HEADER HYDROLASE INHIBITOR 27-SEP-10 3OZQ TITLE CRYSTAL STRUCTURE OF SERPIN48, WHICH IS A HIGHLY SPECIFIC SERPIN IN TITLE 2 THE INSECT TENEBRIO MOLITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERPIN48; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 23-389; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TENEBRIO MOLITOR; SOURCE 3 ORGANISM_COMMON: YELLOW MEALWORM; SOURCE 4 ORGANISM_TAXID: 7067; SOURCE 5 GENE: SPN48; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SERPIN, SERPIN48 INHIBITS SPE SPECIFICALLY, SPE, HYDROLASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR S.H.PARK,S.PIAO,N.-C.HA REVDAT 3 20-MAR-24 3OZQ 1 SEQADV REVDAT 2 09-OCT-13 3OZQ 1 JRNL VERSN REVDAT 1 27-OCT-10 3OZQ 0 JRNL AUTH S.H.PARK,R.JIANG,S.PIAO,B.ZHANG,E.H.KIM,H.M.KWON,X.L.JIN, JRNL AUTH 2 B.L.LEE,N.-C.HA JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF A HIGHLY JRNL TITL 2 SPECIFIC SERPIN IN THE INSECT INNATE IMMUNITY JRNL REF J.BIOL.CHEM. V. 286 1567 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21047786 JRNL DOI 10.1074/JBC.M110.144006 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 27617 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2765 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 2.0200 - 1.9000 0.92 3929 435 0.4400 0.4940 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : 0.30 REMARK 3 B_SOL : 42.16 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -15.06000 REMARK 3 B22 (A**2) : 16.39000 REMARK 3 B33 (A**2) : -1.33000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.98000 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 : 0.007 NULL REMARK 3 ANGLE : 1.100 NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : 25.400 NULL 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: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3OZQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000061775. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27674 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 97.4 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) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13% PEG 8000, 0.11M MES PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 21.28050 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 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 ALA A 19 REMARK 465 THR A 20 REMARK 465 LEU A 21 REMARK 465 ILE A 350 REMARK 465 LEU A 351 REMARK 465 PRO A 352 REMARK 465 GLU A 353 REMARK 465 MET A 354 REMARK 465 ALA A 355 REMARK 465 LEU A 356 REMARK 465 PRO A 357 REMARK 465 ASP A 358 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 GLU A 17 -16.42 -49.96 REMARK 500 ALA A 45 -129.13 -138.84 REMARK 500 HIS A 78 38.65 36.92 REMARK 500 LEU A 97 13.74 -68.39 REMARK 500 ALA A 344 -120.97 -98.78 REMARK 500 THR A 345 112.46 -178.27 REMARK 500 PRO A 348 -166.12 -105.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 15 MET A 16 -149.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NS3 RELATED DB: PDB DBREF 3OZQ A 17 389 UNP D1MYQ6 D1MYQ6_TENMO 17 389 SEQADV 3OZQ GLY A 14 UNP D1MYQ6 EXPRESSION TAG SEQADV 3OZQ HIS A 15 UNP D1MYQ6 EXPRESSION TAG SEQADV 3OZQ MET A 16 UNP D1MYQ6 EXPRESSION TAG SEQRES 1 A 376 GLY HIS MET GLU ASP ALA THR LEU GLN GLU PHE PRO ASN SEQRES 2 A 376 ALA VAL ASN SER PHE THR PRO SER VAL TYR LYS GLU VAL SEQRES 3 A 376 LEU LYS THR GLU LYS ALA ASN PHE LEU VAL SER PRO PHE SEQRES 4 A 376 SER ALA ALA THR LEU LEU ALA LEU ALA GLN SER GLY CYS SEQRES 5 A 376 ARG GLY ASP THR ALA GLU GLU ILE ARG GLN VAL LEU HIS SEQRES 6 A 376 PHE VAL GLY ASP ARG GLU LYS