HEADER LYSINE BINDING SITE 26-AUG-98 4KIV TITLE RECOMBINANT KRINGLE IV-10/W72R MUTANT OF HUMAN APOLIPOPROTEIN(A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOLIPOPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KRINGLE IV-10; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: KIV-10/W72R MUTANT OF HUMAN APOLIPOPROTEIN(A) 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 LYSINE BINDING SITE, SITE MUTATION EXPDTA X-RAY DIFFRACTION AUTHOR I.MOCHALKIN,A.TULINSKY,A.SCANU REVDAT 4 30-OCT-24 4KIV 1 SEQADV REVDAT 3 14-MAR-18 4KIV 1 SEQADV REVDAT 2 24-FEB-09 4KIV 1 VERSN REVDAT 1 18-MAY-99 4KIV 0 JRNL AUTH I.MOCHALKIN,B.CHENG,O.KLEZOVITCH,A.M.SCANU,A.TULINSKY JRNL TITL RECOMBINANT KRINGLE IV-10 MODULES OF HUMAN JRNL TITL 2 APOLIPOPROTEIN(A): STRUCTURE, LIGAND BINDING MODES, AND JRNL TITL 3 BIOLOGICAL RELEVANCE. JRNL REF BIOCHEMISTRY V. 38 1990 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10026282 JRNL DOI 10.1021/BI9820558 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 44.0 REMARK 3 NUMBER OF REFLECTIONS : 2114 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) : 0.162 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) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 633 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.50 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) : 0.011 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.032 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.041 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.028 ; 0.030 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.130 ; 0.120 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.220 ; 0.600 REMARK 3 MULTIPLE TORSION (A) : 0.280 ; 0.600 REMARK 3 H-BOND (X...Y) (A) : 0.290 ; 0.600 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) : 4.000 ; 3.000 REMARK 3 STAGGERED (DEGREES) : 19.000; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 22.300; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.046 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.645 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.748 ; 2.300 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.456 ; 2.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4KIV 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_1000179353. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : OCT-97 REMARK 200 TEMPERATURE (KELVIN) : 130 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 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 : 6494 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 24.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 64.0 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 45.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.17000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 22.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 12.15000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.11500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.91000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.11500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.15000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.91000 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 400 REMARK 400 COMPOUND REMARK 400 N-TERMINAL (VR) AND C-TERMINAL (SDTEGTV) INTERKRINGULAR REMARK 400 PARTS ARE DISORDERED. SIDE CHAIN FOR RESIDUE GLN0 IS REMARK 400 MISSING. THE P30 RESIDUE IS IN CIS CONFORMATION. 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 GLN A 0 CB CG CD OE1 NE2 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. = 4.8 DEGREES REMARK 500 THR A 15 CA - CB - CG2 ANGL. DEV. = 9.7 DEGREES REMARK 500 CYS A 22 CA - CB - SG ANGL. DEV. = 9.5 DEGREES REMARK 500 ARG A 32 CD - NE - CZ ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG A 32 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 35 CD - NE - CZ ANGL. DEV. = 9.9 DEGREES REMARK 500 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 7.4 DEGREES REMARK 500 ARG A 35 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ASN A 49 CA - CB - CG ANGL. DEV. = 15.8 DEGREES REMARK 500 CYS A 51 CA - CB - SG ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A 52 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 71 CD - NE - CZ ANGL. DEV. = 12.1 DEGREES REMARK 500 ARG A 71 NE - CZ - NH1 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 71 NE - CZ - NH2 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 72 NE - CZ - NH2 ANGL. DEV. = -3.0 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 CYS A 1 -131.22 -67.40 REMARK 500 LEU A 46 58.88 -55.68 REMARK 500 MET A 48 -112.61 42.77 REMARK 500 ASP A 57 -155.28 -81.09 REMARK 500 TRP A 62 -148.66 -139.26 REMARK 500 CYS A 63 148.21 165.66 REMARK 500 TYR A 74 -172.98 -65.49 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 A 35 0.11 SIDE CHAIN REMARK 500 ARG A 71 0.07 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 CYS A 1 -10.07 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: W72R MUTATION OF THE LBS RESULTS IN LOSS OF THE REMARK 800 BINDING CAPACITY OF KIV-10. DBREF 4KIV A 0 80 UNP P08519 APOA_HUMAN 4123 4201 SEQADV 4KIV ARG A 72 UNP P08519 TRP 4193 ENGINEERED MUTATION SEQRES 1 A 79 GLN CYS TYR HIS GLY ASN GLY GLN SER TYR ARG GLY THR SEQRES 2 A 79 PHE SER THR THR VAL THR GLY ARG THR CYS GLN SER TRP SEQRES 3 A 79 SER SER MET THR PRO HIS ARG HIS GLN ARG THR PRO GLU SEQRES 4 A 79 ASN TYR PRO ASN ASP GLY LEU THR MET ASN TYR CYS ARG SEQRES 5 A 79 ASN PRO ASP ALA ASP THR GLY PRO TRP CYS PHE THR MET SEQRES 6 A 79 ASP PRO SER ILE ARG ARG GLU TYR CYS ASN LEU THR ARG SEQRES 7 A 79 CYS FORMUL 2 HOH *41(H2 O) SHEET 1 A 2 TRP A 62 PHE A 64 0 SHEET 2 A 2 ARG A 72 TYR A 74 -1 N GLU A 73 O CYS A 63 SSBOND 1 CYS A 1 CYS A 80 1555 1555 2.05 SSBOND 2 CYS A 22 CYS A 63 1555 1555 2.06 SSBOND 3 CYS A 51 CYS A 75 1555 1555 2.00 CISPEP 1 THR A 29 PRO A 30 0 -0.51 SITE 1 LBS 6 ARG A 35 ASP A 55 ASP A 57 TRP A 62 SITE 2 LBS 6 ARG A 71 ARG A 72 CRYST1 24.300 45.820 56.230 90.00 90.00 90.00 P 21 21 21 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 0.041152 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021825 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017784 0.00000