HEADER HYDROLASE/HYDROLASE INHIBITOR 15-NOV-13 4NMX TITLE PCSK9(DELTACRD) IN COMPLEX WITH PHAGE-DERIVED INHIBITORY PEPTIDE 2-8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PROPEPTIDE (UNP RESIDUES 31-152); COMPND 5 SYNONYM: NEURAL APOPTOSIS-REGULATED CONVERTASE 1, NARC-1, PROPROTEIN COMPND 6 CONVERTASE 9, PC9, SUBTILISIN/KEXIN-LIKE PROTEASE PC9; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: CATALYTIC DOMAIN (UNP RESIDUES 153-452); COMPND 12 SYNONYM: NEURAL APOPTOSIS-REGULATED CONVERTASE 1, NARC-1, PROPROTEIN COMPND 13 CONVERTASE 9, PC9, SUBTILISIN/KEXIN-LIKE PROTEASE PC9; COMPND 14 EC: 3.4.21.-; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: PEPTIDE 2-8; COMPND 18 CHAIN: Z; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NARC1, PCSK9, PSEC0052; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: NARC1, PCSK9, PSEC0052; SOURCE 15 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 16 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 OTHER_DETAILS: SYNTHETIC PEPTIDE LIBRARY DISPLAYED ON M13 PHAGE KEYWDS SUBTLISIN, RECEPTOR DEGRADATION, LDL RECEPTOR, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.EIGENBROT,S.SHIA REVDAT 3 20-SEP-23 4NMX 1 SEQADV LINK REVDAT 2 29-JAN-14 4NMX 1 JRNL REVDAT 1 04-DEC-13 4NMX 0 JRNL AUTH Y.ZHANG,C.EIGENBROT,L.ZHOU,S.SHIA,W.LI,C.QUAN,J.TOM,P.MORAN, JRNL AUTH 2 P.DI LELLO,N.J.SKELTON,M.KONG-BELTRAN,A.PETERSON, JRNL AUTH 3 D.KIRCHHOFER JRNL TITL IDENTIFICATION OF A SMALL PEPTIDE THAT INHIBITS PCSK9 JRNL TITL 2 PROTEIN BINDING TO THE LOW DENSITY LIPOPROTEIN RECEPTOR. JRNL REF J.BIOL.CHEM. V. 289 942 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24225950 JRNL DOI 10.1074/JBC.M113.514067 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 38618 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1020 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5556 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2916 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 378 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.70000 REMARK 3 B22 (A**2) : -0.82000 REMARK 3 B33 (A**2) : 0.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.05000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.126 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.122 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.636 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3035 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2942 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4135 ; 1.102 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6753 ; 0.864 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 395 ; 5.230 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 130 ;35.536 ;23.231 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 500 ;12.801 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;18.207 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 480 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3451 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 691 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 