HEADER HYDROLASE 19-NOV-21 7SWB TITLE MICROED STRUCTURE OF PROTEINASE K FROM A 360 NM THICK LAMELLA MEASURED TITLE 2 AT 300 KV 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_COMMON: ENGYODONTIUM ALBUM, TRITIRACHIUM ALBUM; SOURCE 4 ORGANISM_TAXID: 37998 KEYWDS SERINE PROTEASE, HYDROLASE EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR M.W.MARTYNOWYCZ,M.T.B.CLABBERS,J.UNGE,J.HATTNE,T.GONEN REVDAT 2 18-OCT-23 7SWB 1 REMARK REVDAT 1 07-SEP-22 7SWB 0 JRNL AUTH M.W.MARTYNOWYCZ,M.T.B.CLABBERS,J.UNGE,J.HATTNE,T.GONEN JRNL TITL BENCHMARKING THE IDEAL SAMPLE THICKNESS IN CRYO-EM. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 34873060 JRNL DOI 10.1073/PNAS.2108884118 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874+SVN 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 27480 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.520 REMARK 3 FREE R VALUE TEST SET COUNT : 1791 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 30.8200 - 4.8200 0.88 1865 137 0.1690 0.2003 REMARK 3 2 4.8100 - 3.8200 0.92 1939 140 0.1292 0.1547 REMARK 3 3 3.8200 - 3.3400 0.92 1964 134 0.1494 0.1946 REMARK 3 4 3.3400 - 3.0400 0.93 1973 138 0.1818 0.1934 REMARK 3 5 3.0400 - 2.8200 0.94 2000 129 0.2041 0.2685 REMARK 3 6 2.8200 - 2.6500 0.94 1988 138 0.2146 0.2707 REMARK 3 7 2.6500 - 2.5200 0.94 2001 144 0.2279 0.2725 REMARK 3 8 2.5200 - 2.4100 0.94 1989 138 0.2242 0.2991 REMARK 3 9 2.4100 - 2.3200 0.93 2008 136 0.2333 0.3300 REMARK 3 10 2.3200 - 2.2400 0.94 1985 143 0.2309 0.2562 REMARK 3 11 2.2400 - 2.1700 0.94 2000 136 0.2312 0.3331 REMARK 3 12 2.1700 - 2.1100 0.93 1956 134 0.2432 0.3307 REMARK 3 13 2.1100 - 2.0500 0.94 2021 144 0.2526 0.2959 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) : 0.272 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.155 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.54 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 : 0.012 2068 REMARK 3 ANGLE : 1.137 2810 REMARK 3 CHIRALITY : 0.066 312 REMARK 3 PLANARITY : 0.007 370 REMARK 3 DIHEDRAL : 5.717 307 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: NULL REMARK 4 REMARK 4 7SWB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1000260273. 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 : 01-OCT-20 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 CETA (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 300 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 76827 REMARK 240 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 240 RESOLUTION RANGE LOW (A) : 20.000 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 240 DATA REDUNDANCY : 2.800 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :2.05 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :2.10 REMARK 240 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 240 DATA REDUNDANCY IN SHELL : NULL REMARK 240 R MERGE FOR SHELL (I) : 0.76600 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 240 SOFTWARE USED : PHASER 2.8.3 REMARK 240 STARTING MODEL : 6CL7 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 51.76500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.27500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.27500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 77.64750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.27500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.27500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.88250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.27500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.27500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 77.64750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.27500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.27500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.88250 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 51.76500 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 OD1 ASP A 222 O HOH A 401 2.04 REMARK 500 NZ LYS A 347 O HOH A 402 2.07 REMARK 500 O HOH A 407 O HOH A 501 2.11 REMARK 500 O HOH A 535 O HOH A 536 2.14 REMARK 500 NH1 ARG A 185 O HOH A 403 2.16 REMARK 500 OH TYR A 166 O HOH A 404 2.16 REMARK 500 OE1 GLU A 132 O HOH A 405 2.18 REMARK 500 O HOH A 408 O HOH A 529 2.18 REMARK 500 OD2 ASP A 217 O HOH A 406 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 MET A 259 CA - CB - CG ANGL. DEV. = -10.7 DEGREES REMARK 500 MET A 330 CG - SD - CE ANGL. DEV. = -12.9 DEGREES 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 126 24.91 -141.83 REMARK 500 ASP A 144 -140.16 -174.67 REMARK 500 LYS A 162 136.12 -171.00 REMARK 500 ASP A 202 -172.14 -69.10 REMARK 500 SER A 321 -169.71 -112.98 REMARK 500 ASN A 375 72.37 -112.59 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 545 DISTANCE = 5.81 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-25469 RELATED DB: EMDB REMARK 900 MICROED STRUCTURE OF PROTEINASE K FROM A 360 NM THICK LAMELLA REMARK 900 MEASURED AT 300 KV DBREF 7SWB 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 FORMUL 2 HOH *145(H2 O) HELIX 1 AA1 PRO A 112 SER A 119 1 8 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 GLN A 108 0 SHEET 2 AA1 2 TYR A 128 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 LYS A 199 N LYS A 162 SHEET 3 AA2 7 CYS A 139 ASP A 144 1 N VAL A 140 O GLN A 194 SHEET 4 AA2 7 VAL A 232 LEU A 236 1 O VAL A 233 N TYR A 141 SHEET 5 AA2 7 VAL A 258 ALA A 263 1 O ALA A 261 N LEU A 236 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 GLY A 308 N SER A 288 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 TRP A 317 0 SHEET 2 AA4 2 SER A 321 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 2.14 CISPEP 1 SER A 275 PRO A 276 0 0.29 CRYST1 68.550 68.550 103.530 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 0.014588 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014588 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009659 0.00000