HEADER STRUCTURAL GENOMICS 21-SEP-02 1MTP TITLE THE X-RAY CRYSTAL STRUCTURE OF A SERPIN FROM A THERMOPHILIC PROKARYOTE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE PROTEINASE INHIBITOR (SERPIN), CHAIN A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CHAIN A, RESIDUE 55-377; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SERINE PROTEINASE INHIBITOR (SERPIN), CHAIN B; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: CHAIN B, RESIDUE 378-420; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOBIFIDA FUSCA; SOURCE 3 ORGANISM_TAXID: 2021; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: THERMOBIFIDA FUSCA; SOURCE 8 ORGANISM_TAXID: 2021; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STRUCTURAL GENOMICS, PROTEASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR J.A.IRVING,L.D.CABRITA,J.ROSSJOHN,R.N.PIKE,S.P.BOTTOMLEY, AUTHOR 2 J.C.WHISSTOCK REVDAT 4 14-FEB-24 1MTP 1 SEQADV REVDAT 3 11-OCT-17 1MTP 1 REMARK REVDAT 2 24-FEB-09 1MTP 1 VERSN REVDAT 1 15-APR-03 1MTP 0 JRNL AUTH J.A.IRVING,L.D.CABRITA,J.ROSSJOHN,R.N.PIKE,S.P.BOTTOMLEY, JRNL AUTH 2 J.C.WHISSTOCK JRNL TITL THE 1.5 A CRYSTAL STRUCTURE OF A PROKARYOTE SERPIN: JRNL TITL 2 CONTROLLING CONFORMATIONAL CHANGE IN A HEATED ENVIRONMENT JRNL REF STRUCTURE V. 11 387 2003 JRNL REFN ISSN 0969-2126 JRNL PMID 12679017 JRNL DOI 10.1016/S0969-2126(03)00057-1 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 179258 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2714 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 604 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MTP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-SEP-02. REMARK 100 THE DEPOSITION ID IS D_1000017174. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 179258 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : NULL 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: ARP/WARP REMARK 200 STARTING MODEL: PDB ENTRY 1HLE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, 0.1 M TRIS, PH 9.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 20.96800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.36850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.79750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.36850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.96800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.79750 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 3 REMARK 465 SER A 4 REMARK 465 ALA A 325 REMARK 465 GLY B 326 REMARK 465 ALA B 327 REMARK 465 MET B 328 REMARK 465 PRO B 329 REMARK 465 PRO B 330 REMARK 465 ARG B 331 REMARK 465 ARG B 332 REMARK 465 GLN B 368 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 ALA A 52 -131.71 24.23 REMARK 500 ASP A 110 51.82 37.99 REMARK 500 ASN A 230 79.61 -161.70 REMARK 500 REMARK 500 REMARK: NULL DBREF 1MTP A 3 325 GB 23019748 ZP_00059457 55 377 DBREF 1MTP B 326 368 GB 23019748 ZP_00059457 378 420 SEQADV 1MTP THR A 78 GB 23019748 ALA 130 CONFLICT SEQADV 1MTP MET A 105 GB 23019748 VAL 157 CONFLICT SEQADV 1MTP LYS A 165 GB 23019748 ARG 217 CONFLICT SEQADV 1MTP LYS A 198 GB 23019748 GLY 250 CONFLICT SEQADV 1MTP ARG A 209 GB 23019748 GLY 261 CONFLICT SEQRES 1 A 323 MET SER GLY GLY PHE LEU ARG ASP ASP HIS LEU GLU PHE SEQRES 2 A 323 ALA LEU HIS LEU HIS ARG ARG LEU ALA GLU ALA VAL PRO SEQRES 3 A 323 ASP GLY GLU VAL ILE TRP