HEADER HYDROLASE 02-DEC-21 7W70 TITLE CRYSTAL STRUCTURE OF THE PDZ-C DOMAIN FRAGMENT OF KANGIELLA KOREENSIS TITLE 2 RSEP ORTHOLOGUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC METALLOPROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.4.24.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KANGIELLA KOREENSIS DSM 16069; SOURCE 3 ORGANISM_TAXID: 523791; SOURCE 4 STRAIN: DSM 16069 / KCTC 12182 / SW-125; SOURCE 5 GENE: KKOR_1905; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INTRAMEMBRANE PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.MIYOSHI,T.NOGI REVDAT 2 29-NOV-23 7W70 1 REMARK REVDAT 1 07-SEP-22 7W70 0 JRNL AUTH Y.IMAIZUMI,K.TAKANUKI,T.MIYAKE,M.TAKEMOTO,K.HIRATA,M.HIROSE, JRNL AUTH 2 R.OI,T.KOBAYASHI,K.MIYOSHI,R.ARUGA,T.YOKOYAMA,S.KATAGIRI, JRNL AUTH 3 H.MATSUURA,K.IWASAKI,T.KATO,M.K.KANEKO,Y.KATO,M.TAJIRI, JRNL AUTH 4 S.AKASHI,O.NUREKI,Y.HIZUKURI,Y.AKIYAMA,T.NOGI JRNL TITL MECHANISTIC INSIGHTS INTO INTRAMEMBRANE PROTEOLYSIS BY E. JRNL TITL 2 COLI SITE-2 PROTEASE HOMOLOG RSEP. JRNL REF SCI ADV V. 8 P9011 2022 JRNL REFN ESSN 2375-2548 JRNL PMID 36001659 JRNL DOI 10.1126/SCIADV.ABP9011 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 60798 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 5779 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 31.2900 - 3.5700 0.99 3656 190 0.1606 0.1706 REMARK 3 2 3.5700 - 2.8400 0.99 3645 203 0.1822 0.1783 REMARK 3 3 2.8400 - 2.4800 0.99 3622 200 0.2055 0.2091 REMARK 3 4 2.4800 - 2.2500 0.94 3492 147 0.1951 0.2166 REMARK 3 5 2.2500 - 2.0900 0.96 3522 191 0.1869 0.2160 REMARK 3 6 2.0900 - 1.9700 0.97 3574 220 0.1909 0.1744 REMARK 3 7 1.9700 - 1.8700 0.98 3619 187 0.1873 0.1982 REMARK 3 8 1.8700 - 1.7900 0.98 3670 137 0.2042 0.2065 REMARK 3 9 1.7900 - 1.7200 0.99 3667 164 0.2048 0.2403 REMARK 3 10 1.7200 - 1.6600 0.99 3659 185 0.1990 0.1827 REMARK 3 11 1.6600 - 1.6100 0.99 3659 192 0.2000 0.2275 REMARK 3 12 1.6100 - 1.5600 1.00 3584 232 0.1945 0.2254 REMARK 3 13 1.5600 - 1.5200 0.99 3638 231 0.2003 0.2304 REMARK 3 14 1.5200 - 1.4800 1.00 3673 196 0.2050 0.2192 REMARK 3 15 1.4800 - 1.4500 1.00 3703 163 0.2168 0.2208 REMARK 3 16 1.4500 - 1.4200 1.00 3660 210 0.2100 0.2524 REMARK 3 17 1.4200 - 1.3900 0.99 3627 225 0.2290 0.2229 REMARK 3 18 1.3900 - 1.3600 0.97 3503 198 0.2368 0.2402 REMARK 3 19 1.3600 - 1.3400 0.99 3683 195 0.2364 0.2597 REMARK 3 20 1.3400 - 1.3200 0.99 3573 256 0.2481 0.2707 REMARK 3 21 1.3200 - 1.3000 0.99 3655 208 0.2416 0.2579 REMARK 3 22 1.3000 - 1.2800 0.99 3616 179 0.2418 0.3077 REMARK 3 23 1.2800 - 1.2600 0.99 3662 182 0.2567 0.2809 REMARK 3 24 1.2600 - 1.2400 0.99 3707 195 0.2568 0.2760 REMARK 3 25 1.2400 - 1.2200 0.99 3615 195 0.2695 0.2890 REMARK 3 26 1.2200 - 1.2100 0.99 3674 199 0.2685 0.3079 REMARK 3 27 1.2100 - 1.1900 0.99 3619 180 0.2715 0.2995 REMARK 3 28 1.1900 - 1.1800 0.99 3602 176 0.2772 0.2713 REMARK 3 29 1.1800 - 1.1600 0.99 3758 160 0.3014 0.3235 REMARK 3 30 1.1600 - 1.1500 0.98 3582 183 0.3056 0.2759 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) : 0.125 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.314 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.84 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 1461 REMARK 3 ANGLE : 0.822 2015 REMARK 3 CHIRALITY : 0.076 227 REMARK 3 PLANARITY : 0.007 274 REMARK 3 DIHEDRAL : 5.309 221 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): 26.0765 21.9702 14.0976 REMARK 3 T TENSOR REMARK 3 T11: 0.1198 T22: 0.1277 REMARK 3 T33: 0.1410 T12: 0.0166 REMARK 3 T13: 0.0011 T23: -0.0087 REMARK 3 L TENSOR REMARK 3 L11: 0.5470 L22: 0.3669 REMARK 3 L33: 1.0344 L12: 0.6279 REMARK 3 L13: 0.9149 L23: 0.4502 REMARK 3 S TENSOR REMARK 3 S11: -0.0099 S12: -0.0095 S13: 0.0356 REMARK 3 S21: 0.0504 S22: -0.0013 S23: 0.0166 REMARK 3 S31: -0.0481 S32: -0.0463 S33: 0.0070 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 7W70 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1300026112. