HEADER HYDROLASE 24-NOV-20 7KU2 TITLE DATA CLUSTERING AND DYNAMICS OF CHYMOTRYPSINOGEN CLULSTER 140 TITLE 2 (STRUCTURE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHYMOTRYPSINOGEN A; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.21.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS CLUSTERING, DYNAMICS, DATA ANALYSIS, CHYMOTRYPSINOGEN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.NGUYEN,K.L.PHAN,D.F.KREITLER,L.C.ANDREWS,S.B.GABELLI,D.KOZAKOV, AUTHOR 2 J.JAKONCIC,R.M.SWEET,A.S.SOARES,H.J.BERNSTEIN REVDAT 3 18-OCT-23 7KU2 1 REMARK REVDAT 2 16-MAR-22 7KU2 1 JRNL REVDAT 1 10-MAR-21 7KU2 0 JRNL AUTH T.NGUYEN,K.L.PHAN,D.KOZAKOV,S.B.GABELLI,D.F.KREITLER, JRNL AUTH 2 L.C.ANDREWS,J.JAKONCIC,R.M.SWEET,A.S.SOARES,H.J.BERNSTEIN JRNL TITL A SIMPLE TECHNIQUE TO CLASSIFY DIFFRACTION DATA FROM DYNAMIC JRNL TITL 2 PROTEINS ACCORDING TO INDIVIDUAL POLYMORPHS. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 78 268 2022 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 35234141 JRNL DOI 10.1107/S2059798321013425 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 18927 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 916 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 28.8920 - 4.1766 1.00 2757 149 0.1708 0.1796 REMARK 3 2 4.1766 - 3.3167 1.00 2632 117 0.1976 0.2175 REMARK 3 3 3.3167 - 2.8979 1.00 2586 138 0.2528 0.3080 REMARK 3 4 2.8979 - 2.6331 1.00 2581 117 0.2639 0.2941 REMARK 3 5 2.6331 - 2.4445 1.00 2563 121 0.2583 0.3167 REMARK 3 6 2.4445 - 2.3004 1.00 2544 127 0.2664 0.2776 REMARK 3 7 2.3004 - 2.1853 0.93 2348 147 0.2891 0.2911 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.31 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 1822 REMARK 3 ANGLE : 0.864 2488 REMARK 3 CHIRALITY : 0.055 294 REMARK 3 PLANARITY : 0.005 310 REMARK 3 DIHEDRAL : 21.539 638 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 7KU2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1000252809. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-19; 16-OCT-19 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : NSLS-II; NSLS-II REMARK 200 BEAMLINE : 17-ID-1; 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9201; 1.89 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M; DECTRIS REMARK 200 EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18970 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 77.5 REMARK 200 DATA REDUNDANCY : 66.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1EX3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M-2.0 M AMMONIUM SULFATE, 0.1 M REMARK 280 MES PH 6.5, AND 10% OR 15% DIOXANE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 26.46000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 57.78500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 57.78500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 13.23000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 57.78500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 57.78500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.69000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 57.78500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.78500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 13.23000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 57.78500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.78500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.69000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 