HEADER HYDROLASE 24-JAN-18 5Z6O TITLE CRYSTAL STRUCTURE OF PENICILLIUM CYCLOPIUM PROTEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.21.64 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PENICILLIUM CYCLOPIUM; SOURCE 3 ORGANISM_TAXID: 60167 KEYWDS INHIBITOR, METAL ION, PROTEINASE K, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.-P.KO,S.KOSZELAK,J.NG,J.DAY,A.GREENWOOD,A.MCPHERSON REVDAT 3 06-NOV-24 5Z6O 1 REMARK REVDAT 2 22-NOV-23 5Z6O 1 LINK REVDAT 1 28-FEB-18 5Z6O 0 JRNL AUTH S.KOSZELAK,J.D.NG,J.DAY,T.P.KO,A.GREENWOOD,A.MCPHERSON JRNL TITL THE CRYSTALLOGRAPHIC STRUCTURE OF THE SUBTILISIN PROTEASE JRNL TITL 2 FROM PENICILLIUM CYCLOPIUM. JRNL REF BIOCHEMISTRY V. 36 6597 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 9184139 JRNL DOI 10.1021/BI963189T REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.510 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 29195 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.144 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 1398 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 22.7232 - 3.6580 1.00 2924 166 0.1039 0.1367 REMARK 3 2 3.6580 - 2.9054 1.00 2810 144 0.1281 0.1627 REMARK 3 3 2.9054 - 2.5387 1.00 2798 137 0.1429 0.1869 REMARK 3 4 2.5387 - 2.3068 1.00 2740 163 0.1447 0.1914 REMARK 3 5 2.3068 - 2.1416 1.00 2768 125 0.1374 0.1870 REMARK 3 6 2.1416 - 2.0154 1.00 2773 129 0.1431 0.1783 REMARK 3 7 2.0154 - 1.9146 1.00 2734 135 0.1596 0.2059 REMARK 3 8 1.9146 - 1.8313 1.00 2784 114 0.1816 0.2557 REMARK 3 9 1.8313 - 1.7608 1.00 2712 144 0.2087 0.2318 REMARK 3 10 1.7608 - 1.7000 1.00 2754 141 0.2326 0.2763 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.020 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 : 0.011 2062 REMARK 3 ANGLE : 1.073 2811 REMARK 3 CHIRALITY : 0.073 322 REMARK 3 PLANARITY : 0.008 373 REMARK 3 DIHEDRAL : 14.555 1220 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 5Z6O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1300006548. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-95 REMARK 200 TEMPERATURE (KELVIN) : 290 REMARK 200 PH : NULL 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 : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : SUPPER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : UCSD MARK II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : UCSD-SYSTEM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33985 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.36200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: 2PRK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 4000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 298K 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 29.61150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.43100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.82100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.43100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.61150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.82100 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 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 166 O HOH A 401 1.99 REMARK 500 O HOH A 428 O HOH A 503 1.99 REMARK 500 O HOH A 533 O HOH A 601 2.03 REMARK 500 O SER A 265 O HOH A 402 2.09 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 42 -150.08 -166.52 REMARK 500 SER A 136 55.16 -97.23 REMARK 500 SER A 265 -71.78 -78.62 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 A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 181 O REMARK 620 2 ASP A 204 OD1 120.2 REMARK 620 3 ASP A 204 OD2 79.6 51.4 REMARK 620 4 HOH A 494 O 145.8 70.5 86.3 REMARK 620 5 HOH A 499 O 85.3 153.8 149.7 91.9 REMARK 620 6 HOH A 541 O 76.5 115.5 77.2 70.0 73.7 REMARK 620 7 HOH A 558 O 74.9 90.6 110.2 139.3 90.7 148.4 REMARK 620 8 HOH A 