HEADER HYDROLASE 16-FEB-21 7NJJ TITLE PROTEINASE K GROWN INSIDE HARE SERIAL CRYSTALLOGRAPHY CHIP 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: TRITIRACHIUM ALBUM; SOURCE 4 ORGANISM_TAXID: 37998 KEYWDS SERIAL CRYSTALLOGRAPHY, PROTEINASE K, VAPOUR DIFFUSION, SILICON CHIP, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.NORTON-BAKER,P.MEHRABI,J.BOGER,R.SCHONHERR,D.VON STETTEN, AUTHOR 2 H.SCHIKORA,R.W.MARTIN,R.J.D.MILLER,L.REDECKE,E.C.SCHULZ REVDAT 2 31-JAN-24 7NJJ 1 REMARK REVDAT 1 16-JUN-21 7NJJ 0 JRNL AUTH B.NORTON-BAKER,P.MEHRABI,J.BOGER,R.SCHONHERR,D.VON STETTEN, JRNL AUTH 2 H.SCHIKORA,A.O.KWOK,R.W.MARTIN,R.J.D.MILLER,L.REDECKE, JRNL AUTH 3 E.C.SCHULZ JRNL TITL A SIMPLE VAPOR-DIFFUSION METHOD ENABLES PROTEIN JRNL TITL 2 CRYSTALLIZATION INSIDE THE HARE SERIAL CRYSTALLOGRAPHY CHIP. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 77 820 2021 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 34076595 JRNL DOI 10.1107/S2059798321003855 REMARK 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 31835 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1568 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 57.9500 - 3.6700 1.00 2984 146 0.1583 0.1621 REMARK 3 2 3.6700 - 2.9100 1.00 2798 157 0.1639 0.1665 REMARK 3 3 2.9100 - 2.5400 1.00 2765 141 0.1825 0.2293 REMARK 3 4 2.5400 - 2.3100 1.00 2761 137 0.1847 0.2181 REMARK 3 5 2.3100 - 2.1500 1.00 2734 134 0.1748 0.1914 REMARK 3 6 2.1500 - 2.0200 1.00 2715 138 0.1703 0.2318 REMARK 3 7 2.0200 - 1.9200 1.00 2725 154 0.1830 0.2126 REMARK 3 8 1.9200 - 1.8300 1.00 2702 145 0.1897 0.2475 REMARK 3 9 1.8300 - 1.7600 1.00 2702 140 0.2011 0.2267 REMARK 3 10 1.7600 - 1.7000 1.00 2700 149 0.2108 0.2528 REMARK 3 11 1.7000 - 1.6500 0.99 2681 127 0.2561 0.2904 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) : 0.166 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.917 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.29 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 2073 REMARK 3 ANGLE : 0.764 2816 REMARK 3 CHIRALITY : 0.053 312 REMARK 3 PLANARITY : 0.005 372 REMARK 3 DIHEDRAL : 12.997 717 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 7NJJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1292114124. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31851 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 68.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 72.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6J43 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 M NANO3, 0.1 M SODIUM CITRATE PH REMARK 280 6.5, VAPOR DIFFUSION, TEMPERATURE 293K 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 54.32500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.25000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.25000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 81.48750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.25000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.25000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.16250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.25000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.25000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 81.48750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.25000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.25000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.16250 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 54.32500 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: 180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 493 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 597 LIES ON A SPECIAL POSITION. 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 HOH A 405 O HOH A 556 2.16 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 39 -143.99 -165.85 REMARK 500 ASP A 207 62.53 61.42 REMARK 500 ASN A 270 76.86 -111.28 REMARK 500 REMARK 500 REMARK: NULL DBREF 7NJJ A 1 279 UNP P06873 PRTK_PARAQ 106 384 SEQADV 7NJJ ASP A 207 UNP P06873 SER 312 CONFLICT 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 ASP 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 NO3 A 301 4 HETNAM NO3 NITRATE ION FORMUL 2 NO3 N O3 1- FORMUL 3 HOH *209(H2 O) HELIX 1 AA1 PRO A 7 SER A 14 1 8 HELIX 2 AA2 HIS A 46 GLU A 50 5 5 HELIX 3 AA3 GLY A 68 SER A 79 1 12 HELIX 4 AA4 GLN A 103 LYS A 118 1 16 HELIX 5 AA5 ASN A 119 ARG A 121 5 3 HELIX 6 AA6 SER A 138 SER A 151 1 14 HELIX 7 AA7 ASP A 165 ARG A 167 5 3 HELIX 8 AA8 GLY A 222 LEU A 240 1 19 HELIX 9 AA9 SER A 247 THR A 255 1 9 SHEET 1 AA1 2 ALA A 2 GLN A 3 0 SHEET 2 AA1 2 TYR A 23 TYR A 24 -1 O TYR A 23 N GLN A 3 SHEET 1 AA2 7 ALA A 53 THR A 58 0 SHEET 2 AA2 7 GLN A 89 LYS A 94 1 O GLY A 92 N VAL A 56 SHEET 3 AA2 7 SER A 33 ASP A 39 1 N VAL A 37 O PHE A 91 SHEET 4 AA2 7 GLY A 126 LEU A 131 1 O VAL A 128 N TYR A 36 SHEET 5 AA2 7 MET A 154 ALA A 158 1 O MET A 154 N ALA A 129 SHEET 6 AA2 7 CYS A 178 SER A 183 1 O CYS A 178 N VAL A 157 SHEET 7 AA2 7 ILE A 201 PRO A 204 1 O ILE A 201 N GLY A 181 SHEET 1 AA3 2 GLY A 135 GLY A 136 0 SHEET 2 AA3 2 TYR A 169 SER A 170 -1 O SER A 170 N GLY A 135 SHEET 1 AA4 2 ILE A 208 TRP A 212 0 SHEET 2 AA4 2 SER A 216 ILE A 220 -1 O ILE A 220 N ILE A 208 SHEET 1 AA5 2 ASN A 257 LYS A 258 0 SHEET 2 AA5 2 LEU A 271 LEU A 272 -1 O LEU A 272 N ASN A 257 SSBOND 1 CYS A 34 CYS A 123 1555 1555 2.02 SSBOND 2 CYS A 178 CYS A 249 1555 1555 2.03 CISPEP 1 SER A 170 PRO A 171 0 1.26 CRYST1 68.500 68.500 108.650 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 0.014599 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014599 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009204 0.00000