26.46000 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 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 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 THR A 147 REMARK 465 ASN A 148 REMARK 465 ALA A 149 REMARK 465 ASN A 150 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 VAL A 17 -111.27 51.63 REMARK 500 PHE A 71 -55.40 -130.52 REMARK 500 SER A 214 -61.53 -105.13 REMARK 500 REMARK 500 REMARK: NULL DBREF 7KU2 A 1 245 UNP P00766 CTRA_BOVIN 1 245 SEQRES 1 A 245 CYS GLY VAL PRO ALA ILE GLN PRO VAL LEU SER GLY LEU SEQRES 2 A 245 SER ARG ILE VAL ASN GLY GLU GLU ALA VAL PRO GLY SER SEQRES 3 A 245 TRP PRO TRP GLN VAL SER LEU GLN ASP LYS THR GLY PHE SEQRES 4 A 245 HIS PHE CYS GLY GLY SER LEU ILE ASN GLU ASN TRP VAL SEQRES 5 A 245 VAL THR ALA ALA HIS CYS GLY VAL THR THR SER ASP VAL SEQRES 6 A 245 VAL VAL ALA GLY GLU PHE ASP GLN GLY SER SER SER GLU SEQRES 7 A 245 LYS ILE GLN LYS LEU LYS ILE ALA LYS VAL PHE LYS ASN SEQRES 8 A 245 SER LYS TYR ASN SER LEU THR ILE ASN ASN ASP ILE THR SEQRES 9 A 245 LEU LEU LYS LEU SER THR ALA ALA SER PHE SER GLN THR SEQRES 10 A 245 VAL SER ALA VAL CYS LEU PRO SER ALA SER ASP ASP PHE SEQRES 11 A 245 ALA ALA GLY THR THR CYS VAL THR THR GLY TRP GLY LEU SEQRES 12 A 245 THR ARG TYR THR ASN ALA ASN THR PRO ASP ARG LEU GLN SEQRES 13 A 245 GLN ALA SER LEU PRO LEU LEU SER ASN THR ASN CYS LYS SEQRES 14 A 245 LYS TYR TRP GLY THR LYS ILE LYS ASP ALA MET ILE CYS SEQRES 15 A 245 ALA GLY ALA SER GLY VAL SER SER CYS MET GLY ASP SER SEQRES 16 A 245 GLY GLY PRO LEU VAL CYS LYS LYS ASN GLY ALA TRP THR SEQRES 17 A 245 LEU VAL GLY ILE VAL SER TRP GLY SER SER THR CYS SER SEQRES 18 A 245 THR SER THR PRO GLY VAL TYR ALA ARG VAL THR ALA LEU SEQRES 19 A 245 VAL ASN TRP VAL GLN GLN THR LEU ALA ALA ASN HET SO4 A 301 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *44(H2 O) HELIX 1 AA1 SER A 11 ILE A 16 5 6 HELIX 2 AA2 ALA A 55 GLY A 59 5 5 HELIX 3 AA3 TRP A 141 TYR A 146 5 6 HELIX 4 AA4 SER A 164 GLY A 173 1 10 HELIX 5 AA5 THR A 174 ILE A 176 5 3 HELIX 6 AA6 VAL A 231 ASN A 245 1 15 SHEET 1 AA1 8 GLU A 20 GLU A 21 0 SHEET 2 AA1 8 GLN A 156 LEU A 163 -1 O GLN A 157 N GLU A 20 SHEET 3 AA1 8 MET A 180 GLY A 184 -1 O CYS A 182 N LEU A 163 SHEET 4 AA1 8 PRO A 225 ARG A 230 -1 O TYR A 228 N ILE A 181 SHEET 5 AA1 8 ALA A 206 TRP A 215 -1 N ILE A 212 O ALA A 229 SHEET 6 AA1 8 PRO A 198 LYS A 203 -1 N LEU A 199 O VAL A 210 SHEET 7 AA1 8 THR A 135 GLY A 140 -1 N VAL A 137 O VAL A 200 SHEET 8 AA1 8 GLN A 156 LEU A 163 -1 O LEU A 160 N CYS A 136 SHEET 1 AA2 7 GLN A 30 GLN A 34 0 SHEET 2 AA2 7 HIS A 40 ASN A 48 -1 O PHE A 41 N LEU A 33 SHEET 3 AA2 7 TRP A 51 THR A 54 -1 O VAL A 53 N SER A 45 SHEET 4 AA2 7 THR A 104 LEU A 108 -1 O LEU A 106 N VAL A 52 SHEET 5 AA2 7 GLN A 81 LYS A 90 -1 N PHE A 89 O LEU A 105 SHEET 6 AA2 7 VAL A 65 ALA A 68 -1 N VAL A 66 O LEU A 83 SHEET 7 AA2 7 GLN A 30 GLN A 34 -1 N SER A 32 O VAL A 67 SSBOND 1 CYS A 1 CYS A 122 1555 1555 2.07 SSBOND 2 CYS A 42 CYS A 58 1555 1555 2.06 SSBOND 3 CYS A 136 CYS A 201 1555 1555 2.04 SSBOND 4 CYS A 168 CYS A 182 1555 1555 2.03 SSBOND 5 CYS A 191 CYS A 220 1555 1555 2.04 CRYST1 115.570 115.570 52.920 90.00 90.00 90.00 P 41 21 2 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 0.008653 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008653 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018896 0.00000