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9800 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60798 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 42.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 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 : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2ZPM REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS REMARK 200 AND I_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M AMMONIUM SULFATE, 0.1 M HEPES-NA REMARK 280 (PH 7.5), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 20.33650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.97450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.20400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.97450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.33650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.20400 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 PRO A 223 47.82 -86.42 REMARK 500 ASP B 294 93.66 -166.99 REMARK 500 REMARK 500 REMARK: NULL DBREF 7W70 A 221 307 UNP C7R5Z1 C7R5Z1_KANKD 221 307 DBREF 7W70 B 221 307 UNP C7R5Z1 C7R5Z1_KANKD 221 307 SEQRES 1 A 87 GLY GLU PRO SER LEU GLY LEU VAL ALA LYS ASP SER PRO SEQRES 2 A 87 ALA GLU LYS GLY GLY LEU LYS VAL GLY ASP THR VAL VAL SEQRES 3 A 87 SER VAL ASN GLY GLU SER ILE SER LEU TRP SER GLU PHE SEQRES 4 A 87 VAL SER PHE ILE GLU ASN ASN PRO GLY LYS PRO LEU GLU SEQRES 5 A 87 LEU ILE VAL ALA ARG ASP GLY TYR GLN GLN PRO LEU VAL SEQRES 6 A 87 VAL THR PRO GLU ALA ASN GLU ARG ASP ARG THR ILE GLY SEQRES 7 A 87 TYR LEU GLY ILE SER PRO ALA PHE GLN SEQRES 1 B 87 GLY GLU PRO SER LEU GLY LEU VAL ALA LYS ASP SER PRO SEQRES 2 B 87 ALA GLU LYS GLY GLY LEU LYS VAL GLY ASP THR VAL VAL SEQRES 3 B 87 SER VAL ASN GLY GLU SER ILE SER LEU TRP SER GLU PHE SEQRES 4 B 87 VAL SER PHE ILE GLU ASN ASN PRO GLY LYS PRO LEU GLU SEQRES 5 B 87 LEU ILE VAL ALA ARG ASP GLY TYR GLN GLN PRO LEU VAL SEQRES 6 B 87 VAL THR PRO GLU ALA ASN GLU ARG ASP ARG THR ILE GLY SEQRES 7 B 87 TYR LEU GLY ILE SER PRO ALA PHE GLN FORMUL 3 HOH *166(H2 O) HELIX 1 AA1 SER A 232 GLY A 238 1 7 HELIX 2 AA2 LEU A 255 ASN A 266 1 12 HELIX 3 AA3 SER B 232 GLY B 237 1 6 HELIX 4 AA4 LEU B 255 ASN B 265 1 11 SHEET 1 AA1 2 LEU A 225 VAL A 228 0 SHEET 2 AA1 2 ILE A 302 PRO A 304 -1 O SER A 303 N GLY A 226 SHEET 1 AA2 4 GLU A 251 SER A 252 0 SHEET 2 AA2 4 THR A 244 VAL A 248 -1 N VAL A 248 O GLU A 251 SHEET 3 AA2 4 LEU A 271 ARG A 277 -1 O ILE A 274 N VAL A 246 SHEET 4 AA2 4 TYR A 280 VAL A 286 -1 O VAL A 286 N LEU A 271 SHEET 1 AA3 2 GLU A 289 ALA A 290 0 SHEET 2 AA3 2 GLY A 298 TYR A 299 -1 O TYR A 299 N GLU A 289 SHEET 1 AA4 2 LEU B 227 VAL B 228 0 SHEET 2 AA4 2 ILE B 302 SER B 303 -1 O SER B 303 N LEU B 227 SHEET 1 AA5 4 GLU B 251 SER B 252 0 SHEET 2 AA5 4 THR B 244 VAL B 248 -1 N VAL B 248 O GLU B 251 SHEET 3 AA5 4 LEU B 271 ARG B 277 -1 O ALA B 276 N THR B 244 SHEET 4 AA5 4 TYR B 280 VAL B 286 -1 O LEU B 284 N LEU B 273 SHEET 1 AA6 2 GLU B 289 ALA B 290 0 SHEET 2 AA6 2 GLY B 298 TYR B 299 -1 O TYR B 299 N GLU B 289 CRYST1 40.673 42.408 97.949 90.00 90.00 90.00 P 21 21 21 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 0.024586 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023580 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010209 0.00000