A 198 ASP VAL ASP GLU MET THR ARG GLN HIS LEU GLY PHE TRP SEQRES 15 A 198 TYR THR LEU ASP PRO ASN ALA ASP GLY LEU TYR GLY ASN SEQRES 16 A 198 PHE VAL PRO HET CZH A 201 33 HET CA A 202 1 HETNAM CZH C2-HYDROPEROXY-COELENTERAZINE HETNAM CA CALCIUM ION 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 CA CA 2+ FORMUL 4 HOH *128(H2 O) HELIX 1 1 ASP A 18 ASP A 33 1 16 HELIX 2 2 THR A 41 ASP A 51 1 11 HELIX 3 3 ASP A 52 GLY A 58 1 7 HELIX 4 4 THR A 60 ILE A 78 1 19 HELIX 5 5 PHE A 88 GLN A 108 1 21 HELIX 6 6 SER A 112 ASP A 126 1 15 HELIX 7 7 SER A 134 GLY A 146 1 13 HELIX 8 8 SER A 150 CYS A 161 1 12 HELIX 9 9 VAL A 171 TYR A 183 1 13 HELIX 10 10 ASP A 186 ASP A 190 5 5 SHEET 1 A 2 LYS A 39 ILE A 40 0 SHEET 2 A 2 VAL A 86 GLU A 87 -1 O VAL A 86 N ILE A 40 SHEET 1 B 2 SER A 132 ILE A 133 0 SHEET 2 B 2 LEU A 169 ASP A 170 -1 O LEU A 169 N ILE A 133 LINK OD1 ASP A 33 CA CA A 202 1555 1555 2.39 LINK OD1 ASN A 35 CA CA A 202 1555 1555 2.31 LINK OD1 ASN A 37 CA CA A 202 1555 1555 2.47 LINK O LYS A 39 CA CA A 202 1555 1555 2.28 LINK CA CA A 202 O HOH A 223 1555 1555 2.73 SITE 1 AC1 20 HIS A 25 MET A 28 LEU A 32 ILE A 45 SITE 2 AC1 20 ILE A 53 PHE A 91 TRP A 95 ILE A 114 SITE 3 AC1 20 TRP A 117 GLY A 118 PHE A 122 TRP A 138 SITE 4 AC1 20 TYR A 141 ILE A 147 MET A 174 HIS A 178 SITE 5 AC1 20 TRP A 182 TYR A 193 HOH A 213 HOH A 314 SITE 1 AC2 5 ASP A 33 ASN A 35 ASN A 37 LYS A 39 SITE 2 AC2 5 HOH A 223 CRYST1 43.392 68.932 115.348 90.00 90.00 90.00 C 2 2 21 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 0.023046 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014507 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008669 0.00000