HEADER HYDROLASE 19-NOV-21 7SVY TITLE MICROED STRUCTURE OF PROTEINASE K FROM A 130 NM THICK LAMELLA MEASURED TITLE 2 AT 120 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 7SVY 1 REMARK REVDAT 1 07-SEP-22 7SVY 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. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.9 REMARK 3 NUMBER OF REFLECTIONS : 8789 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 433 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 20.0800 - 3.3200 0.82 2862 144 0.1878 0.2321 REMARK 3 2 3.3200 - 2.6300 0.83 2753 149 0.2547 0.2844 REMARK 3 3 2.6300 - 2.3000 0.84 2741 140 0.3011 0.3208 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) : 0.349 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.875 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.29 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 : 0.006 2068 REMARK 3 ANGLE : 0.790 2810 REMARK 3 CHIRALITY : 0.046 312 REMARK 3 PLANARITY : 0.005 370 REMARK 3 DIHEDRAL : 5.679 307 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 7SVY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1000260225. 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 : 11-DEC-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) : 120 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 49740 REMARK 240 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 240 RESOLUTION RANGE LOW (A) : 20.000 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 82.5 REMARK 240 DATA REDUNDANCY : 5.600 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :2.30 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :2.44 REMARK 240 COMPLETENESS FOR SHELL (%) : 84.0 REMARK 240 DATA REDUNDANCY IN SHELL : NULL REMARK 240 R MERGE FOR SHELL (I) : 1.55100 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 50.25100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.41900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.41900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 75.37650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.41900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.41900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.12550 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.41900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.41900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 75.37650 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.41900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.41900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.12550 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 50.25100 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 O SER A 138 OG1 THR A 193 1.94 REMARK 500 OH TYR A 274 O HOH A 401 2.01 REMARK 500 OG1 THR A 127 O HOH A 402 2.02 REMARK 500 N TYR A 242 O HOH A 403 2.10 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 ARG A 169 CD - NE - CZ ANGL. DEV. = 9.4 DEGREES REMARK 500 ARG A 169 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 169 NE - CZ - NH2 ANGL. DEV. = -5.2 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 ASP A 144 -139.44 -163.29 REMARK 500 SER A 237 47.81 -89.15 REMARK 500 ALA A 271 0.79 -68.76 REMARK 500 SER A 321 -163.84 -108.15 REMARK 500 ASN A 375 69.45 -102.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-25456 RELATED DB: EMDB REMARK 900 MICROED STRUCTURE OF PROTEINASE K FROM A 130 NM THICK LAMELLA REMARK 900 MEASURED AT 120 KV DBREF 7SVY 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 *23(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 LEU A 195 LYS A 199 1 O LYS A 199 N LYS A 162 SHEET 3 AA2 7 SER A 138 ASP A 144 1 N VAL A 142 O PHE A 196 SHEET 4 AA2 7 GLY A 231 LEU A 236 1 O SER A 235 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 260 SHEET 7 AA2 7 LEU A 304 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 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 2.03 CISPEP 1 SER A 275 PRO A 276 0 1.44 CRYST1 66.838 66.838 100.502 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 0.014962 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014962 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009950 0.00000