HEADER HYDROLASE 06-APR-23 8SDK TITLE THE MICROED STRUCTURE OF PROTEINASE K CRYSTALLIZED BY SUSPENDED DROP TITLE 2 CRYSTALLIZATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEINASE K; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ENDOPEPTIDASE K, TRITIRACHIUM ALKALINE PROTEINASE; COMPND 5 EC: 3.4.21.64 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARENGYODONTIUM ALBUM; SOURCE 3 ORGANISM_TAXID: 37998 KEYWDS MICROED, SUSPENDED DROP CRYSTALLIZATION, ENZYME, HYDROLASE EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR C.GILLMAN,W.J.NICOLAS,M.W.MARTYNOWYCZ,T.GONEN REVDAT 3 12-JUL-23 8SDK 1 JRNL REVDAT 2 14-JUN-23 8SDK 1 JRNL REVDAT 1 31-MAY-23 8SDK 0 JRNL AUTH C.GILLMAN,W.J.NICOLAS,M.W.MARTYNOWYCZ,T.GONEN JRNL TITL DESIGN AND IMPLEMENTATION OF SUSPENDED DROP CRYSTALLIZATION. JRNL REF IUCRJ V. 10 430 2023 JRNL REFN ESSN 2052-2525 JRNL PMID 37223996 JRNL DOI 10.1107/S2052252523004141 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.2 REMARK 3 NUMBER OF REFLECTIONS : 22074 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.259 REMARK 3 R VALUE (WORKING SET) : 0.255 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2208 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 30.4200 - 5.2800 0.81 1226 145 0.1946 0.1826 REMARK 3 2 5.2800 - 4.2000 0.85 1289 139 0.1547 0.1939 REMARK 3 3 4.2000 - 3.6700 0.86 1299 143 0.1771 0.2193 REMARK 3 4 3.6700 - 3.3300 0.85 1283 143 0.2021 0.2800 REMARK 3 5 3.3300 - 3.0900 0.84 1255 141 0.2504 0.2682 REMARK 3 6 3.0900 - 2.9100 0.83 1263 138 0.2634 0.3243 REMARK 3 7 2.9100 - 2.7700 0.84 1272 140 0.2973 0.3948 REMARK 3 8 2.7700 - 2.6500 0.81 1209 137 0.3004 0.3193 REMARK 3 9 2.6500 - 2.5400 0.83 1240 136 0.3104 0.3657 REMARK 3 10 2.5400 - 2.4600 0.81 1232 139 0.3184 0.3738 REMARK 3 11 2.4600 - 2.3800 0.81 1238 135 0.3161 0.3205 REMARK 3 12 2.3800 - 2.3100 0.82 1223 135 0.3168 0.3181 REMARK 3 13 2.3100 - 2.2500 0.80 1212 142 0.3461 0.3997 REMARK 3 14 2.2500 - 2.2000 0.79 1194 129 0.3422 0.3920 REMARK 3 15 2.2000 - 2.1500 0.81 1225 128 0.3489 0.3662 REMARK 3 16 2.1500 - 2.1000 0.79 1206 138 0.3602 0.4187 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.381 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.451 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.09 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 : 0.001 2072 REMARK 3 ANGLE : 0.383 2816 REMARK 3 CHIRALITY : 0.039 312 REMARK 3 PLANARITY : 0.002 370 REMARK 3 DIHEDRAL : 3.607 307 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: NONE REMARK 4 REMARK 4 8SDK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-23. REMARK 100 THE DEPOSITION ID IS D_1000273253. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : NULL REMARK 240 TEMPERATURE (KELVIN) : NULL REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 240 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 300 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 240 RESOLUTION RANGE HIGH (A) : NULL REMARK 240 RESOLUTION RANGE LOW (A) : NULL REMARK 240 DATA SCALING SOFTWARE : NULL REMARK 240 COMPLETENESS FOR RANGE (%) : NULL REMARK 240 DATA REDUNDANCY : NULL REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :NULL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :NULL REMARK 240 COMPLETENESS FOR SHELL (%) : NULL REMARK 240 DATA REDUNDANCY IN SHELL : NULL REMARK 240 R MERGE FOR SHELL (I) : NULL REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 240 SOFTWARE USED : NULL REMARK 240 STARTING MODEL : NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 50.97500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.13000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.13000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 76.46250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.13000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.13000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.48750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.13000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.13000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 76.46250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.13000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.13000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.48750 