HEADER BLOOD CLOTTING 21-JAN-00 1DVN TITLE LATENT FORM OF PLASMINOGEN ACTIVATOR INHIBITOR-1 (PAI-1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLASMINOGEN ACTIVATOR INHIBITOR-1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UMBILICAL VEIN ENDOTHELIUM LIBRARY; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTRCHIS2A KEYWDS SERPIN, PAI-1, INHIBITOR, BLOOD CLOTTING EXPDTA X-RAY DIFFRACTION AUTHOR T.J.STOUT,H.GRAHAM,D.I.BUCKLEY,D.J.MATTHEWS REVDAT 5 07-FEB-24 1DVN 1 REMARK REVDAT 4 03-NOV-21 1DVN 1 REMARK SEQADV REVDAT 3 04-OCT-17 1DVN 1 REMARK REVDAT 2 24-FEB-09 1DVN 1 VERSN REVDAT 1 13-SEP-00 1DVN 0 JRNL AUTH T.J.STOUT,H.GRAHAM,D.I.BUCKLEY,D.J.MATTHEWS JRNL TITL STRUCTURES OF ACTIVE AND LATENT PAI-1: A POSSIBLE JRNL TITL 2 STABILIZING ROLE FOR CHLORIDE IONS. JRNL REF BIOCHEMISTRY V. 39 8460 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10913251 JRNL DOI 10.1021/BI000290W REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 98.0 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.5 REMARK 3 NUMBER OF REFLECTIONS : 21869 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) : 0.236 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1108 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3040 REMARK 3 BIN R VALUE (WORKING SET) : 0.2840 REMARK 3 BIN FREE R VALUE : 0.3330 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 172 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3013 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 313 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.33 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) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.32 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.070 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) : 2.060 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.170 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.390 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.820 ; 2.500 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DVN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-00. REMARK 100 THE DEPOSITION ID IS D_1000010412. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-98 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 7.9 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 : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23999 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 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: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG1000, MPD, MGSO4, TRIS, PH 7.9, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 77.29050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.34850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 77.29050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.34850 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 TYR A 79 CG CD1 CD2 CE1 CE2 CZ OH REMARK 480 ARG A 115 CD NE CZ NH1 NH2 REMARK 480 LYS A 154 CD CE NZ 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 LYS A 88 -59.46 69.40 REMARK 500 LEU A 103 101.42 -34.85 REMARK 500 ARG A 118 -17.51 64.80 REMARK 500 THR A 120 116.19 63.23 REMARK 500 HIS A 185 51.50 -112.82 REMARK 500 ASP A 217 34.31 -77.33 REMARK 500 SER A 344 99.91 82.51 REMARK 500 ARG A 356 100.78 -32.