HEADER HYDROLASE 30-DEC-16 5MS3 TITLE KALLIKREIN-RELATED PEPTIDASE 8 CALCIUM COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: KALLIKREIN-8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HK8,NEUROPSIN,NP,OVASIN,SERINE PROTEASE 19,SERINE PROTEASE COMPND 5 TADG-14,TUMOR-ASSOCIATED DIFFERENTIALLY EXPRESSED GENE 14 PROTEIN; COMPND 6 EC: 3.4.21.118; 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: KLK8, NRPN, PRSS19, TADG14, UNQ283/PRO322; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRYPSIN-LIKE SERINE PROTEASE, CA2+ COMPLEX, FREE ACTIVE SITE, KEYWDS 2 SYNAPTIC REMODELING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.DEBELA,V.MAGDOLEN,W.SKALA,W.BODE,H.BRANDSTETTER,P.GOETTIG REVDAT 3 17-JAN-24 5MS3 1 REMARK REVDAT 2 17-JUL-19 5MS3 1 REMARK REVDAT 1 17-JAN-18 5MS3 0 JRNL AUTH M.DEBELA,V.MAGDOLEN,W.SKALA,C.S.CRAIK,E.L.SCHNEIDER, JRNL AUTH 2 M.L.BINIOSSEK,O.SCHILLING,B.ELSAESSER,W.BODE,H.BRANDSTETTER, JRNL AUTH 3 P.GOETTIG JRNL TITL SPECIFICITY PROFILES AND ANTAGONISTIC CA2+ AND ZN2+ JRNL TITL 2 REGULATION OF HUMAN KLK8/NEUROPSIN ACTIVITY BY MODULES JRNL TITL 3 IDENTIFIED IN CRYSTAL STRUCTURES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1-2155 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 9190 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.730 REMARK 3 FREE R VALUE TEST SET COUNT : 435 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 43.8958 - 4.9534 1.00 945 60 0.2123 0.2281 REMARK 3 2 4.9534 - 3.9324 1.00 894 43 0.1686 0.1722 REMARK 3 3 3.9324 - 3.4356 1.00 892 40 0.1926 0.2887 REMARK 3 4 3.4356 - 3.1215 1.00 886 40 0.2089 0.3315 REMARK 3 5 3.1215 - 2.8979 1.00 869 35 0.2434 0.2685 REMARK 3 6 2.8979 - 2.7270 0.99 866 43 0.2541 0.2854 REMARK 3 7 2.7270 - 2.5905 1.00 870 36 0.2493 0.2956 REMARK 3 8 2.5905 - 2.4777 1.00 853 48 0.2734 0.3236 REMARK 3 9 2.4777 - 2.3823 1.00 852 46 0.2752 0.3504 REMARK 3 10 2.3823 - 2.3001 0.98 828 44 0.2998 0.3320 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.34 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 : 0.006 1764 REMARK 3 ANGLE : 0.721 2392 REMARK 3 CHIRALITY : 0.048 255 REMARK 3 PLANARITY : 0.006 317 REMARK 3 DIHEDRAL : 12.409 1064 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 5MS3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1200002923. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X12 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97469 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9263 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 82.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.15800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.40300 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 2.6.1 REMARK 200 STARTING MODEL: 1NPM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% (V/V) TERT-BUTANOL, 0.1 M TRI-NA REMARK 280 CITRATE/CITRIC ACID, PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 22.99850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.43150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.87050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.43150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.99850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.87050 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10290 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 GLN A 27 73.26 -117.64 REMARK 500 LEU A 41 -65.60 -98.55 REMARK 500 HIS A 71 -64.72 -129.77 REMARK 500 GLU A 97 -0.23 72.66 REMARK 500 LYS A 119 142.33 -174.47 REMARK 500 SER A 146 140.09 -174.