577 O 148.7 76.2 126.0 62.1 78.4 122.9 78.7 REMARK 620 N 1 2 3 4 5 6 7 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PMS A 302 DBREF 5Z6O A 1 282 PDB 5Z6O 5Z6O 1 282 SEQRES 1 A 282 ALA ASN VAL VAL GLN ARG ASN SER PRO SER TRP GLY LEU SEQRES 2 A 282 SER ARG ILE SER SER LYS LYS SER GLY ALA THR ASP TYR SEQRES 3 A 282 VAL TYR ASP SER THR ALA GLY GLU GLY ILE VAL ILE TYR SEQRES 4 A 282 GLY VAL ASP THR GLY ILE ASP ILE GLY HIS ALA ASP PHE SEQRES 5 A 282 GLY GLY ARG ALA GLU TRP GLY THR ASN THR ALA ASP ASN SEQRES 6 A 282 ASP ASP THR ASP GLY ASN GLY HIS GLY THR HIS THR ALA SEQRES 7 A 282 SER THR ALA ALA GLY SER LYS PHE GLY VAL ALA LYS LYS SEQRES 8 A 282 ALA SER VAL VAL ALA VAL LYS VAL LEU GLY ALA ASP GLY SEQRES 9 A 282 SER GLY THR ASN SER GLN VAL ILE ALA GLY MET ASP TRP SEQRES 10 A 282 ALA VAL LYS ASP SER LYS SER ARG GLY ALA THR GLY LYS SEQRES 11 A 282 SER VAL MET ASN MET SER LEU GLY GLY ALA TYR SER ARG SEQRES 12 A 282 ALA MET ASN ASP ALA ALA ALA ASN VAL VAL ARG SER GLY SEQRES 13 A 282 VAL PHE LEU SER VAL ALA ALA GLY ASN GLU ALA GLN ASP SEQRES 14 A 282 ALA SER ASN SER SER PRO ALA SER ALA PRO ASN VAL CYS SEQRES 15 A 282 THR ILE ALA ALA SER THR ASN SER ASP GLY SER ALA SER SEQRES 16 A 282 PHE THR ASN PHE GLY SER VAL VAL ASP LEU TYR ALA PRO SEQRES 17 A 282 GLY LYS ASP ILE THR ALA ALA TYR PRO GLY GLY GLY SER SEQRES 18 A 282 LYS THR LEU SER GLY THR SER MET ALA ALA PRO HIS VAL SEQRES 19 A 282 ALA GLY ALA ALA ALA TYR LEU MET ALA LEU GLU GLY THR SEQRES 20 A 282 THR THR SER SER ALA CYS ALA ARG ILE VAL GLN ASP ALA SEQRES 21 A 282 ILE THR LYS ILE SER GLY ALA PRO LYS GLY THR THR THR SEQRES 22 A 282 LYS LEU LEU TYR ASN GLY ILE ASN GLY HET CA A 301 1 HET PMS A 302 16 HETNAM CA CALCIUM ION HETNAM PMS PHENYLMETHANESULFONIC ACID FORMUL 2 CA CA 2+ FORMUL 3 PMS C7 H8 O3 S FORMUL 4 HOH *214(H2 O) HELIX 1 AA1 SER A 10 SER A 17 1 8 HELIX 2 AA2 HIS A 49 GLY A 53 5 5 HELIX 3 AA3 GLY A 72 GLY A 83 1 12 HELIX 4 AA4 THR A 107 ARG A 125 1 19 HELIX 5 AA5 SER A 142 SER A 155 1 14 HELIX 6 AA6 ASP A 169 SER A 171 5 3 HELIX 7 AA7 GLY A 226 GLY A 246 1 21 HELIX 8 AA8 THR A 248 ALA A 260 1 13 SHEET 1 AA1 2 ASN A 2 GLN A 5 0 SHEET 2 AA1 2 TYR A 26 ASP A 29 -1 O TYR A 26 N GLN A 5 SHEET 1 AA2 7 ALA A 56 ASN A 61 0 SHEET 2 AA2 7 SER A 93 LYS A 98 1 O LYS A 98 N THR A 60 SHEET 3 AA2 7 VAL A 37 ASP A 42 1 N GLY A 40 O VAL A 97 SHEET 4 AA2 7 SER A 131 MET A 135 1 O VAL A 132 N TYR A 39 SHEET 5 AA2 7 VAL A 157 ALA A 162 1 O SER A 160 N MET A 135 SHEET 6 AA2 7 CYS A 182 SER A 187 1 O CYS A 182 N LEU A 159 SHEET 7 AA2 7 LEU A 205 PRO A 208 1 O LEU A 205 N ALA A 185 SHEET 1 AA3 2 GLY A 139 ALA A 140 0 SHEET 2 AA3 2 SER A 173 SER A 174 -1 O SER A 174 N GLY A 139 SHEET 1 AA4 2 ILE A 212 ALA A 215 0 SHEET 2 AA4 2 SER A 221 LEU A 224 -1 O LEU A 224 N ILE A 212 SHEET 1 AA5 2 ILE A 261 THR A 262 0 SHEET 2 AA5 2 LYS A 274 LEU A 275 -1 O LEU A 275 N ILE A 261 SSBOND 1 CYS A 182 CYS A 253 1555 1555 2.05 LINK OG SER A 228 S PMS A 302 1555 1555 1.59 LINK O VAL A 181 CA CA A 301 1555 1555 2.57 LINK OD1 ASP A 204 CA CA A 301 1555 1555 2.62 LINK OD2 ASP A 204 CA CA A 301 1555 1555 2.42 LINK CA CA A 301 O HOH A 494 1555 1555 2.25 LINK CA CA A 301 O HOH A 499 1555 1555 2.64 LINK CA CA A 301 O HOH A 541 1555 1555 2.30 LINK CA CA A 301 O HOH A 558 1555 1555 2.36 LINK CA CA A 301 O HOH A 577 1555 1555 2.41 CISPEP 1 SER A 174 PRO A 175 0 5.55 SITE 1 AC1 7 VAL A 181 ASP A 204 HOH A 494 HOH A 499 SITE 2 AC1 7 HOH A 541 HOH A 558 HOH A 577 SITE 1 AC2 11 HIS A 73 SER A 136 GLY A 138 ALA A 162 SITE 2 AC2 11 ASN A 165 GLY A 226 SER A 228 HOH A 401 SITE 3 AC2 11 HOH A 480 HOH A 542 HOH A 586 CRYST1 59.223 61.642 70.862 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 0.016885 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016223 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014112 0.00000