ALA GLU GLY ALA VAL LYS SEQRES 7 A 376 GLU VAL LEU SER LYS LEU THR ASN GLU GLU TYR THR LEU SEQRES 8 A 376 HIS THR ALA ASN LYS ILE TYR VAL LYS THR ASN PHE SER SEQRES 9 A 376 VAL ARG GLU GLU PHE GLN LYS ILE ALA VAL GLU VAL TYR SEQRES 10 A 376 GLY ALA GLN SER GLU ASN VAL ASP PHE SER GLU LYS ASN SEQRES 11 A 376 ASP ALA ALA LYS LEU MET ASN ALA TRP VAL GLU GLU GLN SEQRES 12 A 376 THR GLN HIS LYS ILE GLN ASN LEU VAL ASP PRO GLU ILE SEQRES 13 A 376 LEU ASN ASN LEU THR ARG VAL VAL LEU ILE ASN ALA LEU SEQRES 14 A 376 TYR PHE ASN ALA LYS TRP LEU VAL PRO PHE PRO PRO PHE SEQRES 15 A 376 HIS THR ARG LYS SER ASP PHE HIS LYS SER ALA LYS GLU SEQRES 16 A 376 VAL VAL GLN VAL ASP THR MET TYR LEU ASP GLU GLN TYR SEQRES 17 A 376 PHE ASN TYR TYR GLU CYS HIS HIS LEU ASP ALA LYS LEU SEQRES 18 A 376 LEU GLU LEU PRO PHE LYS GLY GLY ALA SER LEU THR ILE SEQRES 19 A 376 VAL LEU SER ASN GLN ILE GLU GLY LEU VAL SER LEU GLU SEQRES 20 A 376 SER LYS ILE LYS ARG SER PHE LEU PRO HIS ASN LEU THR SEQRES 21 A 376 LYS GLN LEU VAL ASN VAL ALA LEU PRO LYS PHE LYS ILE SEQRES 22 A 376 GLU SER THR VAL ASP PHE LYS LYS VAL LEU LYS LYS LEU SEQRES 23 A 376 GLY VAL LYS LYS ALA PHE GLY ASP GLU ALA ASP LEU SER SEQRES 24 A 376 GLY ILE ALA GLY GLU LYS GLY ASP LEU VAL ILE SER ASN SEQRES 25 A 376 ILE VAL GLN LYS SER PHE ILE ASP VAL SER GLU GLU GLY SEQRES 26 A 376 VAL GLU ALA ALA ALA ALA THR TYR ILE PRO VAL ILE LEU SEQRES 27 A 376 PRO GLU MET ALA LEU PRO ASP SER PRO LYS GLN PHE ILE SEQRES 28 A 376 VAL ASP HIS PRO PHE ILE PHE TYR ILE LYS VAL LYS GLY SEQRES 29 A 376 MET ILE LEU PHE ALA GLY ARG VAL THR THR LEU ASN FORMUL 2 HOH *105(H2 O) HELIX 1 1 GLN A 22 GLU A 43 1 22 HELIX 2 2 SER A 50 GLY A 64 1 15 HELIX 3 3 ARG A 66 LEU A 77 1 12 HELIX 4 4 ASP A 82 LEU A 97 1 16 HELIX 5 5 ARG A 119 VAL A 129 1 11 HELIX 6 6 GLU A 141 THR A 157 1 17 HELIX 7 7 ASP A 166 LEU A 170 5 5 HELIX 8 8 PRO A 193 THR A 197 5 5 HELIX 9 9 GLY A 255 LYS A 262 1 8 HELIX 10 10 LYS A 262 LEU A 268 1 7 HELIX 11 11 PHE A 292 GLY A 300 1 9 HELIX 12 12 LYS A 302 GLY A 306 5 5 SHEET 1 A 7 PHE A 47 VAL A 49 0 SHEET 2 A 7 MET A 378 VAL A 385 -1 O ALA A 382 N VAL A 49 SHEET 3 A 7 PHE A 369 VAL A 375 -1 N ILE A 373 O LEU A 380 SHEET 4 A 7 SER A 244 SER A 250 -1 N THR A 246 O TYR A 372 SHEET 5 A 7 ALA A 232 PRO A 238 -1 N LEU A 237 O LEU A 245 SHEET 6 A 7 VAL A 209 CYS A 227 -1 N TYR A 225 O LEU A 234 SHEET 7 A 7 ARG A 198 HIS A 203 -1 N ARG A 198 O THR A 214 SHEET 1 B 8 PHE A 47 VAL A 49 0 SHEET 2 B 8 MET A 378 VAL A 385 -1 O ALA A 382 N VAL A 49 SHEET 3 B 8 PHE A 369 VAL A 375 -1 N ILE A 373 O LEU A 380 SHEET 4 B 8 SER A 244 SER A 250 -1 N THR A 246 O TYR A 372 SHEET 5 B 8 ALA A 232 PRO A 238 -1 N LEU A 237 O LEU A 245 SHEET 6 B 8 VAL A 209 CYS A 227 -1 N TYR A 225 O LEU A 234 SHEET 7 B 8 THR A 273 PRO A 282 -1 O VAL A 279 N LEU A 217 SHEET 8 B 8 LYS A 361 ILE A 364 1 O LYS A 361 N LEU A 276 SHEET 1 C 5 GLN A 133 VAL A 137 0 SHEET 2 C 5 THR A 103 LYS A 113 1 N VAL A 112 O GLU A 135 SHEET 3 C 5 VAL A 176 LYS A 187 -1 O ILE A 179 N LYS A 109 SHEET 4 C 5 ILE A 323 VAL A 334 1 O SER A 324 N VAL A 176 SHEET 5 C 5 PHE A 284 ASP A 291 -1 N PHE A 284 O VAL A 334 SHEET 1 D 4 GLN A 133 VAL A 137 0 SHEET 2 D 4 THR A 103 LYS A 113 1 N VAL A 112 O GLU A 135 SHEET 3 D 4 VAL A 176 LYS A 187 -1 O ILE A 179 N LYS A 109 SHEET 4 D 4 GLY A 338 VAL A 339 -1 O VAL A 339 N ALA A 186 CRYST1 66.061 42.561 66.178 90.00 105.16 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 0.015138 0.000000 0.004102 0.00000 SCALE2 0.000000 0.023496 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015656 0.00000