176 B 260 REMARK 3 ORIGIN FOR THE GROUP (A): 13.8649 9.9543 -16.5008 REMARK 3 T TENSOR REMARK 3 T11: 0.0484 T22: 0.0663 REMARK 3 T33: 0.0449 T12: -0.0036 REMARK 3 T13: -0.0027 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 0.0267 L22: 0.1938 REMARK 3 L33: 0.2713 L12: 0.0241 REMARK 3 L13: 0.0625 L23: 0.0235 REMARK 3 S TENSOR REMARK 3 S11: -0.0049 S12: 0.0112 S13: 0.0108 REMARK 3 S21: -0.0130 S22: 0.0044 S23: 0.0010 REMARK 3 S31: 0.0296 S32: -0.0413 S33: 0.0005 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 261 B 339 REMARK 3 ORIGIN FOR THE GROUP (A): 24.4396 13.5408 -5.1823 REMARK 3 T TENSOR REMARK 3 T11: 0.0528 T22: 0.0548 REMARK 3 T33: 0.0582 T12: 0.0016 REMARK 3 T13: -0.0017 T23: 0.0003 REMARK 3 L TENSOR REMARK 3 L11: 0.0418 L22: 0.1452 REMARK 3 L33: 0.0091 L12: -0.0139 REMARK 3 L13: 0.0185 L23: 0.0044 REMARK 3 S TENSOR REMARK 3 S11: 0.0004 S12: 0.0046 S13: -0.0009 REMARK 3 S21: 0.0173 S22: 0.0013 S23: -0.0166 REMARK 3 S31: 0.0039 S32: 0.0018 S33: -0.0017 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 340 B 446 REMARK 3 ORIGIN FOR THE GROUP (A): 31.4808 17.9031 -19.4687 REMARK 3 T TENSOR REMARK 3 T11: 0.0478 T22: 0.0529 REMARK 3 T33: 0.0625 T12: 0.0022 REMARK 3 T13: 0.0079 T23: 0.0024 REMARK 3 L TENSOR REMARK 3 L11: 0.0353 L22: 0.1821 REMARK 3 L33: 0.1321 L12: 0.0664 REMARK 3 L13: -0.0034 L23: 0.0561 REMARK 3 S TENSOR REMARK 3 S11: -0.0010 S12: 0.0096 S13: -0.0022 REMARK 3 S21: -0.0287 S22: 0.0094 S23: -0.0442 REMARK 3 S31: -0.0042 S32: 0.0004 S33: -0.0083 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 61 A 87 REMARK 3 ORIGIN FOR THE GROUP (A): 18.5627 22.5818 7.8657 REMARK 3 T TENSOR REMARK 3 T11: 0.0432 T22: 0.0529 REMARK 3 T33: 0.0551 T12: -0.0004 REMARK 3 T13: -0.0022 T23: 0.0006 REMARK 3 L TENSOR REMARK 3 L11: 0.1908 L22: 0.4749 REMARK 3 L33: 0.3384 L12: 0.0185 REMARK 3 L13: 0.0138 L23: -0.3648 REMARK 3 S TENSOR REMARK 3 S11: -0.0184 S12: 0.0039 S13: 0.0169 REMARK 3 S21: 0.0113 S22: -0.0184 S23: -0.0337 REMARK 3 S31: -0.0105 S32: -0.0001 S33: 0.0368 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 88 A 105 REMARK 3 ORIGIN FOR THE GROUP (A): 10.5141 13.5321 20.1379 REMARK 3 T TENSOR REMARK 3 T11: 0.0654 T22: 0.0531 REMARK 3 T33: 0.0466 T12: 0.0026 REMARK 3 T13: 0.0121 T23: 0.0010 REMARK 3 L TENSOR REMARK 3 L11: 1.1318 L22: 1.2011 REMARK 3 L33: 0.7600 L12: -1.0010 REMARK 3 L13: -0.6286 L23: 0.9161 REMARK 3 S TENSOR REMARK 3 S11: 0.0001 S12: -0.0312 S13: -0.0184 REMARK 3 S21: 0.0678 S22: -0.0099 S23: 0.0162 REMARK 3 S31: 0.0766 S32: -0.0269 S33: 0.0098 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 106 A 152 REMARK 3 ORIGIN FOR THE GROUP (A): 13.8024 18.8545 10.3622 REMARK 3 T TENSOR REMARK 3 T11: 0.0505 T22: 0.0510 REMARK 3 T33: 0.0561 T12: -0.0025 REMARK 3 T13: -0.0004 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 0.0969 L22: 0.1093 REMARK 3 L33: 0.4127 L12: 0.0195 REMARK 3 L13: -0.1981 L23: -0.0196 REMARK 3 S TENSOR REMARK 3 S11: -0.0051 S12: 0.0066 S13: -0.0001 REMARK 3 S21: 0.0128 S22: -0.0065 S23: 0.0007 REMARK 3 S31: 0.0194 S32: -0.0062 S33: 