HEADER SERINE PROTEASE 19-SEP-97 5HPG TITLE STRUCTURE AND LIGAND DETERMINANTS OF THE RECOMBINANT KRINGLE 5 DOMAIN TITLE 2 OF HUMAN PLASMINOGEN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLASMINOGEN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: KRINGLE 5; COMPND 5 EC: 3.4.21.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SERINE PROTEASE, KRINGLE 5, HUMAN PLASMINOGEN, FIBRINOLYSIS EXPDTA X-RAY DIFFRACTION AUTHOR A.TULINSKY,I.MOCHALKIN,F.J.CASTELLINO REVDAT 4 09-AUG-23 5HPG 1 SEQADV REVDAT 3 24-FEB-09 5HPG 1 VERSN REVDAT 2 12-APR-05 5HPG 1 AUTHOR JRNL REMARK REVDAT 1 25-MAR-98 5HPG 0 JRNL AUTH Y.CHANG,I.MOCHALKIN,S.G.MCCANCE,B.CHENG,A.TULINSKY, JRNL AUTH 2 F.J.CASTELLINO JRNL TITL STRUCTURE AND LIGAND BINDING DETERMINANTS OF THE RECOMBINANT JRNL TITL 2 KRINGLE 5 DOMAIN OF HUMAN PLASMINOGEN. JRNL REF BIOCHEMISTRY V. 37 3258 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9521645 JRNL DOI 10.1021/BI972284E REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROFFT REMARK 3 AUTHORS : KONNERT,HENDRICKSON,FINZEL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.0 REMARK 3 NUMBER OF REFLECTIONS : 15014 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) : 0.166 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. 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) : 16720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1296 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 193 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.40 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.016 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.034 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.050 ; 0.040 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) : 0.160 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.180 ; 0.800 REMARK 3 MULTIPLE TORSION (A) : 0.240 ; 0.800 REMARK 3 H-BOND (X...Y) (A) : 0.230 ; 0.800 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) : 5.200 ; 3.000 REMARK 3 STAGGERED (DEGREES) : 17.800; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 22.400; 20.000 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 5HPG 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_1000179725. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : APR-97 REMARK 200 TEMPERATURE (KELVIN) : 123 REMARK 200 PH : 7.0 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MSC-YALE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : RIGAKU R-AXIS, R-AXIS (RIGAKU) REMARK 200 DATA SCALING SOFTWARE : R-AXIS (RIGAKU) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16720 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 35.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 72.0 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : 0.05100 REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 37.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.08700 REMARK 200 R SYM FOR SHELL (I) : 0.13000 REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1PKR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% (W/V) PEG 8000, 0.1 M NA-HEPES, PH REMARK 280 7.0, 0.15 M LI2(SO4) REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 38.71500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.60000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.71500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.60000 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 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 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 ARG A 43 NE CZ NH1 NH2 REMARK 470 GLU A 47 CG CD OE1 OE2 REMARK 470 LYS A 48 CE NZ REMARK 470 ARG B 43 NE CZ NH1 NH2 REMARK 470 GLU B 47 CD OE1 OE2 REMARK 470 LYS B 48 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 ARG A 10 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 GLU A 29 CG - CD - OE2 ANGL. DEV. = 12.8 DEGREES REMARK 500 ARG A 32 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 52 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 52 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 57 CB - CG - OD1 ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG A 69 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 TYR A 74 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG B 10 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 32 CD - NE - CZ ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG B 32 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 69 NE - CZ - NH2 ANGL. DEV. = 3.7 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 LYS A 48 -124.75 59.19 REMARK 500 VAL B 14 21.52 -142.78 REMARK 500 LYS B 48 -131.04 43.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 69 0.20 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ARG A 43 -14.36 REMARK 500 CYS A 75 -13.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: LBS REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: LYSINE BINDING SITE. DBREF 5HPG A 0 83 UNP P00747 PLMN_HUMAN 480 563 DBREF 5HPG B 0 83 UNP P00747 PLMN_HUMAN 480 563 SEQADV 5HPG VAL A 14 UNP P00747 ALA 494 CONFLICT SEQADV 5HPG VAL B 14 UNP P00747 ALA 494 CONFLICT SEQRES 1 A 84 ASP CYS MET PHE GLY ASN GLY LYS GLY TYR ARG GLY LYS SEQRES 2 A 84 ARG VAL THR THR VAL THR GLY THR PRO CYS GLN ASP TRP SEQRES 3 A 84 ALA ALA GLN GLU PRO HIS ARG HIS SER ILE PHE THR PRO SEQRES 4 A 84 GLU THR ASN PRO ARG ALA GLY LEU GLU LYS ASN TYR CYS SEQRES 5 A 84 ARG ASN PRO ASP GLY ASP VAL GLY GLY PRO TRP CYS TYR SEQRES 6 A 84 THR THR ASN PRO ARG LYS LEU TYR ASP TYR CYS ASP VAL SEQRES 7 A 84 PRO GLN CYS ALA ALA PRO SEQRES 1 B 84 ASP CYS MET PHE GLY ASN GLY LYS GLY TYR ARG GLY LYS SEQRES 2 B 84 ARG VAL THR THR VAL THR GLY THR PRO CYS GLN ASP TRP SEQRES 3 B 84 ALA ALA GLN GLU PRO HIS ARG HIS SER ILE PHE THR PRO SEQRES 4 B 84 GLU THR ASN PRO ARG ALA GLY LEU GLU LYS ASN TYR CYS SEQRES 5 B 84 ARG ASN PRO ASP GLY ASP VAL GLY GLY PRO TRP CYS TYR SEQRES 6 B 84 THR THR ASN PRO ARG LYS LEU TYR ASP TYR CYS ASP VAL SEQRES 7 B 84 PRO GLN CYS ALA ALA PRO FORMUL 3 HOH *193(H2 O) SHEET 1 A 2 TRP A 62 TYR A 64 0 SHEET 2 A 2 TYR A 72 TYR A 74 -1 N ASP A 73 O CYS A 63 SHEET 1 B 2 TRP B 62 TYR B 64 0 SHEET 2 B 2 TYR B 72 TYR B 74 -1 N ASP B 73 O CYS B 63 SSBOND 1 CYS A 1 CYS A 80 1555 1555 2.04 SSBOND 2 CYS A 22 CYS A 63 1555 1555 2.08 SSBOND 3 CYS A 51 CYS A 75 1555 1555 2.05 SSBOND 4 CYS B 1 CYS B 80 1555 1555 2.02 SSBOND 5 CYS B 22 CYS B 63 1555 1555 2.06 SSBOND 6 CYS B 51 CYS B 75 1555 1555 2.07 CISPEP 1 GLU A 29 PRO A 30 0 2.58 CISPEP 2 GLU B 29 PRO B 30 0 -2.20 SITE 1 LBS 4 ASP A 55 ASP A 57 ASP B 55 ASP B 57 CRYST1 77.430 79.200 30.780 90.00 90.00 90.00 P 21 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 0.012915 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012626 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032489 0.00000 MTRIX1 1 -0.847210 -0.074010 -0.526070 31.74900 1 MTRIX2 1 -0.030510 -0.981840 0.187260 53.68800 1 MTRIX3 1 -0.530370 0.174700 0.829570 3.80200 1