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DVM RELATED DB: PDB REMARK 900 ACTIVE FORM OF PLASMINOGEN ACTIVATOR INHIBITOR-1 (PAI-1) DBREF 1DVN A 1 379 UNP P05121 PAI1_HUMAN 24 402 SEQADV 1DVN ASN A 150 UNP P05121 HIS 173 ENGINEERED MUTATION SEQADV 1DVN LYS A 154 UNP P05121 THR 177 ENGINEERED MUTATION SEQADV 1DVN GLN A 319 UNP P05121 LEU 342 ENGINEERED MUTATION SEQADV 1DVN MET A 354 UNP P05121 ILE 377 ENGINEERED MUTATION SEQRES 1 A 379 VAL HIS HIS PRO PRO SER TYR VAL ALA HIS LEU ALA SER SEQRES 2 A 379 ASP PHE GLY VAL ARG VAL PHE GLN GLN VAL ALA GLN ALA SEQRES 3 A 379 SER LYS ASP ARG ASN VAL VAL PHE SER PRO TYR GLY VAL SEQRES 4 A 379 ALA SER VAL LEU ALA MET LEU GLN LEU THR THR GLY GLY SEQRES 5 A 379 GLU THR GLN GLN GLN ILE GLN ALA ALA MET GLY PHE LYS SEQRES 6 A 379 ILE ASP ASP LYS GLY MET ALA PRO ALA LEU ARG HIS LEU SEQRES 7 A 379 TYR LYS GLU LEU MET GLY PRO TRP ASN LYS ASP GLU ILE SEQRES 8 A 379 SER THR THR ASP ALA ILE PHE VAL GLN ARG ASP LEU LYS SEQRES 9 A 379 LEU VAL GLN GLY PHE MET PRO HIS PHE PHE ARG LEU PHE SEQRES 10 A 379 ARG SER THR VAL LYS GLN VAL ASP PHE SER GLU VAL GLU SEQRES 11 A 379 ARG ALA ARG PHE ILE ILE ASN ASP TRP VAL LYS THR HIS SEQRES 12 A 379 THR LYS GLY MET ILE SER ASN LEU LEU GLY LYS GLY ALA SEQRES 13 A 379 VAL ASP GLN LEU THR ARG LEU VAL LEU VAL ASN ALA LEU SEQRES 14 A 379 TYR PHE ASN GLY GLN TRP LYS THR PRO PHE PRO ASP SER SEQRES 15 A 379 SER THR HIS ARG ARG LEU PHE HIS LYS SER ASP GLY SER SEQRES 16 A 379 THR VAL SER VAL PRO MET MET ALA GLN THR ASN LYS PHE SEQRES 17 A 379 ASN TYR THR GLU PHE THR THR PRO ASP GLY HIS TYR TYR SEQRES 18 A 379 ASP ILE LEU GLU LEU PRO TYR HIS GLY ASP THR LEU SER SEQRES 19 A 379 MET PHE ILE ALA ALA PRO TYR GLU LYS GLU VAL PRO LEU SEQRES 20 A 379 SER ALA LEU THR ASN ILE LEU SER ALA GLN LEU ILE SER SEQRES 21 A 379 HIS TRP LYS GLY ASN MET THR ARG LEU PRO ARG LEU LEU SEQRES 22 A 379 VAL LEU PRO LYS PHE SER LEU GLU THR GLU VAL ASP LEU SEQRES 23 A 379 ARG LYS PRO LEU GLU ASN LEU GLY MET THR ASP MET PHE SEQRES 24 A 379 ARG GLN PHE GLN ALA ASP PHE THR SER LEU SER ASP GLN SEQRES 25 A 379 GLU PRO LEU HIS VAL ALA GLN ALA LEU GLN LYS VAL LYS SEQRES 26 A 379 ILE GLU VAL ASN GLU SER GLY THR VAL ALA SER SER SER SEQRES 27 A 379 THR ALA VAL ILE VAL SER ALA ARG MET ALA PRO GLU GLU SEQRES 28 A 379 ILE ILE MET ASP ARG PRO PHE LEU PHE VAL VAL ARG HIS SEQRES 29 A 379 ASN PRO THR GLY THR VAL LEU PHE MET GLY GLN VAL MET SEQRES 30 A 379 GLU PRO FORMUL 2 HOH *313(H2 O) HELIX 1 1 HIS A 3 SER A 27 1 25 HELIX 2 2 SER A 35 THR A 50 1 16 HELIX 3 3 GLY A 51 GLY A 63 1 13 HELIX 4 4 GLY A 70 GLY A 84 1 15 HELIX 5 5 PRO A 85 LYS A 88 5 4 HELIX 6 6 GLY A 108 ARG A 118 1 11 HELIX 7 7 GLU A 128 THR A 144 1 17 HELIX 8 8 LEU A 247 ASN A 252 1 6 HELIX 9 9 SER A 255 ASN A 265 1 11 HELIX 10 10 LEU A 286 LEU A 293 1 8 HELIX 11 11 THR A 296 ARG A 300 5 5 SHEET 1 A 3 THR A 267 PRO A 276 0 SHEET 2 A 3 THR A 196 THR A 214 -1 O MET A 202 N LEU A 275 SHEET 3 A 3 ARG A 186 HIS A 190 -1 O ARG A 187 N VAL A 199 SHEET 1 B 7 THR A 267 PRO A 276 0 SHEET 2 B 7 THR A 196 THR A 214 -1 O MET A 202 N LEU A 275 SHEET 3 B 7 TYR A 220 PRO A 227 -1 N TYR A 221 O PHE A 213 SHEET 4 B 7 LEU A 233 PRO A 240 -1 N MET A 235 O LEU A 226 SHEET 5 B 7 PRO A 357 HIS A 364 -1 O LEU A 359 N ALA A 238 SHEET 6 B 7 THR A 369 MET A 377 -1 O THR A 369 N HIS A 364 SHEET 7 B 7 VAL A 32 PHE A 34 -1 O VAL A 32 N GLN A 375 SHEET 1 C 6 LYS A 122 VAL A 124 0 SHEET 2 C 6 GLU A 90 GLN A 100 1 O ILE A 97 N LYS A 122 SHEET 3 C 6 LEU A 163 GLN A 174 -1 O VAL A 164 N PHE A 98 SHEET 4 C 6 GLY A 332 VAL A 343 -1 O THR A 333 N GLY A 173 SHEET 5 C 6 GLN A 319 VAL A 328 -1 O GLN A 319 N ILE A 342 SHEET 6 C 6 PHE A 278 ASP A 285 -1 O PHE A 278 N VAL A 328 CRYST1 154.581 46.697 61.966 90.00 107.11 90.00 C 1 2 1 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 0.006469 0.000000 0.001992 0.00000 SCALE2 0.000000 0.021415 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016886 0.00000