0.0115 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 153 B 163 REMARK 3 ORIGIN FOR THE GROUP (A): 29.9777 13.1368 -31.2549 REMARK 3 T TENSOR REMARK 3 T11: 0.0606 T22: 0.0691 REMARK 3 T33: 0.0499 T12: -0.0023 REMARK 3 T13: 0.0196 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: 3.9446 L22: 0.6551 REMARK 3 L33: 1.0681 L12: -1.0084 REMARK 3 L13: 1.2312 L23: -0.5725 REMARK 3 S TENSOR REMARK 3 S11: -0.0478 S12: 0.2214 S13: -0.1828 REMARK 3 S21: -0.0064 S22: 0.0352 S23: 0.0742 REMARK 3 S31: 0.0251 S32: 0.1276 S33: 0.0126 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : Z 0 Z 14 REMARK 3 ORIGIN FOR THE GROUP (A): 15.2674 14.4426 -37.1262 REMARK 3 T TENSOR REMARK 3 T11: 0.0724 T22: 0.0788 REMARK 3 T33: 0.0424 T12: 0.0032 REMARK 3 T13: 0.0009 T23: 0.0185 REMARK 3 L TENSOR REMARK 3 L11: 3.4831 L22: 0.9556 REMARK 3 L33: 1.9142 L12: 1.0827 REMARK 3 L13: -1.0506 L23: -0.2699 REMARK 3 S TENSOR REMARK 3 S11: 0.0519 S12: 0.1014 S13: 0.1592 REMARK 3 S21: -0.0972 S22: -0.0408 S23: -0.0673 REMARK 3 S31: 0.0237 S32: -0.1260 S33: -0.0110 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4NMX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000083403. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39638 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09900 REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2QTW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M LITHIUM CHLORIDE, 10% W/V REMARK 280 PEG6000, 0.05 M TRIS, PH 8, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292K 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 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 47.55100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.38250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.55100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.38250 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, Z 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 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 ALA A 28 REMARK 465 GLY A 29 REMARK 465 SER A 30 REMARK 465 GLN A 31 REMARK 465 GLU A 32 REMARK 465 ASP A 33 REMARK 465 GLU A 34 REMARK 465 ASP A 35 REMARK 465 GLY A 36 REMARK 465 ASP A 37 REMARK 465 TYR A 38 REMARK 465 GLU A 39 REMARK 465 GLU A 40 REMARK 465 LEU A 41 REMARK 465 VAL A 42 REMARK 465 LEU A 43 REMARK 465 ALA A 44 REMARK 465 LEU A 45 REMARK 465 ARG A 46 REMARK 465 SER A 47 REMARK 465 GLU A 48 REMARK 465 GLU A 49 REMARK 465 ASP A 50 REMARK 465 GLY A 51 REMARK 465 LEU A 52 REMARK 465 ALA A 53 REMARK 465 GLU A 54 REMARK 465 ALA A 55 REMARK 465 PRO A 56 REMARK 465 GLU A 57 REMARK 465 HIS A 58 REMARK 465 GLY A 59 REMARK 465 THR A 60 REMARK 465 PRO B 164 REMARK 465 ARG B 165 REMARK 465 TYR B 166 REMARK 465 ARG B 167 REMARK 465 ALA B 168 REMARK 465 ASP B 169 REMARK 465 GLU B 170 REMARK 465 TYR B 171 REMARK 465 GLN B 172 REMARK 465 PRO B 173 REMARK 465 PRO B 174 REMARK 465 ASP B 175 REMARK 465 HIS B 217 REMARK 465 ARG B 218 REMARK 465 GLN B 219 REMARK 465 ALA B 220 REMARK 465 SER B 447 REMARK 465 THR B 448 REMARK 465 HIS B 449 REMARK 465 GLY B 450 REMARK 