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 50.97500 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 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 O PRO A 112 O HOH A 501 2.14 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 144 -135.53 -152.67 REMARK 500 SER A 237 47.04 -91.86 REMARK 500 ASN A 375 63.00 -102.99 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 608 DISTANCE = 5.82 ANGSTROMS 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 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 280 O REMARK 620 2 VAL A 282 O 87.1 REMARK 620 3 ASP A 305 OD2 161.5 75.3 REMARK 620 4 HOH A 512 O 85.5 58.3 89.7 REMARK 620 5 HOH A 530 O 63.8 63.3 102.5 114.3 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-40351 RELATED DB: EMDB REMARK 900 THE MICROED STRUCTURE OF PROTEINASE K CRYSTALLIZED BY SUSPENDED REMARK 900 DROP CRYSTALLIZATION DBREF 8SDK A 106 384 UNP P06873 PRTK_PARAQ 106 384 SEQRES 1 A 279 ALA ALA GLN THR ASN ALA PRO TRP GLY LEU ALA ARG ILE SEQRES 2 A 279 SER SER THR SER PRO GLY THR SER THR TYR TYR TYR ASP SEQRES 3 A 279 GLU SER ALA GLY GLN GLY SER CYS VAL TYR VAL ILE ASP SEQRES 4 A 279 THR GLY ILE GLU ALA SER HIS PRO GLU PHE GLU GLY ARG SEQRES 5 A 279 ALA GLN MET VAL LYS THR TYR TYR TYR SER SER ARG ASP SEQRES 6 A 279 GLY ASN GLY HIS GLY THR HIS CYS ALA GLY THR VAL GLY SEQRES 7 A 279 SER ARG THR TYR GLY VAL ALA LYS LYS THR GLN LEU PHE SEQRES 8 A 279 GLY VAL LYS VAL LEU ASP ASP ASN GLY SER GLY GLN TYR SEQRES 9 A 279 SER THR ILE ILE ALA GLY MET ASP PHE VAL ALA SER ASP SEQRES 10 A 279 LYS ASN ASN ARG ASN CYS PRO LYS GLY VAL VAL ALA SER SEQRES 11 A 279 LEU SER LEU GLY GLY GLY TYR SER SER SER VAL ASN SER SEQRES 12 A 279 ALA ALA ALA ARG LEU GLN SER SER GLY VAL MET VAL ALA SEQRES 13 A 279 VAL ALA ALA GLY ASN ASN ASN ALA ASP ALA ARG ASN TYR SEQRES 14 A 279 SER PRO ALA SER GLU PRO SER VAL CYS THR VAL GLY ALA SEQRES 15 A 279 SER ASP ARG TYR ASP ARG ARG SER SER PHE SER ASN TYR SEQRES 16 A 279 GLY SER VAL LEU ASP ILE PHE GLY PRO GLY THR SER ILE SEQRES 17 A 279 LEU SER THR TRP ILE GLY GLY SER THR ARG SER ILE SER SEQRES 18 A 279 GLY THR SER MET ALA THR PRO HIS VAL ALA GLY LEU ALA SEQRES 19 A 279 ALA TYR LEU MET THR LEU GLY LYS THR THR ALA ALA SER SEQRES 20 A 279 ALA CYS ARG TYR ILE ALA ASP THR ALA ASN LYS GLY ASP SEQRES 21 A 279 LEU SER ASN ILE PRO PHE GLY THR VAL ASN LEU LEU ALA SEQRES 22 A 279 TYR ASN ASN TYR GLN ALA HET SO4 A 401 5 HET CA A 402 1 HETNAM SO4 SULFATE ION HETNAM CA CALCIUM ION FORMUL 2 SO4 O4 S 2- FORMUL 3 CA CA 2+ FORMUL 4 HOH *108(H2 O) HELIX 1 AA1 PRO A 112 ILE A 118 1 7 HELIX 2 AA2 HIS A 151 GLU A 155 5 5 HELIX 3 AA3 GLY A 173 SER A 184 1 12 HELIX 4 AA4 GLN A 208 LYS A 223 1 16 HELIX 5 AA5 ASN A 224 ARG A 226 5 3 HELIX 6 AA6 SER A 243 SER A 256 1 14 HELIX 7 AA7 ASP A 270 ARG A 272 5 3 HELIX 8 AA8 GLY A 327 LEU A 345 1 19 HELIX 9 AA9 SER A 352 THR A 360 1 9 SHEET 1 AA1 2 ALA A 107 THR A 109 0 SHEET 2 AA1 2 THR A 127 TYR A 129 -1 O TYR A 128 N GLN A 108 SHEET 1 AA2 7 ALA A 158 THR A 163 0 SHEET 2 AA2 7 GLN A 194 LYS A 199 1 O GLY A 197 N GLN A 159 SHEET 3 AA2 7 SER A 138 ASP A 144 1 N VAL A 140 O GLN A 194 SHEET 4 AA2 7 GLY A 231 LEU A 236 1 O VAL A 233 N TYR A 141 SHEET 5 AA2 7 MET A 259 ALA A 263 1 O MET A 259 N ALA A 234 SHEET 6 AA2 7 CYS A 283 SER A 288 1 O CYS A 283 N VAL A 262 SHEET 7 AA2 7 ILE A 306 PRO A 309 1 O ILE A 306 N GLY A 286 SHEET 1 AA3 2 GLY A 240 GLY A 241 0 SHEET 2 AA3 2 TYR A 274 SER A 275 -1 O SER A 275 N GLY A 240 SHEET 1 AA4 2 ILE A 313 THR A 316 0 SHEET 2 AA4 2 THR A 322 ILE A 325 -1 O ILE A 325 N ILE A 313 SHEET 1 AA5 2 ASN A 362 LYS A 363 0 SHEET 2 AA5 2 LEU A 376 LEU A 377 -1 O LEU A 377 N ASN A 362 SSBOND 1 CYS A 139 CYS A 228 1555 1555 2.03 SSBOND 2 CYS A 283 CYS A 354 1555 1555 2.03 LINK O PRO A 280 CA CA A 402 1555 1555 2.46 LINK O VAL A 282 CA CA A 402 1555 1555 2.78 LINK OD2 ASP A 305 CA CA A 402 1555 1555 2.35 LINK CA CA A 402 O HOH A 512 1555 1555 2.52 LINK CA CA A 402 O HOH A 530 1555 1555 2.36 CISPEP 1 SER A 275 PRO A 276 0 1.50 CRYST1 68.260 68.260 101.950 90.00 90.00 90.00 P 43 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 0.014650 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014650 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009809 0.00000