HEADER HYDROLASE 01-SEP-16 5T6U TITLE CRYSTAL STRUCTURE OF MOUSE CATHEPSIN K AT 2.9 ANGSTROMS RESOLUTION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN K; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.22.38; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: CTSK; SOURCE 6 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS GS115; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 644223; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PPIC9K KEYWDS CATHEPSIN K, N-ACETYL-D-GLUCOSAMINE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.LAW,A.AGUDA,N.NGUYEN,G.BRAYER,D.BROMME REVDAT 6 04-OCT-23 5T6U 1 HETSYN REVDAT 5 29-JUL-20 5T6U 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE REVDAT 4 08-JAN-20 5T6U 1 REMARK REVDAT 3 27-SEP-17 5T6U 1 REMARK REVDAT 2 08-MAR-17 5T6U 1 JRNL REVDAT 1 18-JAN-17 5T6U 0 JRNL AUTH S.LAW,P.M.ANDRAULT,A.H.AGUDA,N.T.NGUYEN,N.KRUGLYAK, JRNL AUTH 2 G.D.BRAYER,D.BROMME JRNL TITL IDENTIFICATION OF MOUSE CATHEPSIN K STRUCTURAL ELEMENTS THAT JRNL TITL 2 REGULATE THE POTENCY OF ODANACATIB. JRNL REF BIOCHEM. J. V. 474 851 2017 JRNL REFN ESSN 1470-8728 JRNL PMID 28049758 JRNL DOI 10.1042/BCJ20160985 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 5241 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 261 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.2648 - 3.6534 1.00 2568 136 0.1977 0.2258 REMARK 3 2 3.6534 - 2.9000 0.99 2412 125 0.2173 0.2125 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 1709 REMARK 3 ANGLE : 0.611 2307 REMARK 3 CHIRALITY : 0.045 238 REMARK 3 PLANARITY : 0.002 299 REMARK 3 DIHEDRAL : 11.798 618 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5T6U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1000223823. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 7.2.1 REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5243 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 43.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: 4X6H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM PHOSPHATE PH 6.2 25% REMARK 280 (V/V) 1,2-PROPANEDIOL 10% (V/V) GLYCEROL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 18.96000 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.98500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 18.96000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 66.98500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 37.92000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 422 LIES ON A SPECIAL POSITION. 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 VAL A 128 -66.12 -103.50 REMARK 500 SER A 146 -32.12 -148.41 REMARK 500 ASN A 161 15.46 -147.61 REMARK 500 LYS A 200 41.27 -91.52 REMARK 500 REMARK 500 REMARK: NULL DBREF 5T6U A 1 215 UNP P55097 CATK_MOUSE 115 329 SEQRES 1 A 215 VAL PRO ASP SER ILE ASP TYR ARG LYS LYS GLY TYR VAL SEQRES 2 A 215 THR PRO VAL LYS ASN GLN GLY GLN CYS GLY SER CYS TRP SEQRES 3 A 215 ALA PHE SER SER ALA GLY ALA LEU GLU GLY GLN LEU LYS SEQRES 4 A 215 LYS LYS THR GLY LYS LEU LEU ALA LEU SER PRO GLN ASN SEQRES 5 A 215 LEU VAL ASP CYS VAL THR GLU ASN TYR GLY CYS GLY GLY SEQRES 6 A 215 GLY TYR MET THR THR ALA PHE GLN TYR VAL GLN GLN ASN SEQRES 7 A 215 GLY GLY ILE ASP SER GLU ASP ALA TYR PRO TYR VAL GLY SEQRES 8 A 215 GLN ASP GLU SER CYS MET TYR ASN ALA THR ALA LYS ALA SEQRES 9 A 215 ALA LYS CYS ARG GLY TYR ARG GLU ILE PRO VAL GLY ASN SEQRES 10 A 215 GLU LYS ALA LEU LYS ARG ALA VAL ALA ARG VAL GLY PRO SEQRES 11 A 215 ILE SER VAL SER ILE ASP ALA SER LEU ALA SER PHE GLN SEQRES 12 A 215 PHE TYR SER ARG GLY VAL TYR TYR ASP GLU ASN CYS ASP SEQRES 13 A 215 ARG ASP ASN VAL ASN HIS ALA VAL LEU VAL VAL GLY TYR SEQRES 14 A 215 GLY THR GLN LYS GLY SER LYS HIS TRP ILE ILE LYS ASN SEQRES 15 A 215 SER TRP GLY GLU SER TRP GLY ASN LYS GLY TYR ALA LEU SEQRES 16 A 215 LEU ALA ARG ASN LYS ASN ASN ALA CYS GLY ILE THR ASN SEQRES 17 A 215 MET ALA SER PHE PRO LYS MET HET SO4 A 301 5 HET SO4 A 302 5 HET SO4 A 303 5 HET NAG A 304 14 HETNAM SO4 SULFATE ION HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 NAG C8 H15 N O6 FORMUL 6 HOH *22(H2 O) HELIX 1 AA1 SER A 24 GLY A 43 1 20 HELIX 2 AA2 SER A 49 VAL A 57 1 9 HELIX 3 AA3 TYR A 61 GLY A 65 5 5 HELIX 4 AA4 TYR A 67 GLY A 79 1 13 HELIX 5 AA5 ASN A 99 THR A 101 5 3 HELIX 6 AA6 ASN A 117 VAL A 128 1 12 HELIX 7 AA7 LEU A 139 PHE A 144 1 6 HELIX 8 AA8 ASN A 202 ILE A 206 5 5 SHEET 1 AA1 3 ILE A 5 ASP A 6 0 SHEET 2 AA1 3 HIS A 162 GLN A 172 -1 O TYR A 169 N ILE A 5 SHEET 3 AA1 3 ILE A 131 ILE A 135 -1 N ILE A 135 O HIS A 162 SHEET 1 AA2 5 ILE A 5 ASP A 6 0 SHEET 2 AA2 5 HIS A 162 GLN A 172 -1 O TYR A 169 N ILE A 5 SHEET 3 AA2 5 SER A 175 LYS A 181 -1 O ILE A 179 N GLY A 168 SHEET 4 AA2 5 TYR A 193 ALA A 197 -1 O ALA A 194 N ILE A 180 SHEET 5 AA2 5 VAL A 149 TYR A 150 1 N TYR A 150 O LEU A 195 SHEET 1 AA3 2 ILE A 81 ASP A 82 0 SHEET 2 AA3 2 LYS A 103 ALA A 105 -1 O ALA A 104 N ILE A 81 SHEET 1 AA4 2 TYR A 110 GLU A 112 0 SHEET 2 AA4 2 SER A 211 PRO A 213 -1 O PHE A 212 N ARG A 111 SSBOND 1 CYS A 22 CYS A 63 1555 1555 2.03 SSBOND 2 CYS A 56 CYS A 96 1555 1555 2.03 SSBOND 3 CYS A 155 CYS A 204 1555 1555 2.03 LINK ND2 ASN A 99 C1 NAG A 304 1555 1555 1.44 CRYST1 37.920 43.260 133.970 90.00 90.00 90.00 P 21 2 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 0.026372 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023116 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007464 0.00000