465 ALA B 451 REMARK 465 GLY B 452 REMARK 465 ASN B 453 REMARK 465 SER B 454 REMARK 465 HIS B 455 REMARK 465 HIS B 456 REMARK 465 HIS B 457 REMARK 465 HIS B 458 REMARK 465 HIS B 459 REMARK 465 HIS B 460 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 DISTANCE REMARK 500 O HOH B 657 O HOH B 749 2.07 REMARK 500 OD1 ASP A 70 O HOH A 219 2.10 REMARK 500 O HOH B 548 O HOH B 618 2.13 REMARK 500 NH1 ARG A 66 O HOH A 221 2.17 REMARK 500 O HOH A 311 O HOH A 312 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 ACE Z 0 O - C - N ANGL. DEV. = -31.0 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 HIS A 139 -8.79 81.07 REMARK 500 ASP B 186 -155.75 -160.43 REMARK 500 THR B 187 -178.94 -68.24 REMARK 500 ARG B 215 -111.48 -54.70 REMARK 500 VAL B 280 -139.64 -122.57 REMARK 500 PRO B 288 47.61 -88.13 REMARK 500 LEU B 351 -145.71 -116.59 REMARK 500 REMARK 500 REMARK: NULL DBREF 4NMX A 31 152 UNP Q8NBP7 PCSK9_HUMAN 31 152 DBREF 4NMX B 153 452 UNP Q8NBP7 PCSK9_HUMAN 153 452 DBREF 4NMX Z 0 14 PDB 4NMX 4NMX 0 14 SEQADV 4NMX ALA A 28 UNP Q8NBP7 EXPRESSION TAG SEQADV 4NMX GLY A 29 UNP Q8NBP7 EXPRESSION TAG SEQADV 4NMX SER A 30 UNP Q8NBP7 EXPRESSION TAG SEQADV 4NMX ASN B 453 UNP Q8NBP7 EXPRESSION TAG SEQADV 4NMX SER B 454 UNP Q8NBP7 EXPRESSION TAG SEQADV 4NMX HIS B 455 UNP Q8NBP7 EXPRESSION TAG SEQADV 4NMX HIS B 456 UNP Q8NBP7 EXPRESSION TAG SEQADV 4NMX HIS B 457 UNP Q8NBP7 EXPRESSION TAG SEQADV 4NMX HIS B 458 UNP Q8NBP7 EXPRESSION TAG SEQADV 4NMX HIS B 459 UNP Q8NBP7 EXPRESSION TAG SEQADV 4NMX HIS B 460 UNP Q8NBP7 EXPRESSION TAG SEQRES 1 A 125 ALA GLY SER GLN GLU ASP GLU ASP GLY ASP TYR GLU GLU SEQRES 2 A 125 LEU VAL LEU ALA LEU ARG SER GLU GLU ASP GLY LEU ALA SEQRES 3 A 125 GLU ALA PRO GLU HIS GLY THR THR ALA THR PHE HIS ARG SEQRES 4 A 125 CYS ALA LYS ASP PRO TRP ARG LEU PRO GLY THR TYR VAL SEQRES 5 A 125 VAL VAL LEU LYS GLU GLU THR HIS LEU SER GLN SER GLU SEQRES 6 A 125 ARG THR ALA ARG ARG LEU GLN ALA GLN ALA ALA ARG ARG SEQRES 7 A 125 GLY TYR LEU THR LYS ILE LEU HIS VAL PHE HIS GLY LEU SEQRES 8 A 125 LEU PRO GLY PHE LEU VAL LYS MET SER GLY ASP LEU LEU SEQRES 9 A 125 GLU LEU ALA LEU LYS LEU PRO HIS VAL ASP TYR ILE GLU SEQRES 10 A 125 GLU ASP SER SER VAL PHE ALA GLN SEQRES 1 B 308 SER ILE PRO TRP ASN LEU GLU ARG ILE THR PRO PRO ARG SEQRES 2 B 308 TYR ARG ALA ASP GLU TYR GLN PRO PRO ASP GLY GLY SER SEQRES 3 B 308 LEU VAL GLU VAL TYR LEU LEU ASP THR SER ILE GLN SER SEQRES 4 B 308 ASP HIS ARG GLU ILE GLU GLY ARG VAL MET VAL THR ASP SEQRES 5 B 308 PHE GLU ASN VAL PRO GLU GLU ASP GLY THR ARG PHE HIS SEQRES 6 B 308 ARG GLN ALA SER LYS CYS ASP SER HIS GLY THR HIS LEU SEQRES 7 B 308 ALA GLY VAL VAL SER GLY ARG ASP ALA GLY VAL ALA LYS SEQRES 8 B 308 GLY ALA SER MET ARG SER LEU ARG VAL LEU ASN CYS GLN SEQRES 9 B 308 GLY LYS GLY THR VAL SER GLY THR LEU ILE GLY LEU GLU SEQRES 10 B 308 PHE ILE ARG LYS SER GLN LEU VAL GLN PRO VAL GLY PRO SEQRES 11 B 308 LEU VAL VAL LEU LEU PRO LEU ALA GLY GLY TYR SER ARG SEQRES 12 B 308 VAL LEU ASN ALA ALA CYS GLN ARG LEU ALA ARG ALA GLY SEQRES 13 B 308 VAL VAL LEU VAL THR ALA ALA GLY ASN PHE