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A3001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 70 OD1 REMARK 620 2 SER A 72 O 82.3 REMARK 620 3 ASN A 75 O 166.2 85.9 REMARK 620 4 ASP A 77 OD2 80.1 87.9 92.4 REMARK 620 5 GLU A 80 OE2 95.5 172.8 95.3 85.0 REMARK 620 6 HOH A3139 O 95.2 90.1 91.9 175.1 96.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 3001 DBREF 5MS3 A 16 246 UNP O60259 KLK8_HUMAN 78 305 SEQRES 1 A 228 VAL LEU GLY GLY HIS GLU CYS GLN PRO HIS SER GLN PRO SEQRES 2 A 228 TRP GLN ALA ALA LEU PHE GLN GLY GLN GLN LEU LEU CYS SEQRES 3 A 228 GLY GLY VAL LEU VAL GLY GLY ASN TRP VAL LEU THR ALA SEQRES 4 A 228 ALA HIS CYS LYS LYS PRO LYS TYR THR VAL ARG LEU GLY SEQRES 5 A 228 ASP HIS SER LEU GLN ASN LYS ASP GLY PRO GLU GLN GLU SEQRES 6 A 228 ILE PRO VAL VAL GLN SER ILE PRO HIS PRO CYS TYR ASN SEQRES 7 A 228 SER SER ASP VAL GLU ASP HIS ASN HIS ASP LEU MET LEU SEQRES 8 A 228 LEU GLN LEU ARG ASP GLN ALA SER LEU GLY SER LYS VAL SEQRES 9 A 228 LYS PRO ILE SER LEU ALA ASP HIS CYS THR GLN PRO GLY SEQRES 10 A 228 GLN LYS CYS THR VAL SER GLY TRP GLY THR VAL THR SER SEQRES 11 A 228 PRO ARG GLU ASN PHE PRO ASP THR LEU ASN CYS ALA GLU SEQRES 12 A 228 VAL LYS ILE PHE PRO GLN LYS LYS CYS GLU ASP ALA TYR SEQRES 13 A 228 PRO GLY GLN ILE THR ASP GLY MET VAL CYS ALA GLY SER SEQRES 14 A 228 SER LYS GLY ALA ASP THR CYS GLN GLY ASP SER GLY GLY SEQRES 15 A 228 PRO LEU VAL CYS ASP GLY ALA LEU GLN GLY ILE THR SER SEQRES 16 A 228 TRP GLY SER ASP PRO CYS GLY ARG SER ASP LYS PRO GLY SEQRES 17 A 228 VAL TYR THR ASN ILE CYS ARG TYR LEU ASP TRP ILE LYS SEQRES 18 A 228 LYS ILE ILE GLY SER LYS GLY HET CA A3001 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *84(H2 O) HELIX 1 AA1 ALA A 55 LYS A 59 5 5 HELIX 2 AA2 PRO A 164 TYR A 172 1 9 HELIX 3 AA3 TYR A 234 GLY A 243 1 10 SHEET 1 AA1 8 HIS A 20 GLU A 21 0 SHEET 2 AA1 8 ASN A 156 ILE A 162 -1 O CYS A 157 N HIS A 20 SHEET 3 AA1 8 MET A 180 GLY A 184 -1 O GLY A 184 N LYS A 161 SHEET 4 AA1 8 GLY A 226 ASN A 230 -1 O TYR A 228 N VAL A 181 SHEET 5 AA1 8 ALA A 208 TRP A 215 -1 N ILE A 212 O THR A 229 SHEET 6 AA1 8 PRO A 198 CYS A 201 -1 N LEU A 199 O GLN A 210 SHEET 7 AA1 8 LYS A 135 GLY A 140 -1 N THR A 137 O VAL A 200 SHEET 8 AA1 8 ASN A 156 ILE A 162 -1 O VAL A 160 N CYS A 136 SHEET 1 AA2 7 GLN A 30 GLN A 35 0 SHEET 2 AA2 7 GLN A 39 LEU A 46 -1 O LEU A 41 N LEU A 33 SHEET 3 AA2 7 TRP A 51 THR A 54 -1 O LEU A 53 N VAL A 45 SHEET 4 AA2 7 MET A 104 LEU A 108 -1 O LEU A 106 N VAL A 52 SHEET 5 AA2 7 GLN A 81 PRO A 90 -1 N ILE A 89 O LEU A 105 SHEET 6 AA2 7 THR A 64 LEU A 67 -1 N VAL A 65 O ILE A 83 SHEET 7 AA2 7 GLN A 30 GLN A 35 -1 N PHE A 34 O THR A 64 SSBOND 1 CYS A 22 CYS A 157 1555 1555 2.03 SSBOND 2 CYS A 42 CYS A 58 1555 1555 2.02 SSBOND 3 CYS A 129 CYS A 232 1555 1555 2.03 SSBOND 4 CYS A 136 CYS A 201 1555 1555 2.02 SSBOND 5 CYS A 168 CYS A 182 1555 1555 2.03 SSBOND 6 CYS A 191 CYS A 220 1555 1555 2.03 LINK OD1 ASP A 70 CA CA A3001 1555 1555 2.30 LINK O SER A 72 CA CA A3001 1555 1555 2.22 LINK O ASN A 75 CA CA A3001 1555 1555 2.31 LINK OD2 ASP A 77 CA CA A3001 1555 1555 2.35 LINK OE2 GLU A 80 CA CA A3001 1555 1555 2.36 LINK CA CA A3001 O HOH A3139 1555 1555 2.36 CISPEP 1 SER A 146 PRO A 147 0 -1.22 CISPEP 2 ASP A 218 PRO A 219 0 4.29 SITE 1 AC1 6 ASP A 70 SER A 72 ASN A 75 ASP A 77 SITE 2 AC1 6 GLU A 80 HOH A3139 CRYST1 45.997 51.741 82.863 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 0.021741 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019327 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012068 0.00000