HEADER HYDROLASE 08-APR-16 5J94 TITLE HUMAN CATHEPSIN K MUTANT C25S IN COMPLEX WITH THE ALLOSTERIC EFFECTOR TITLE 2 NSC13345 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN K; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CATHEPSIN O,CATHEPSIN O2,CATHEPSIN X; COMPND 5 EC: 3.4.22.38; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: 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: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA-GAMI 2 PLYSS KEYWDS CYSTEINE PROTEASES, ALLOSTERIC REGULATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.NOVINEC,M.KORENC,B.LENARCIC,A.BAICI REVDAT 2 10-JAN-24 5J94 1 REMARK REVDAT 1 20-APR-16 5J94 0 SPRSDE 20-APR-16 5J94 4LEG JRNL AUTH M.NOVINEC,M.KORENC,A.CAFLISCH,R.RANGANATHAN,B.LENARCIC, JRNL AUTH 2 A.BAICI JRNL TITL A NOVEL ALLOSTERIC MECHANISM IN THE CYSTEINE PEPTIDASE JRNL TITL 2 CATHEPSIN K DISCOVERED BY COMPUTATIONAL METHODS. JRNL REF NAT COMMUN V. 5 3287 2014 JRNL REFN ESSN 2041-1723 JRNL PMID 24518821 JRNL DOI 10.1038/NCOMMS4287 REMARK 2 REMARK 2 RESOLUTION. 2.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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) : 2.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.338 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 3 NUMBER OF REFLECTIONS : 16999 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.006 REMARK 3 FREE R VALUE TEST SET COUNT : 851 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 44.8368 - 4.0332 1.00 3124 164 0.1894 0.1965 REMARK 3 2 4.0332 - 3.2016 1.00 3122 161 0.1737 0.1881 REMARK 3 3 3.2016 - 2.7969 1.00 3124 165 0.2094 0.2491 REMARK 3 4 2.7969 - 2.5412 0.92 2847 156 0.2384 0.2531 REMARK 3 5 2.5412 - 2.3591 0.75 2342 121 0.2635 0.3071 REMARK 3 6 2.3591 - 2.2200 0.51 1589 84 0.2999 0.3237 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) : 0.221 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.201 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.28 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 : 0.003 1786 REMARK 3 ANGLE : 0.521 2413 REMARK 3 CHIRALITY : 0.043 239 REMARK 3 PLANARITY : 0.004 318 REMARK 3 DIHEDRAL : 17.762 660 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 5J94 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220101. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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 : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT 1.0 REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17003 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.220 REMARK 200 RESOLUTION RANGE LOW (A) : 49.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.30 REMARK 200 R MERGE FOR SHELL (I) : 0.10200 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 2.1 REMARK 200 STARTING MODEL: 4LEG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 30% PEG 8000, REMARK 280 PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, VAPOR REMARK 280 DIFFUSION, HANGING DROP 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 24.67250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.27800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.05050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.27800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.67250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.05050 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 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 SER A 146 -33.18 -141.45 REMARK 500 LYS A 200 53.90 -111.62 REMARK 500 CYS A 204 16.76 59.61 REMARK 500 LEU A 209 47.90 -140.02 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 1XF A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 DBREF 5J94 A -7 215 UNP P43235 CATK_HUMAN 107 329 SEQADV 5J94 SER A 25 UNP P43235 CYS 139 ENGINEERED MUTATION SEQRES 1 A 223 TYR ILE PRO GLU TRP GLU GLY ARG ALA PRO ASP SER VAL SEQRES 2 A 223 ASP TYR ARG LYS LYS GLY TYR VAL THR PRO VAL LYS ASN SEQRES 3 A 223 GLN GLY GLN CYS GLY SER SER TRP ALA PHE SER SER VAL SEQRES 4 A 223 GLY ALA LEU GLU GLY GLN LEU LYS LYS LYS THR GLY LYS SEQRES 5 A 223 LEU LEU ASN LEU SER PRO GLN ASN LEU VAL ASP CYS VAL SEQRES 6 A 223 SER GLU ASN ASP GLY CYS GLY GLY GLY TYR MET THR ASN SEQRES 7 A 223 ALA PHE GLN TYR VAL GLN LYS ASN ARG GLY ILE ASP SER SEQRES 8 A 223 GLU ASP ALA TYR PRO TYR VAL GLY GLN GLU GLU SER CYS SEQRES 9 A 223 MET TYR ASN PRO THR GLY LYS ALA ALA LYS CYS ARG GLY SEQRES 10 A 223 TYR ARG GLU ILE PRO GLU GLY ASN GLU LYS ALA LEU LYS SEQRES 11 A 223 ARG ALA VAL ALA ARG VAL GLY PRO VAL SER VAL ALA ILE SEQRES 12 A 223 ASP ALA SER LEU THR SER PHE GLN PHE TYR SER LYS GLY SEQRES 13 A 223 VAL TYR TYR ASP GLU SER CYS ASN SER ASP ASN LEU ASN SEQRES 14 A 223 HIS ALA VAL LEU ALA VAL GLY TYR GLY ILE GLN LYS GLY SEQRES 15 A 223 ASN LYS HIS TRP ILE ILE LYS ASN SER TRP GLY GLU ASN SEQRES 16 A 223 TRP GLY ASN LYS GLY TYR ILE LEU MET ALA ARG ASN LYS SEQRES 17 A 223 ASN ASN ALA CYS GLY ILE ALA ASN LEU ALA SER PHE PRO SEQRES 18 A 223 LYS MET HET 1XF A 301 17 HET SO4 A 302 5 HETNAM 1XF 2-{[(CARBAMOYLSULFANYL)ACETYL]AMINO}BENZOIC ACID HETNAM SO4 SULFATE ION FORMUL 2 1XF C10 H10 N2 O4 S FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *132(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 ARG 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 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 ILE A 135 O HIS A 162 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 MET A 196 N TRP A 178 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 GLY A 109 GLU A 112 0 SHEET 2 AA4 2 SER A 211 LYS A 214 -1 O LYS A 214 N GLY A 109 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 SITE 1 AC1 10 GLY A -1 ALA A 1 LYS A 119 LYS A 122 SITE 2 AC1 10 ARG A 123 LYS A 176 ASN A 199 HOH A 404 SITE 3 AC1 10 HOH A 428 HOH A 495 SITE 1 AC2 5 ASN A 18 GLY A 185 GLU A 186 ASN A 187 SITE 2 AC2 5 HOH A 419 CRYST1 49.345 56.101 74.556 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 0.020265 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017825 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013413 0.00000