ARG ASP ASP SEQRES 14 B 308 ALA CYS LEU TYR SER PRO ALA SER ALA PRO GLU VAL ILE SEQRES 15 B 308 THR VAL GLY ALA THR ASN ALA GLN ASP GLN PRO VAL THR SEQRES 16 B 308 LEU GLY THR LEU GLY THR ASN PHE GLY ARG CYS VAL ASP SEQRES 17 B 308 LEU PHE ALA PRO GLY GLU ASP ILE ILE GLY ALA SER SER SEQRES 18 B 308 ASP CYS SER THR CYS PHE VAL SER GLN SER GLY THR SER SEQRES 19 B 308 GLN ALA ALA ALA HIS VAL ALA GLY ILE ALA ALA MET MET SEQRES 20 B 308 LEU SER ALA GLU PRO GLU LEU THR LEU ALA GLU LEU ARG SEQRES 21 B 308 GLN ARG LEU ILE HIS PHE SER ALA LYS ASP VAL ILE ASN SEQRES 22 B 308 GLU ALA TRP PHE PRO GLU ASP GLN ARG VAL LEU THR PRO SEQRES 23 B 308 ASN LEU VAL ALA ALA LEU PRO PRO SER THR HIS GLY ALA SEQRES 24 B 308 GLY ASN SER HIS HIS HIS HIS HIS HIS SEQRES 1 Z 15 ACE THR VAL PHE THR SER TRP GLU GLU TYR LEU ASP TRP SEQRES 2 Z 15 VAL NH2 HET ACE Z 0 3 HET NH2 Z 14 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 3 ACE C2 H4 O FORMUL 3 NH2 H2 N FORMUL 4 HOH *378(H2 O) HELIX 1 1 LYS A 69 PRO A 71 5 3 HELIX 2 2 HIS A 87 ARG A 105 1 19 HELIX 3 3 SER A 127 ASP A 129 5 3 HELIX 4 4 LEU A 130 LYS A 136 1 7 HELIX 5 5 PRO B 155 ILE B 161 1 7 HELIX 6 6 ASP B 224 GLY B 236 1 13 HELIX 7 7 VAL B 261 GLN B 278 1 18 HELIX 8 8 SER B 294 ALA B 307 1 14 HELIX 9 9 ASP B 321 CYS B 323 5 3 HELIX 10 10 GLY B 384 GLU B 403 1 20 HELIX 11 11 THR B 407 PHE B 418 1 12 HELIX 12 12 ASN B 425 PHE B 429 5 5 HELIX 13 13 PRO B 430 ARG B 434 5 5 HELIX 14 14 SER Z 5 VAL Z 13 1 9 SHEET 1 A 3 THR A 63 HIS A 65 0 SHEET 2 A 3 VAL A 140 ALA A 151 1 O GLU A 145 N HIS A 65 SHEET 3 A 3 LYS B 258 THR B 260 -1 O GLY B 259 N VAL A 149 SHEET 1 B 6 LYS A 110 PHE A 115 0 SHEET 2 B 6 GLY A 121 LYS A 125 -1 O LEU A 123 N HIS A 113 SHEET 3 B 6 ARG A 73 LEU A 82 -1 N VAL A 80 O PHE A 122 SHEET 4 B 6 VAL A 140 ALA A 151 -1 O GLU A 144 N VAL A 79 SHEET 5 B 6 LEU B 289 GLY B 292 -1 O ALA B 290 N PHE A 150 SHEET 6 B 6 TYR B 325 SER B 326 -1 O SER B 326 N GLY B 291 SHEET 1 C 7 VAL B 200 GLU B 206 0 SHEET 2 C 7 SER B 246 ARG B 251 1 O MET B 247 N MET B 201 SHEET 3 C 7 GLU B 181 ASP B 186 1 N LEU B 184 O LEU B 250 SHEET 4 C 7 LEU B 283 LEU B 287 1 O LEU B 286 N TYR B 183 SHEET 5 C 7 VAL B 310 ALA B 314 1 O VAL B 312 N LEU B 287 SHEET 6 C 7 ILE B 334 THR B 339 1 O ILE B 334 N LEU B 311 SHEET 7 C 7 LEU B 361 PRO B 364 1 O LEU B 361 N GLY B 337 SHEET 1 D 2 THR B 347 LEU B 348 0 SHEET 2 D 2 LEU B 351 GLY B 352 -1 O LEU B 351 N LEU B 348 SHEET 1 E 2 ILE B 368 SER B 372 0 SHEET 2 E 2 CYS B 378 GLN B 382 -1 O VAL B 380 N GLY B 370 SHEET 1 F 2 ALA B 420 LYS B 421 0 SHEET 2 F 2 LEU B 440 VAL B 441 -1 O VAL B 441 N ALA B 420 SSBOND 1 CYS B 223 CYS B 255 1555 1555 2.09 SSBOND 2 CYS B 323 CYS B 358 1555 1555 2.07 SSBOND 3 CYS B 375 CYS B 378 1555 1555 2.05 LINK C ACE Z 0 N THR Z 1 1555 1555 1.42 LINK C VAL Z 13 N NH2 Z 14 1555 1555 1.38 CISPEP 1 SER B 326 PRO B 327 0 3.74 CRYST1 95.102 70.765 70.413 90.00 96.08 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 0.010515 0.000000 0.001120 0.00000 SCALE2 0.000000 0.014131 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014282 0.00000