HEADER HYDROLASE 02-SEP-15 5DK1 TITLE S. ERYTHRAEA TRYPSIN MIXED CATALYTIC INTERMEDIATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPSIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SET; COMPND 5 EC: 3.4.21.4; COMPND 6 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 5 27-SEP-23 5DK1 1 REMARK REVDAT 4 11-DEC-19 5DK1 1 REMARK REVDAT 3 22-NOV-17 5DK1 1 REMARK REVDAT 2 13-SEP-17 5DK1 1 REMARK REVDAT 1 08-MAR-17 5DK1 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. 0.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2356: ???) 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) : 0.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 173750 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.107 REMARK 3 R VALUE (WORKING SET) : 0.107 REMARK 3 FREE R VALUE : 0.117 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3473 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 39.4031 - 2.7431 1.00 7052 132 0.1300 0.1524 REMARK 3 2 2.7431 - 2.1773 1.00 6941 139 0.1028 0.1037 REMARK 3 3 2.1773 - 1.9021 1.00 6925 144 0.0897 0.0981 REMARK 3 4 1.9021 - 1.7282 1.00 6892 139 0.0859 0.0959 REMARK 3 5 1.7282 - 1.6043 1.00 6880 152 0.0817 0.0958 REMARK 3 6 1.6043 - 1.5097 1.00 6942 116 0.0768 0.0778 REMARK 3 7 1.5097 - 1.4341 1.00 6861 140 0.0733 0.0840 REMARK 3 8 1.4341 - 1.3717 1.00 6839 139 0.0718 0.0909 REMARK 3 9 1.3717 - 1.3189 1.00 6900 145 0.0770 0.0962 REMARK 3 10 1.3189 - 1.2734 1.00 6843 148 0.0759 0.0754 REMARK 3 11 1.2734 - 1.2335 1.00 6868 147 0.0744 0.1002 REMARK 3 12 1.2335 - 1.1983 1.00 6863 153 0.0751 0.1090 REMARK 3 13 1.1983 - 1.1667 1.00 6856 127 0.0805 0.0849 REMARK 3 14 1.1667 - 1.1383 1.00 6854 141 0.0878 0.0921 REMARK 3 15 1.1383 - 1.1124 1.00 6892 131 0.0967 0.0973 REMARK 3 16 1.1124 - 1.0887 1.00 6825 164 0.1180 0.1233 REMARK 3 17 1.0887 - 1.0669 1.00 6834 135 0.1249 0.1225 REMARK 3 18 1.0669 - 1.0468 1.00 6853 146 0.1377 0.1157 REMARK 3 19 1.0468 - 1.0281 1.00 6896 125 0.1530 0.1708 REMARK 3 20 1.0281 - 1.0107 1.00 6818 161 0.1780 0.1883 REMARK 3 21 1.0107 - 0.9944 1.00 6849 132 0.2054 0.2324 REMARK 3 22 0.9944 - 0.9791 1.00 6781 147 0.2411 0.2203 REMARK 3 23 0.9791 - 0.9647 1.00 6891 128 0.2705 0.2996 REMARK 3 24 0.9647 - 0.9511 0.97 6615 129 0.3108 0.3241 REMARK 3 25 0.9511 - 0.9382 0.80 5507 113 0.3416 0.3281 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) : 11.370 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 : 0.005 2141 REMARK 3 ANGLE : 1.129 2951 REMARK 3 CHIRALITY : 0.072 319 REMARK 3 PLANARITY : 0.006 423 REMARK 3 DIHEDRAL : 13.942 799 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 5DK1 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_1000213326. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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 : 173768 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.938 REMARK 200 RESOLUTION RANGE LOW (A) : 62.426 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.06400 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) : 0.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 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 (%): 57.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, PH 8.0, 2.3 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 18.37124 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.64850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 62.42658 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 18.37124 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.64850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 62.42658 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: 9910 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: 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 81 -40.04 -130.92 REMARK 500 ASP A 116 -4.36 84.85 REMARK 500 SER A 194 -60.96 -131.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 625 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A 626 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A 627 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A 628 DISTANCE = 6.58 ANGSTROMS REMARK 525 HOH A 629 DISTANCE = 7.01 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DJ7 RELATED DB: PDB REMARK 900 RELATED ID: 5DJM RELATED DB: PDB REMARK 900 RELATED ID: 4M7G RELATED DB: PDB REMARK 900 RELATED ID: 5KWM RELATED DB: PDB DBREF 5DK1 A 1 227 UNP P24664 TRYP_SACER 1 227 SEQADV 5DK1 GLU A 65 UNP P24664 ILE 65 VARIANT SEQADV 5DK1 SER A 228 UNP P24664 CLONING ARTIFACT SEQADV 5DK1 ALA A 229 UNP P24664 CLONING ARTIFACT SEQADV 5DK1 ARG A 230 UNP P24664 CLONING ARTIFACT 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 ASN 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 *328(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 ALA A 224 1 11 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 PHE A 26 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 2.02 SSBOND 3 CYS A 175 CYS A 199 1555 1555 2.08 CRYST1 41.037 53.297 124.927 90.00 91.97 90.00 I 1 2 1 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 0.024368 0.000000 0.000840 0.00000 SCALE2 0.000000 0.018763 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008009 0.00000