HEADER HYDROLASE 03-SEP-15 5DKM TITLE S. ERYTHRAEA TRYPSIN MICHAELIS-MENTEN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPSIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 43-272; COMPND 5 SYNONYM: SET; COMPND 6 EC: 3.4.21.4; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROPOLYSPORA ERYTHRAEA; SOURCE 3 ORGANISM_TAXID: 1836; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PQE-80L KEYWDS SERINE PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR E.BLANKENSHIP,D.T.LODOWSKI REVDAT 6 09-OCT-24 5DKM 1 REMARK REVDAT 5 27-SEP-23 5DKM 1 REMARK REVDAT 4 11-DEC-19 5DKM 1 REMARK REVDAT 3 22-NOV-17 5DKM 1 REMARK REVDAT 2 13-SEP-17 5DKM 1 REMARK REVDAT 1 08-MAR-17 5DKM 0 JRNL AUTH E.BLANKENSHIP,D.T.LODOWSKI JRNL TITL HIGH RESOLUTION STRUCTURES OF S. ERYTHRAEUS TRYPSIN JRNL TITL 2 THROUGHOUT THE CATALYTIC CYCLE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2328: ???) 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) : 0.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 139424 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.120 REMARK 3 R VALUE (WORKING SET) : 0.119 REMARK 3 FREE R VALUE : 0.130 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 6931 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 28.2077 - 2.8577 1.00 4538 253 0.1375 0.1402 REMARK 3 2 2.8577 - 2.2686 0.99 4460 231 0.1126 0.1174 REMARK 3 3 2.2686 - 1.9819 1.00 4462 218 0.0999 0.1024 REMARK 3 4 1.9819 - 1.8007 1.00 4447 261 0.0917 0.1126 REMARK 3 5 1.8007 - 1.6717 1.00 4382 248 0.0883 0.1039 REMARK 3 6 1.6717 - 1.5731 1.00 4461 230 0.0839 0.0941 REMARK 3 7 1.5731 - 1.4943 1.00 4415 249 0.0852 0.1050 REMARK 3 8 1.4943 - 1.4293 1.00 4442 238 0.0833 0.0925 REMARK 3 9 1.4293 - 1.3743 1.00 4417 230 0.0788 0.0909 REMARK 3 10 1.3743 - 1.3268 0.99 4354 232 0.0938 0.1197 REMARK 3 11 1.3268 - 1.2854 1.00 4444 234 0.0882 0.1096 REMARK 3 12 1.2854 - 1.2486 1.00 4372 249 0.0880 0.0979 REMARK 3 13 1.2486 - 1.2157 1.00 4455 200 0.0866 0.1017 REMARK 3 14 1.2157 - 1.1861 1.00 4412 242 0.0891 0.1068 REMARK 3 15 1.1861 - 1.1591 1.00 4463 211 0.0997 0.1126 REMARK 3 16 1.1591 - 1.1344 0.99 4328 235 0.1241 0.1441 REMARK 3 17 1.1344 - 1.1118 1.00 4451 214 0.1149 0.1361 REMARK 3 18 1.1118 - 1.0908 0.98 4336 212 0.1416 0.1485 REMARK 3 19 1.0908 - 1.0713 1.00 4387 247 0.1300 0.1337 REMARK 3 20 1.0713 - 1.0531 1.00 4409 210 0.1395 0.1555 REMARK 3 21 1.0531 - 1.0361 1.00 4415 241 0.1533 0.1822 REMARK 3 22 1.0361 - 1.0202 1.00 4424 224 0.1652 0.1817 REMARK 3 23 1.0202 - 1.0052 1.00 4381 246 0.1804 0.2039 REMARK 3 24 1.0052 - 0.9910 1.00 4445 217 0.2027 0.2105 REMARK 3 25 0.9910 - 0.9776 1.00 4390 229 0.2171 0.2218 REMARK 3 26 0.9776 - 0.9649 1.00 4443 226 0.2315 0.2384 REMARK 3 27 0.9649 - 0.9529 1.00 4372 227 0.2764 0.2609 REMARK 3 28 0.9529 - 0.9414 1.00 4398 263 0.2767 0.2893 REMARK 3 29 0.9414 - 0.9305 1.00 4398 193 0.3086 0.3137 REMARK 3 30 0.9305 - 0.9200 0.99 4392 221 0.3419 0.3442 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.22 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 : 0.008 1978 REMARK 3 ANGLE : 1.067 2742 REMARK 3 CHIRALITY : 0.092 302 REMARK 3 PLANARITY : 0.008 385 REMARK 3 DIHEDRAL : 16.210 735 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 5DKM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213320. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.688 REMARK 200 MONOCHROMATOR : CRYO-COOLED DOUBLE CRYSTAL REMARK 200 SI(111) 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 : XDS, AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 159546 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.870 REMARK 200 RESOLUTION RANGE LOW (A) : 28.