HEADER SERINE PROTEASE INHIBITOR 11-NOV-97 2PSI OBSLTE 27-SEP-99 2PSI 1QLP TITLE INTACT WILDTYPE RECOMBINANT ALPHA-1-ANTITRYPSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-1-ANTITRYPSIN; COMPND 3 CHAIN: NULL; COMPND 4 SYNONYM: ALPHA-1-PROTEINASE INHIBITOR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGAN: LIVER; SOURCE 5 TISSUE: HEPATOCYTES; SOURCE 6 CELL: NEUTROPHILS; SOURCE 7 CELLULAR_LOCATION: SECRETED; SOURCE 8 GENE: ALPHA-1-ANTITRYPSIN; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: BL21 DE3; SOURCE 11 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PTERMAT; SOURCE 13 EXPRESSION_SYSTEM_GENE: ALPHA-1-ANTITRYPSIN KEYWDS SERINE PROTEASE INHIBITOR, SERPIN, GLYCOPROTEIN, SIGNAL, KEYWDS 2 POLYMORPHISM, EMPHYSEMA, DISEASE MUTATION, ACUTE PHASE EXPDTA X-RAY DIFFRACTION AUTHOR P.R.ELLIOTT,J.-P.ABRAHAMS,D.A.LOMAS REVDAT 2 27-SEP-99 2PSI 1 OBSLTE REVDAT 1 28-JAN-98 2PSI 0 JRNL AUTH P.R.ELLIOTT,J.-P.ABRAHAMS,D.A.LOMAS JRNL TITL WILDTYPE ALPHA1-ANTITRYPSIN IS IN THE CANONICAL JRNL TITL 2 INHIBITORY CONFORMATION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5D REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 7612 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD :FREE R REMARK 3 FREE R VALUE TEST SET SELECTION :RANDOM REMARK 3 R VALUE (WORKING + TEST SET) :0.222 REMARK 3 R VALUE (WORKING SET) :0.219 REMARK 3 FREE R VALUE :0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) :11.000 REMARK 3 FREE R VALUE TEST SET COUNT :970 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2956 REMARK 3 NUCLEIC ACID ATOMS : NULL REMARK 3 HETEROGEN ATOMS : NULL REMARK 3 SOLVENT ATOMS : NULL REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 72.562 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.005 ; 0.800 ; 3016 REMARK 3 BOND ANGLES (DEGREES) : 0.946 ; 1.200 ; 4060 REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : TNT REMARK 3 KSOL : 0.80 REMARK 3 BSOL : 215.00 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : PROTGEO.DAT, PARHCSDX.PRO REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : BCORREL.DAT REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2PSI COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-1997 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ELLIOT GX-11 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NICKEL COATED DOUBLE REMARK 200 REMARK 200 DETECTOR TYPE : 18 CM IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7612 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.910 REMARK 200 RESOLUTION RANGE LOW (A) : 24.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : 0.08900 REMARK 200 FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.22000 REMARK 200 R SYM FOR SHELL (I) : 0.22000 REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: THERMOSTABLE VARIANT ALPHA1-ANTITRYPSIN (PDB REMARK 200 ENTRY 1PSI) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.0 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 1/2+X,1/2+Y,Z REMARK 290 4555 1/2-X,1/2+Y,-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 56.86000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.21000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.86000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.21000 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 1 REMARK 465 ASP 2 REMARK 465 PRO 3 REMARK 465 GLN 4 REMARK 465 GLY 5 REMARK 465 ASP 6 REMARK 465 ALA 7 REMARK 465 ALA 8 REMARK 465 GLN 9 REMARK 465 LYS 10 REMARK 465 THR 11 REMARK 465 ASP 12 REMARK 465 THR 13 REMARK 465 SER 14 REMARK 465 HIS 15 REMARK 465 HIS 16 REMARK 465 ASP 17 REMARK 465 GLN 18 REMARK 465 ASP 19 REMARK 465 HIS 20 REMARK 465 PRO 21 REMARK 465 THR 22 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 NH1 ARG 223 OE2 GLU 354 2.19 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE 23 CB PHE 23 CG -0.062 REMARK 500 PHE 23 CD1 PHE 23 CE1 -0.065 REMARK 500 PHE 23 CE1 PHE 23 CZ -0.056 REMARK 500 PHE 23 CE2 PHE 23 CD2 -0.075 REMARK 500 HIS 139 CB HIS 139 CG 0.059 REMARK 500 HIS 262 CA HIS 262 CB 0.053 REMARK 500 LEU 263 