HEADER HYDROLASE 29-JUN-19 6PKS TITLE MICROED STRUCTURE OF PROTEINASE K FROM LOW-DOSE MERGED LAMELLAE THAT TITLE 2 WERE NOT PRE-COATED WITH PLATINUM 2.16A RESOLUTION (LD) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEINASE K; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 106-384; COMPND 5 SYNONYM: ENDOPEPTIDASE K, TRITIRACHIUM ALKALINE PROTEINASE; COMPND 6 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 HYDROLASE EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR M.W.MARTYNOWYCZ,W.ZHAO,J.HATTNE,G.J.JENSEN,T.GONEN REVDAT 4 09-OCT-24 6PKS 1 REMARK REVDAT 3 18-DEC-19 6PKS 1 REMARK REVDAT 2 16-OCT-19 6PKS 1 JRNL REVDAT 1 04-SEP-19 6PKS 0 JRNL AUTH M.W.MARTYNOWYCZ,W.ZHAO,J.HATTNE,G.J.JENSEN,T.GONEN JRNL TITL QUALITATIVE ANALYSES OF POLISHING AND PRECOATING FIB MILLED JRNL TITL 2 CRYSTALS FOR MICROED. JRNL REF STRUCTURE V. 27 1594 2019 JRNL REFN ISSN 0969-2126 JRNL PMID 31422911 JRNL DOI 10.1016/J.STR.2019.07.004 REMARK 2 REMARK 2 RESOLUTION. 2.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 13527 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.470 REMARK 3 FREE R VALUE TEST SET COUNT : 1589 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 43.4700 - 4.8023 0.98 2074 144 0.1870 0.2098 REMARK 3 2 4.8023 - 3.8125 0.99 2100 151 0.1629 0.1823 REMARK 3 3 3.8125 - 3.3307 0.99 2113 151 0.1955 0.2489 REMARK 3 4 3.3307 - 3.0263 0.99 2100 143 0.2291 0.2249 REMARK 3 5 3.0263 - 2.8094 0.99 2095 139 0.2663 0.3103 REMARK 3 6 2.8094 - 2.6438 0.99 2119 144 0.2611 0.3043 REMARK 3 7 2.6438 - 2.5114 0.99 2092 133 0.2758 0.2975 REMARK 3 8 2.5114 - 2.4021 0.99 2077 163 0.2941 0.2987 REMARK 3 9 2.4021 - 2.3096 0.99 2145 137 0.3093 0.3530 REMARK 3 10 2.3096 - 2.2299 0.98 2050 152 0.3375 0.3258 REMARK 3 11 2.2299 - 2.1602 0.95 2007 132 0.3567 0.4223 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.580 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 : 0.002 2070 REMARK 3 ANGLE : 0.537 2814 REMARK 3 CHIRALITY : 0.040 312 REMARK 3 PLANARITY : 0.003 370 REMARK 3 DIHEDRAL : 3.146 1208 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 6PKS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000242625. 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 TALOS ARCTICA REMARK 240 DETECTOR TYPE : FEI CETA (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 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 52.68500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.73500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.73500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 79.02750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.73500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.73500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.34250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.73500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.73500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 79.02750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.73500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.73500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.34250 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 52.68500 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: 10140 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: 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 OH TYR A 356 O HOH A 401 2.08 REMARK 500 OG SER A 122 O HOH A 402 2.17 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 -149.61 -159.07 REMARK 500 LYS A 191 3.34 -66.85 REMARK 500 ASP A 202 -177.12 -66.53 REMARK 500 ASN A 266 40.57 -102.65 REMARK 500 ASN A 375 67.10 -117.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-20365 RELATED DB: EMDB REMARK 900 MICROED STRUCTURE OF PROTEINASE K FROM LOW-DOSE MERGED, LAMELLAE REMARK 900 THAT WERE NOT PRE-COATED WITH PLATINUM 2.16A RESOLUTION (LD) REMARK 900 RELATED ID: EMD-20356 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-20357 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-20358 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-20359 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-20360 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-20361 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-20362 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-20363 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-20364 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-20366 RELATED DB: EMDB DBREF 6PKS 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 *55(H2 O) HELIX 1 AA1 PRO A 112 SER A 119 1 8 HELIX 2 AA2 GLY A 173 SER A 184 1 12 HELIX 3 AA3 GLN A 208 LYS A 223 1 16 HELIX 4 AA4 ASN A 224 ARG A 226 5 3 HELIX 5 AA5 SER A 243 SER A 256 1 14 HELIX 6 AA6 ASP A 270 ARG A 272 5 3 HELIX 7 AA7 GLY A 327 LEU A 345 1 19 HELIX 8 AA8 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 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 VAL A 258 ALA A 263 1 O MET A 259 N ALA A 234 SHEET 6 AA2 7 CYS A 283 SER A 288 1 O VAL A 285 N VAL A 262 SHEET 7 AA2 7 ILE A 306 PRO A 309 1 O GLY A 308 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 0.96 CRYST1 67.470 67.470 105.370 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 0.014821 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014821 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009490 0.00000