SER PRO TYR SER VAL ALA CYS SEQRES 4 A 323 ALA LEU GLY VAL LEU ALA ALA GLY ALA ARG ALA THR THR SEQRES 5 A 323 ARG THR GLU LEU THR THR LEU LEU GLY THR ASP PRO ALA SEQRES 6 A 323 PRO LEU LEU ALA ALA LEU ASP ARG ALA VAL THR ASP SER SEQRES 7 A 323 PRO ASP LEU ALA SER ARG THR VAL LEU TRP VAL SER ALA SEQRES 8 A 323 ASP VAL PRO VAL ARG SER SER PHE ARG ALA THR MET HIS SEQRES 9 A 323 ASP ARG PRO ASP SER ASP VAL ARG THR ALA ASP PHE ARG SEQRES 10 A 323 THR ASN PRO GLU GLY VAL ARG ALA THR VAL ASN ALA ASP SEQRES 11 A 323 ILE ALA ASP ALA THR ARG GLY MET ILE ARG GLU LEU LEU SEQRES 12 A 323 PRO GLN GLY ALA VAL THR PRO ASP LEU ARG ALA ILE LEU SEQRES 13 A 323 THR ASN ALA LEU TRP ALA LYS ALA ARG TRP THR THR PRO SEQRES 14 A 323 PHE GLU ALA HIS LEU THR ARG GLU GLY THR PHE ARG THR SEQRES 15 A 323 PRO ARG GLY PRO LYS ARG VAL PRO PHE MET HIS ARG THR SEQRES 16 A 323 LYS THR MET PRO TYR ALA THR ALA ARG GLY TRP ARG MET SEQRES 17 A 323 VAL THR LEU HIS ALA HIS ASP GLU LEU ALA VAL ASP VAL SEQRES 18 A 323 LEU LEU PRO PRO GLY THR ASN ALA ALA ALA VAL PRO THR SEQRES 19 A 323 ALA PRO LEU LEU THR ALA LEU HIS ARG ARG SER ALA SER SEQRES 20 A 323 THR SER VAL GLU LEU ALA LEU PRO ARG PHE GLU LEU THR SEQRES 21 A 323 GLN PRO HIS GLN LEU VAL GLU VAL LEU ALA GLU ALA GLY SEQRES 22 A 323 VAL ARG THR LEU PHE THR ALA SER ALA ASP LEU SER GLY SEQRES 23 A 323 ILE SER THR VAL PRO LEU TYR VAL ASP THR VAL ILE HIS SEQRES 24 A 323 GLN ALA ARG LEU ARG VAL ASP GLU ARG GLY ALA GLU GLY SEQRES 25 A 323 ALA ALA ALA THR ALA ALA MET MET LEU LEU ALA SEQRES 1 B 43 GLY ALA MET PRO PRO ARG ARG THR ILE ARG PHE SER VAL SEQRES 2 B 43 ASP ARG PRO PHE HIS ILE VAL VAL ARG ARG ARG GLY ALA SEQRES 3 B 43 ILE LEU PHE LEU GLY SER ILE ALA ASP PRO HIS ASP PRO SEQRES 4 B 43 GLY PRO ALA GLN FORMUL 3 HOH *604(H2 O) HELIX 1 1 ARG A 9 VAL A 27 1 19 HELIX 2 2 SER A 35 GLY A 49 1 15 HELIX 3 3 ARG A 51 GLY A 63 1 13 HELIX 4 4 ASP A 65 VAL A 77 1 13 HELIX 5 5 ARG A 98 ARG A 108 1 11 HELIX 6 6 ASN A 121 THR A 137 1 17 HELIX 7 7 GLU A 173 THR A 177 5 5 HELIX 8 8 PRO A 227 ALA A 231 5 5 HELIX 9 9 THR A 236 SER A 247 1 12 HELIX 10 10 LEU A 267 ALA A 274 1 8 HELIX 11 11 ARG A 277 THR A 281 5 5 SHEET 1 A 4 ILE B 334 SER B 337 0 SHEET 2 A 4 ALA A 248 PRO A 257 1 N GLU A 253 O ILE B 334 SHEET 3 A 4 GLY A 187 ALA A 205 -1 N MET A 194 O LEU A 256 SHEET 4 A 4 ARG A 178 THR A 184 -1 N ARG A 178 O PHE A 193 SHEET 1 B 8 ILE B 334 SER B 337 0 SHEET 2 B 8 ALA A 248 PRO A 257 1 N GLU A 253 O ILE B 334 SHEET 3 B 8 GLY A 187 ALA A 205 -1 N MET A 194 O LEU A 256 SHEET 4 B 8 TRP A 208 HIS A 214 -1 O TRP A 208 N ALA A 205 SHEET 5 B 8 LEU A 219 LEU A 225 -1 O VAL A 221 N LEU A 213 SHEET 6 B 8 PHE B 342 ARG B 348 -1 O HIS B 343 N LEU A 224 SHEET 7 B 8 ALA B 351 ILE B 358 -1 O PHE B 354 N VAL B 346 SHEET 8 B 8 VAL A 32 TRP A 34 -1 N VAL A 32 O SER B 357 SHEET 1 C 6 ASP A 112 THR A 115 0 SHEET 2 C 6 LEU A 83 VAL A 91 1 N VAL A 91 O ARG A 114 SHEET 3 C 6 LEU A 154 ARG A 167 -1 O ILE A 157 N TRP A 90 SHEET 4 C 6 GLY A 311 LEU A 323 -1 O MET A 322 N ALA A 156 SHEET 5 C 6 TYR A 295 ASP A 308 -1 N ILE A 300 O ALA A 319 SHEET 6 C 6 PHE A 259 GLN A 266 -1 N PHE A 259 O VAL A 307 CRYST1 41.936 65.595 124.737 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 0.023846 -0.000001 -0.000001 0.00000 SCALE2 0.000000 0.015245 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008017 0.00000