CG LEU 263 CD1 -0.060 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLN 97 OE1 - CD - NE2 ANGL. DEV. = -9.8 DEGREES REMARK 500 GLN 97 CG - CD - NE2 ANGL. DEV. = 9.9 DEGREES REMARK 500 HIS 139 CB - CA - C ANGL. DEV. = -9.5 DEGREES REMARK 500 HIS 262 N - CA - C ANGL. DEV. =-10.7 DEGREES REMARK 500 LYS 290 N - CA - C ANGL. DEV. = -8.1 DEGREES REMARK 500 MET 385 N - CA - C ANGL. DEV. = -7.0 DEGREES REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 1PSI REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 1PSI REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: NUL REMARK 800 SITE_DESCRIPTION: ACTIVE SITE RESIDUES. REMARK 999 REMARK 999 SEQUENCE REMARK 999 2PSI SWS P01009 1 - 46 NOT IN ATOMS LIST DBREF 2PSI 23 394 UNP P01009 A1AT_HUMAN 47 418 SEQRES 1 394 MET ASP PRO GLN GLY ASP ALA ALA GLN LYS THR ASP THR SEQRES 2 394 SER HIS HIS ASP GLN ASP HIS PRO THR PHE ASN LYS ILE SEQRES 3 394 THR PRO ASN LEU ALA GLU PHE ALA PHE SER LEU TYR ARG SEQRES 4 394 GLN LEU ALA HIS GLN SER ASN SER THR ASN ILE PHE PHE SEQRES 5 394 SER PRO VAL SER ILE ALA THR ALA PHE ALA MET LEU SER SEQRES 6 394 LEU GLY THR LYS ALA ASP THR HIS ASP GLU ILE LEU GLU SEQRES 7 394 GLY LEU ASN PHE ASN LEU THR GLU ILE PRO GLU ALA GLN SEQRES 8 394 ILE HIS GLU GLY PHE GLN GLU LEU LEU ARG THR LEU ASN SEQRES 9 394 GLN PRO ASP SER GLN LEU GLN LEU THR THR GLY ASN GLY SEQRES 10 394 LEU PHE LEU SER GLU GLY LEU LYS LEU VAL ASP LYS PHE SEQRES 11 394 LEU GLU ASP VAL LYS LYS LEU TYR HIS SER GLU ALA PHE SEQRES 12 394 THR VAL ASN PHE GLY ASP THR GLU GLU ALA LYS LYS GLN SEQRES 13 394 ILE ASN ASP TYR VAL GLU LYS GLY THR GLN GLY LYS ILE SEQRES 14 394 VAL ASP LEU VAL LYS GLU LEU ASP ARG ASP THR VAL PHE SEQRES 15 394 ALA LEU VAL ASN TYR ILE PHE PHE LYS GLY LYS TRP GLU SEQRES 16 394 ARG PRO PHE GLU VAL LYS ASP THR GLU GLU GLU ASP PHE SEQRES 17 394 HIS VAL ASP GLN VAL THR THR VAL LYS VAL PRO MET MET SEQRES 18 394 LYS ARG LEU GLY MET PHE ASN ILE GLN HIS CYS LYS LYS SEQRES 19 394 LEU SER SER TRP VAL LEU LEU MET LYS TYR LEU GLY ASN SEQRES 20 394 ALA THR ALA ILE PHE PHE LEU PRO ASP GLU GLY LYS LEU SEQRES 21 394 GLN HIS LEU GLU ASN GLU LEU THR HIS ASP ILE ILE THR SEQRES 22 394 LYS PHE LEU GLU ASN GLU ASP ARG ARG SER ALA SER LEU SEQRES 23 394 HIS LEU PRO LYS LEU SER ILE THR GLY THR TYR ASP LEU SEQRES 24 394 LYS SER VAL LEU GLY GLN LEU GLY ILE THR LYS VAL PHE SEQRES 25 394 SER ASN GLY ALA ASP LEU SER GLY VAL THR GLU GLU ALA SEQRES 26 394 PRO LEU LYS LEU SER LYS ALA VAL HIS LYS ALA VAL LEU SEQRES 27 394 THR ILE ASP GLU LYS GLY THR GLU ALA ALA GLY ALA MET SEQRES 28 394 PHE LEU GLU ALA ILE PRO MET SER ILE PRO PRO GLU VAL SEQRES 29 394 LYS PHE ASN LYS PRO PHE VAL PHE LEU MET ILE GLU GLN SEQRES 30 394 ASN THR LYS SER PRO LEU PHE MET GLY LYS VAL VAL ASN SEQRES 31 394 PRO THR GLN LYS HELIX 1 1 THR 27 GLN 44 1 18 HELIX 2 2 PRO 54 GLY 67 1 14 HELIX 3 3 ALA 70 GLY 79 1 10 HELIX 4 4 GLU 89 ASN 104 1 16 HELIX 5 5 ASP 128 LYS 135 1 8 HELIX 6 6 THR 150 GLY 164 1 15 HELIX 7 7 VAL 200 ASP 202 5 3 HELIX 8 8 LEU 260 GLU 266 1 7 HELIX 9 9 HIS 269 LEU 276 1 8 HELIX 10 10 LEU 299 GLN 305 1 7 HELIX 11 11 LYS 310 PHE 312 5 3 SHEET 1 A 6 ILE 50 PHE 52 0 SHEET 2 A 6 PRO 382 VAL 388 -1 N LYS 387 O ILE 50 SHEET 3 A 6 PHE 370 GLU 376 -1 N MET 374 O LEU 383 SHEET 4 A 6 ALA 248 PRO 255 -1 N PHE 253 O VAL 371 SHEET 5 A 6 SER 237 LYS 243 -1 N MET 242 O ALA 250 SHEET 6 A 6 ILE 229 CYS 232 -1 N CYS 232 O SER 237 SHEET 1 B 5 GLU 141 VAL 145 0 SHEET 2 B 5 LEU 112 SER 121 1 N LEU 118 O GLU 141 SHEET 3 B 5 PHE 182 PHE 190 -1 N PHE 189 O THR 113 SHEET 4 B 5 LYS 331 ILE 340 1 N LYS 331 O LEU 184 SHEET 5 B 5 LEU 291 ASP 298 -1 N TYR 297 O HIS 334 SHEET 1 C 4 GLU 204 HIS 209 0 SHEET 2 C 4 THR 215 PHE 227 -1 N MET 220 O GLU 204 SHEET 3 C 4 ARG 282 PRO 289 -1 N LEU 288 O MET 221 SHEET 4 C 4 PRO 362 PHE 366 1 N PRO 362 O SER 285 SITE 1 NUL 1 MET 358 CRYST1 113.720 38.420 89.200 90.00 105.40 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 0.008794 0.000000 0.002422 0.00000 SCALE2 0.000000 0.026028 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011628 0.00000