PDB Short entry for 1D0D HEADER BLOOD CLOTTING INHIBITOR 09-SEP-99 1D0D TITLE CRYSTAL STRUCTURE OF TICK ANTICOAGULANT PROTEIN COMPLEXED WITH BOVINE TITLE 2 PANCREATIC TRYPSIN INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTICOAGULANT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TAP; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PANCREATIC TRYPSIN INHIBITOR; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: BPTI SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORNITHODOROS MOUBATA; SOURCE 3 ORGANISM_TAXID: 6938; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 6 ORGANISM_COMMON: CATTLE; SOURCE 7 ORGANISM_TAXID: 9913; SOURCE 8 ORGAN: PANCREAS KEYWDS FACTOR XA INHIBITOR, KUNITZ INHIBITOR, BLOOD CLOTTING INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR R.ST.CHARLES,K.PADMANABHAN,R.V.ARNI,K.P.PADMANABHAN,A.TULINSKY REVDAT 9 04-APR-18 1D0D 1 REMARK REVDAT 8 31-JAN-18 1D0D 1 AUTHOR JRNL REVDAT 7 24-JAN-18 1D0D 1 JRNL REVDAT 6 11-OCT-17 1D0D 1 REMARK REVDAT 5 04-OCT-17 1D0D 1 REMARK REVDAT 4 01-FEB-17 1D0D 1 AUTHOR JRNL VERSN REVDAT 3 24-FEB-09 1D0D 1 VERSN REVDAT 2 01-APR-03 1D0D 1 JRNL REVDAT 1 09-SEP-00 1D0D 0 JRNL AUTH R.ST.CHARLES,K.PADMANABHAN,R.V.ARNI,K.P.PADMANABHAN, JRNL AUTH 2 A.TULINSKY JRNL TITL STRUCTURE OF TICK ANTICOAGULANT PEPTIDE AT 1.6 A RESOLUTION JRNL TITL 2 COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR. JRNL REF PROTEIN SCI. V. 9 265 2000 JRNL REFN ISSN 0961-8368 JRNL PMID 10716178 REMARK 2 REMARK 2 RESOLUTION. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 12942 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 665 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 943 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 124 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.80 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1D0D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-99. REMARK 100 THE DEPOSITION ID IS D_1000009676. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-93 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 6.5 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 RU200 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 II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13056 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 47.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.33600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, ADA, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 25.20542 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 12.60271 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.80814 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 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 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 ASN B 44 111.96 -160.48 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 B 59 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 60 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 61 DBREF 1D0D A 1 60 UNP P17726 TAP_ORNMO 1 60 DBREF 1D0D B 1 58 UNP P00974 BPT1_BOVIN 36 93 SEQRES 1 A 60 TYR ASN ARG LEU CYS ILE LYS PRO ARG ASP TRP ILE ASP SEQRES 2 A 60 GLU CYS ASP SER ASN GLU GLY GLY GLU ARG ALA TYR PHE SEQRES 3 A 60 ARG ASN GLY LYS GLY GLY CYS ASP SER PHE TRP ILE CYS SEQRES 4 A 60 PRO GLU ASP HIS THR GLY ALA ASP TYR TYR SER SER TYR SEQRES 5 A 60 ARG ASP CYS PHE ASN ALA CYS ILE SEQRES 1 B 58 ARG PRO ASP PHE CYS LEU GLU PRO PRO TYR THR GLY PRO SEQRES 2 B 58 CYS LYS ALA ARG ILE ILE ARG TYR PHE TYR ASN ALA LYS SEQRES 3 B 58 ALA GLY LEU CYS GLN THR PHE VAL TYR GLY GLY CYS ARG SEQRES 4 B 58 ALA LYS ARG ASN ASN PHE LYS SER ALA GLU ASP CYS MET SEQRES 5 B 58 ARG THR CYS GLY GLY ALA HET SO4 B 59 5 HET SO4 B 60 5 HET SO4 B 61 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 HOH *124(H2 O) HELIX 1 1 ASN A 2 ILE A 6 5 5 HELIX 2 2 ASP A 16 GLY A 20 5 5 HELIX 3 3 SER A 51 ILE A 60 1 10 HELIX 4 4 PRO B 2 GLU B 7 5 6 HELIX 5 5 SER B 47 GLY B 56 1 10 SHEET 1 A 2 GLU A 22 ARG A 27 0 SHEET 2 A 2 CYS A 33 ILE A 38 -1 N ASP A 34 O PHE A 26 SHEET 1 B 2 ILE B 18 ASN B 24 0 SHEET 2 B 2 LEU B 29 TYR B 35 -1 O LEU B 29 N ASN B 24 SSBOND 1 CYS A 5 CYS A 59 1555 1555 2.03 SSBOND 2 CYS A 15 CYS A 39 1555 1555 2.03 SSBOND 3 CYS A 33 CYS A 55 1555 1555 2.03 SSBOND 4 CYS B 5 CYS B 55 1555 1555 2.03 SSBOND 5 CYS B 14 CYS B 38 1555 1555 2.04 SSBOND 6 CYS B 30 CYS B 51 1555 1555 2.04 SITE 1 AC1 6 ASN A 2 TYR A 49 ARG B 42 HOH B 121 SITE 2 AC1 6 HOH B 253 HOH B 279 SITE 1 AC2 5 LYS B 15 ALA B 16 ARG B 17 HOH B 217 SITE 2 AC2 5 HOH B 254 SITE 1 AC3 3 ARG B 20 TYR B 35 ALA B 40 CRYST1 46.870 46.870 50.350 90.00 90.00 90.00 P 41 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 0.021277 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021277 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019837 0.00000