HEADER HYDROLASE 19-MAR-15 4YVA TITLE CATHEPSIN K CO-CRYSTALLIZED WITH ACTINOMYCETES EXTRACT COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN K; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 115-329; COMPND 5 SYNONYM: CATHEPSIN O,CATHEPSIN O2,CATHEPSIN X; COMPND 6 EC: 3.4.22.38; COMPND 7 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: CTSK, CTSO, CTSO2; SOURCE 6 EXPRESSION_SYSTEM: PICHIA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4919 KEYWDS CATHEPSIN K, ACTINOMYCETES, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.H.AGUDA,N.T.NGUYEN,D.BROMME,G.D.BRAYER REVDAT 6 27-SEP-23 4YVA 1 REMARK REVDAT 5 08-JAN-20 4YVA 1 REMARK REVDAT 4 27-SEP-17 4YVA 1 REMARK REVDAT 3 07-SEP-16 4YVA 1 JRNL REVDAT 2 24-AUG-16 4YVA 1 JRNL REVDAT 1 04-MAY-16 4YVA 0 JRNL AUTH A.H.AGUDA,V.LAVALLEE,P.CHENG,T.M.BOTT,L.G.MEIMETIS,S.LAW, JRNL AUTH 2 N.T.NGUYEN,D.E.WILLIAMS,J.KALETA,I.VILLANUEVA,J.DAVIES, JRNL AUTH 3 R.J.ANDERSEN,G.D.BRAYER,D.BROMME JRNL TITL AFFINITY CRYSTALLOGRAPHY: A NEW APPROACH TO EXTRACTING JRNL TITL 2 HIGH-AFFINITY ENZYME INHIBITORS FROM NATURAL EXTRACTS. JRNL REF J.NAT.PROD. V. 79 1962 2016 JRNL REFN ESSN 1520-6025 JRNL PMID 27498895 JRNL DOI 10.1021/ACS.JNATPROD.6B00215 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 20365 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1005 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 52.0030 - 3.4431 1.00 2977 146 0.1723 0.1855 REMARK 3 2 3.4431 - 2.7329 1.00 2793 153 0.1874 0.2197 REMARK 3 3 2.7329 - 2.3875 1.00 2741 152 0.1960 0.2408 REMARK 3 4 2.3875 - 2.1692 1.00 2732 142 0.1872 0.2077 REMARK 3 5 2.1692 - 2.0137 0.99 2698 142 0.1834 0.2401 REMARK 3 6 2.0137 - 1.8950 0.99 2708 126 0.1839 0.2292 REMARK 3 7 1.8950 - 1.8001 0.99 2711 144 0.1974 0.2216 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.290 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 : 0.004 1719 REMARK 3 ANGLE : 0.801 2306 REMARK 3 CHIRALITY : 0.032 233 REMARK 3 PLANARITY : 0.004 301 REMARK 3 DIHEDRAL : 13.889 626 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -21.6299 4.2270 -12.6522 REMARK 3 T TENSOR REMARK 3 T11: 0.1864 T22: 0.1791 REMARK 3 T33: 0.1803 T12: 0.0364 REMARK 3 T13: 0.0100 T23: 0.0171 REMARK 3 L TENSOR REMARK 3 L11: 0.6162 L22: 0.9564 REMARK 3 L33: 1.3947 L12: 0.3692 REMARK 3 L13: 0.1769 L23: 0.2838 REMARK 3 S TENSOR REMARK 3 S11: -0.0054 S12: -0.0427 S13: -0.0421 REMARK 3 S21: -0.0936 S22: -0.0175 S23: -0.0653 REMARK 3 S31: -0.1268 S32: -0.1646 S33: 0.0000 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 4YVA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000208155. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20402 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 51.981 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : 0.49500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.200 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: 3C9E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG 8000, 0.2M AMMONIUM SULFATE, REMARK 280 PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 64.95500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.36000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.36000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 97.43250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.36000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.36000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.47750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.36000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.36000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 97.43250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.36000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.36000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 32.47750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 64.95500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 1 REMARK 465 PRO A 2 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 200 59.95 -109.88 REMARK 500 LEU A 209 55.52 -144.57 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 A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YV8 RELATED DB: PDB DBREF 4YVA A 1 215 UNP P43235 CATK_HUMAN 115 329 SEQRES 1 A 215 ALA PRO ASP SER VAL 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 VAL GLY ALA LEU GLU GLY GLN LEU LYS SEQRES 4 A 215 LYS LYS THR GLY LYS LEU LEU ASN LEU SER PRO GLN ASN SEQRES 5 A 215 LEU VAL ASP CYS VAL SER GLU ASN ASP GLY CYS GLY GLY SEQRES 6 A 215 GLY TYR MET THR ASN ALA PHE GLN TYR VAL GLN LYS ASN SEQRES 7 A 215 ARG GLY ILE ASP SER GLU ASP ALA TYR PRO TYR VAL GLY SEQRES 8 A 215 GLN GLU GLU SER CYS MET TYR ASN PRO THR GLY LYS ALA SEQRES 9 A 215 ALA LYS CYS ARG GLY TYR ARG GLU ILE PRO GLU GLY ASN SEQRES 10 A 215 GLU LYS ALA LEU LYS ARG ALA VAL ALA ARG VAL GLY PRO SEQRES 11 A 215 VAL SER VAL ALA ILE ASP ALA SER LEU THR SER PHE GLN SEQRES 12 A 215 PHE TYR SER LYS GLY VAL TYR TYR ASP GLU SER CYS ASN SEQRES 13 A 215 SER ASP ASN LEU ASN HIS ALA VAL LEU ALA VAL GLY TYR SEQRES 14 A 215 GLY ILE GLN LYS GLY ASN LYS HIS TRP ILE ILE LYS ASN SEQRES 15 A 215 SER TRP GLY GLU ASN TRP GLY ASN LYS GLY TYR ILE LEU SEQRES 16 A 215 MET ALA ARG ASN LYS ASN ASN ALA CYS GLY ILE ALA ASN SEQRES 17 A 215 LEU ALA SER PHE PRO LYS MET HET SO4 A 301 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *125(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 ASP A 61 GLY A 65 5 5 HELIX 4 AA4 TYR A 67 ASN A 78 1 12 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 VAL A 5 ASP A 6 0 SHEET 2 AA1 3 HIS A 162 GLN A 172 -1 O TYR A 169 N VAL A 5 SHEET 3 AA1 3 VAL A 131 ILE A 135 -1 N VAL A 131 O ALA A 166 SHEET 1 AA2 5 VAL A 5 ASP A 6 0 SHEET 2 AA2 5 HIS A 162 GLN A 172 -1 O TYR A 169 N VAL A 5 SHEET 3 AA2 5 ASN A 175 LYS A 181 -1 O LYS A 181 N LEU A 165 SHEET 4 AA2 5 TYR A 193 ALA A 197 -1 O ILE 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 2.04 SSBOND 3 CYS A 155 CYS A 204 1555 1555 2.04 SITE 1 AC1 10 ASN A 18 ARG A 108 ARG A 111 GLY A 185 SITE 2 AC1 10 GLU A 186 ASN A 187 LYS A 214 HOH A 412 SITE 3 AC1 10 HOH A 417 HOH A 477 CRYST1 56.720 56.720 129.910 90.00 90.00 90.00 P 43 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 0.017630 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017630 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007698 0.00000