HEADER HYDROLASE 29-JUN-19 6PKP
TITLE MICROED STRUCTURE OF PROTEINASE K FROM A PLATINUM-COATED, POLISHED,
TITLE 2 SINGLE LAMELLA AT 1.91A RESOLUTION (#10)
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 3 18-DEC-19 6PKP 1 REMARK
REVDAT 2 16-OCT-19 6PKP 1 JRNL
REVDAT 1 04-SEP-19 6PKP 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. 1.91 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) : 1.91
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.39
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 90.4
REMARK 3 NUMBER OF REFLECTIONS : 17803
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.199
REMARK 3 R VALUE (WORKING SET) : 0.197
REMARK 3 FREE R VALUE : 0.234
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.500
REMARK 3 FREE R VALUE TEST SET COUNT : 2130
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 29.0387 - 4.7044 0.85 1938 137 0.1481 0.1835
REMARK 3 2 4.7044 - 3.7365 0.88 1985 144 0.1271 0.1482
REMARK 3 3 3.7365 - 3.2649 0.89 2016 146 0.1491 0.2053
REMARK 3 4 3.2649 - 2.9667 0.90 2024 136 0.1819 0.1760
REMARK 3 5 2.9667 - 2.7543 0.91 2071 138 0.2009 0.2636
REMARK 3 6 2.7543 - 2.5920 0.92 2047 142 0.2055 0.2549
REMARK 3 7 2.5920 - 2.4622 0.92 2094 136 0.2286 0.2764
REMARK 3 8 2.4622 - 2.3551 0.92 2107 133 0.2385 0.2807
REMARK 3 9 2.3551 - 2.2645 0.92 2056 160 0.2548 0.2891
REMARK 3 10 2.2645 - 2.1864 0.92 2076 132 0.2475 0.2960
REMARK 3 11 2.1864 - 2.1180 0.92 2071 143 0.2669 0.3096
REMARK 3 12 2.1180 - 2.0575 0.92 2107 150 0.2879 0.3362
REMARK 3 13 2.0575 - 2.0034 0.92 2077 140 0.3018 0.3235
REMARK 3 14 2.0034 - 1.9545 0.91 2032 147 0.3233 0.3996
REMARK 3 15 1.9545 - 1.9101 0.86 1947 146 0.3331 0.3651
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) : 0.290
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.810
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 : 0.011 2070
REMARK 3 ANGLE : 1.132 2814
REMARK 3 CHIRALITY : 0.063 312
REMARK 3 PLANARITY : 0.006 370
REMARK 3 DIHEDRAL : 3.137 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 6PKP 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_1000242613.
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 52.97000
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.75500
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.75500
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 79.45500
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.75500
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.75500
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.48500
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.75500
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.75500
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 79.45500
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.75500
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.75500
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.48500
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 52.97000
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: 10040 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 ND1 HIS A 177 O HOH A 401 2.10
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 -148.65 -171.00
REMARK 500 ASN A 172 -50.58 -123.85
REMARK 500 SER A 256 0.07 -65.97
REMARK 500 ASN A 266 50.98 -106.77
REMARK 500 SER A 321 -164.55 -103.37
REMARK 500 ASN A 375 75.39 -114.95
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: EMD-20362 RELATED DB: EMDB
REMARK 900 MICROED STRUCTURE OF PROTEINASE K FROM A PLATINUM COATED, POLISHED
REMARK 900 SINGLE LAMELLA AT 1.91A RESOLUTION (#10)
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-20363 RELATED DB: EMDB
REMARK 900 RELATED ID: EMD-20364 RELATED DB: EMDB
REMARK 900 RELATED ID: EMD-20365 RELATED DB: EMDB
REMARK 900 RELATED ID: EMD-20366 RELATED DB: EMDB
DBREF 6PKP 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 *91(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 THR A 349 THR A 360 1 12
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 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 VAL A 233 N CYS A 139
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 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 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 2.05
SSBOND 2 CYS A 283 CYS A 354 1555 1555 2.11
CISPEP 1 SER A 275 PRO A 276 0 4.78
CRYST1 67.510 67.510 105.940 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 0.014813 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014813 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009439 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
