HEADER ANTI-COAGULANT 14-OCT-98 1BX7 TITLE HIRUSTASIN FROM HIRUDO MEDICINALIS AT 1.2 ANGSTROMS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIRUSTASIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 3 ORGANISM_COMMON: MEDICINAL LEECH; SOURCE 4 ORGANISM_TAXID: 6421; SOURCE 5 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 6 EXPRESSION_SYSTEM_COMMON: BAKER'S YEAST; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932 KEYWDS ANTI-COAGULANT, PEPTIDIC INHIBITORS, CONFORMATIONAL FLEXIBILITY, KEYWDS 2 SERINE PROTEASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR I.USON,G.M.SHELDRICK,E.DE LA FORTELLE,G.BRICOGNE,S.DI MARCO, AUTHOR 2 J.P.PRIESTLE,M.G.GRUETTER,P.R.E.MITTL REVDAT 5 23-OCT-24 1BX7 1 REMARK REVDAT 4 05-JUN-24 1BX7 1 REMARK REVDAT 3 24-FEB-09 1BX7 1 VERSN REVDAT 2 01-APR-03 1BX7 1 JRNL REVDAT 1 27-APR-99 1BX7 0 JRNL AUTH I.USON,G.M.SHELDRICK,E.DE LA FORTELLE,G.BRICOGNE,S.DI MARCO, JRNL AUTH 2 J.P.PRIESTLE,M.G.GRUTTER,P.R.MITTL JRNL TITL THE 1.2 A CRYSTAL STRUCTURE OF HIRUSTASIN REVEALS THE JRNL TITL 2 INTRINSIC FLEXIBILITY OF A FAMILY OF HIGHLY JRNL TITL 3 DISULPHIDE-BRIDGED INHIBITORS. JRNL REF STRUCTURE FOLD.DES. V. 7 55 1999 JRNL REFN ISSN 0969-2126 JRNL PMID 10368273 JRNL DOI 10.1016/S0969-2126(99)80009-4 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.R.MITTL,S.DI MARCO,G.FENDRICH,G.POHLIG,J.HEIM, REMARK 1 AUTH 2 C.SOMMERHOFF,H.FRITZ,J.P.PRIESTLE,M.G.GRUTTER REMARK 1 TITL A NEW STRUCTURAL CLASS OF SERINE PROTEASE INHIBITORS REMARK 1 TITL 2 REVEALED BY THE STRUCTURE OF THE HIRUSTASIN-KALLIKREIN REMARK 1 TITL 3 COMPLEX REMARK 1 REF STRUCTURE V. 5 253 1997 REMARK 1 REFN ISSN 0969-2126 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.R.MITTL,S.DI MARCO,G.FENDRICH,G.POHLIG,J.HEIM, REMARK 1 AUTH 2 C.SOMMERHOFF,H.FRITZ,J.P.PRIESTLE,M.G.GRUTTER REMARK 1 TITL ERRATUM. A NEW STRUCTURAL CLASS OF SERINE PROTEASE REMARK 1 TITL 2 INHIBITORS REVEALED BY THE STRUCTURE OF THE REMARK 1 TITL 3 HIRUSTASIN-KALLIKREIN COMPLEX REMARK 1 REF STRUCTURE V. 5 585 1997 REMARK 1 REFN ISSN 0969-2126 REMARK 1 REFERENCE 3 REMARK 1 AUTH S.DI MARCO,G.FENDRICH,R.KNECHT,A.STRAUSS,G.POHLIG,J.HEIM, REMARK 1 AUTH 2 J.P.PRIESTLE,C.P.SOMMERHOFF,M.G.GRUTTER REMARK 1 TITL RECOMBINANT HIRUSTASIN: PRODUCTION IN YEAST, REMARK 1 TITL 2 CRYSTALLIZATION, AND INTERACTION WITH SERINE PROTEASES REMARK 1 REF PROTEIN SCI. V. 6 109 1997 REMARK 1 REFN ISSN 0961-8368 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.180 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.179 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 792 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 15894 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.129 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.127 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 522 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 10289 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 366 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 52 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 417.02 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 342.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 5 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 4045 REMARK 3 NUMBER OF RESTRAINTS : 4895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.036 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.029 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.140 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.120 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.042 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.097 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.096 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY 2% REMARK 4 REMARK 4 1BX7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172130. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NOV-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.45 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.050 REMARK 200 MONOCHROMATOR : GE(111) REMARK 200 OPTICS : BENT CRYSTAL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MARSCALE, MARXDS REMARK 200 DATA SCALING SOFTWARE : MARSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15928 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 25.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.37600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.610 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELXL-97 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: TWO DIFFERENT INDEPENDENT METHODS WERE USED FOR STRUCTURE REMARK 200 SOLUTION REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.45 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 33.90600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 18.85650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 18.85650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.85900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 18.85650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 18.85650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 16.95300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 18.85650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 18.85650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 50.85900 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 18.85650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 18.85650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 16.95300 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 33.90600 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 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 130 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 THR A 1 REMARK 465 GLN A 2 REMARK 465 SER A 54 REMARK 465 GLN A 55 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 21 CD CE NZ 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLU A 9 CB - CG - CD ANGL. DEV. = 18.0 DEGREES REMARK 500 GLU A 26 CA - CB - CG ANGL. DEV. = 13.2 DEGREES REMARK 500 ARG A 32 CD - NE - CZ ANGL. DEV. = 12.1 DEGREES REMARK 500 GLU A 45 OE1 - CD - OE2 ANGL. DEV. = -11.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 45 62.60 -106.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 101 DBREF 1BX7 A 1 55 UNP P80302 ANTA_HIRME 1 55 SEQRES 1 A 55 THR GLN GLY ASN THR CYS GLY GLY GLU THR CYS SER ALA SEQRES 2 A 55 ALA GLN VAL CYS LEU LYS GLY LYS CYS VAL CYS ASN GLU SEQRES 3 A 55 VAL HIS CYS ARG ILE ARG CYS LYS TYR GLY LEU LYS LYS SEQRES 4 A 55 ASP GLU ASN GLY CYS GLU TYR PRO CYS SER CYS ALA LYS SEQRES 5 A 55 ALA SER GLN HET SO4 A 100 5 HET SO4 A 101 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *52(H2 O) SHEET 1 A 2 GLN A 15 LEU A 18 0 SHEET 2 A 2 LYS A 21 CYS A 24 -1 N VAL A 23 O VAL A 16 SSBOND 1 CYS A 6 CYS A 17 1555 1555 2.04 SSBOND 2 CYS A 11 CYS A 22 1555 1555 2.03 SSBOND 3 CYS A 24 CYS A 44 1555 1555 2.05 SSBOND 4 CYS A 29 CYS A 48 1555 1555 2.03 SSBOND 5 CYS A 33 CYS A 50 1555 1555 2.04 CISPEP 1 TYR A 46 PRO A 47 0 -9.16 SITE 1 AC1 6 ARG A 30 LYS A 38 ALA A 51 LYS A 52 SITE 2 AC1 6 ALA A 53 HOH A 112 SITE 1 AC2 5 HIS A 28 ARG A 30 LYS A 38 LYS A 52 SITE 2 AC2 5 HOH A 139 CRYST1 37.713 37.713 67.812 90.00 90.00 90.00 P 43 21 2 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 0.026516 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026516 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014747 0.00000