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 2.60100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.400 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: PDB ENTRY 4M7G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES, PH 6.0, 36% PEG400, 100 MM REMARK 280 BTP , 120 MM SODIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 23.72050 REMARK 290 SMTRY3 2 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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: 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 OG1 THR A 20 OD1 ASP A 22 1.95 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 SER A 194 -63.98 -131.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DJ7 RELATED DB: PDB REMARK 900 RELATED ID: 5DK1 RELATED DB: PDB REMARK 900 RELATED ID: 5KWM RELATED DB: PDB DBREF 5DKM A 1 230 UNP Q54137 Q54137_SACER 43 272 SEQRES 1 A 230 ILE VAL GLY GLY GLU ASP ALA ASN VAL GLN ASP HIS PRO SEQRES 2 A 230 PHE THR VAL ALA LEU VAL THR PRO ASP GLY GLN GLN PHE SEQRES 3 A 230 CYS GLY GLY THR LEU ALA ALA PRO ASN LYS VAL VAL THR SEQRES 4 A 230 ALA ALA HIS CYS THR VAL GLY SER GLN PRO ALA ASP ILE SEQRES 5 A 230 ASN VAL VAL SER GLY ARG THR VAL MET SER SER ASN GLU SEQRES 6 A 230 GLY THR VAL SER LYS VAL THR ASN VAL TRP VAL HIS PRO SEQRES 7 A 230 GLU TYR GLN ASP ALA ALA LYS GLY PHE ASP VAL SER VAL SEQRES 8 A 230 LEU THR LEU GLU ALA PRO VAL LYS GLU ALA PRO ILE GLU SEQRES 9 A 230 LEU ALA LYS ALA ASP ASP ALA GLY TYR ALA PRO ASP THR SEQRES 10 A 230 ALA ALA THR ILE LEU GLY TRP GLY ASN THR SER GLU GLY SEQRES 11 A 230 GLY GLN GLN ALA ASP HIS LEU GLN LYS ALA THR VAL PRO SEQRES 12 A 230 VAL ASN SER ASP ASP THR CYS LYS GLN ALA TYR GLY GLU SEQRES 13 A 230 TYR THR PRO ASP ALA MET VAL CYS ALA GLY VAL PRO GLU SEQRES 14 A 230 GLY GLY VAL ASP THR CYS GLN GLY ASP SER GLY GLY PRO SEQRES 15 A 230 MET VAL VAL ASN ASN LYS LEU ILE GLY VAL THR SER TRP SEQRES 16 A 230 GLY GLU GLY CYS ALA ARG PRO GLY LYS PRO GLY VAL TYR SEQRES 17 A 230 ALA ARG VAL GLY ALA TYR TYR ASP VAL LEU MET GLU GLN SEQRES 18 A 230 ILE ASN ALA GLY ALA VAL SER ALA ARG FORMUL 2 HOH *306(H2 O) HELIX 1 AA1 ASN A 8 HIS A 12 5 5 HELIX 2 AA2 ALA A 40 VAL A 45 1 6 HELIX 3 AA3 GLN A 48 ASP A 51 5 4 HELIX 4 AA4 ASP A 82 GLY A 86 5 5 HELIX 5 AA5 ASP A 110 ALA A 114 5 5 HELIX 6 AA6 SER A 146 TYR A 154 1 9 HELIX 7 AA7 TYR A 214 ASN A 223 1 10 SHEET 1 AA1 6 GLU A 5 ASP A 6 0 SHEET 2 AA1 6 GLN A 138 PRO A 143 -1 O LYS A 139 N GLU A 5 SHEET 3 AA1 6 ALA A 118 GLY A 123 -1 N ALA A 119 O VAL A 142 SHEET 4 AA1 6 PRO A 182 VAL A 185 -1 O VAL A 184 N THR A 120 SHEET 5 AA1 6 LYS A 188 TRP A 195 -1 O ILE A 190 N MET A 183 SHEET 6 AA1 6 GLU A 104 LEU A 105 1 N GLU A 104 O LEU A 189 SHEET 1 AA2 7 GLU A 5 ASP A 6 0 SHEET 2 AA2 7 GLN A 138 PRO A 143 -1 O LYS A 139 N GLU A 5 SHEET 3 AA2 7 ALA A 118 GLY A 123 -1 N ALA A 119 O VAL A 142 SHEET 4 AA2 7 PRO A 182 VAL A 185 -1 O VAL A 184 N THR A 120 SHEET 5 AA2 7 LYS A 188 TRP A 195 -1 O ILE A 190 N MET A 183 SHEET 6 AA2 7 GLY A 206 ARG A 210 -1 O VAL A 207 N TRP A 195 SHEET 7 AA2 7 MET A 162 ALA A 165 -1 N VAL A 163 O TYR A 208 SHEET 1 AA3 7 THR A 15 VAL A 19 0 SHEET 2 AA3 7 GLN A 25 ALA A 33 -1 O CYS A 27 N LEU A 18 SHEET 3 AA3 7 LYS A 36 THR A 39 -1 O VAL A 38 N THR A 30 SHEET 4 AA3 7 SER A 90 LEU A 94 -1 O LEU A 92 N VAL A 37 SHEET 5 AA3 7 THR A 67 VAL A 76 -1 N THR A 72 O THR A 93 SHEET 6 AA3 7 ASN A 53 SER A 56 -1 N VAL A 54 O SER A 69 SHEET 7 AA3 7 THR A 15 VAL A 19 -1 N ALA A 17 O VAL A 55 SSBOND 1 CYS A 27 CYS A 43 1555 1555 2.08 SSBOND 2 CYS A 150 CYS A 164 1555 1555 2.06 SSBOND 3 CYS A 175 CYS A 199 1555 1555 2.08 CRYST1 42.072 47.441 53.471 90.00 106.10 90.00 P 1 21 1 2 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 0.023769 0.000000 0.006860 0.00000 SCALE2 0.000000 0.021079 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019465 0.00000