HEADER HYDROLASE INHIBITOR 16-NOV-15 5FNW TITLE CRYSTAL STRUCTURE AT PH 7.0 OF A POTATO STI-KUNITZ BI-FUNCTIONAL TITLE 2 INHIBITOR OF SERINE AND ASPARTIC PROTEASES IN SPACE GROUP P4322 AND TITLE 3 PH 9.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: POTATO STI-KUNITZ BI-FUNCTIONAL INHIBITOR E3AD_N19D; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: THE SEQUENCE OF THE POTATO STI-KUNITZ BI- FUNCTIONAL COMPND 6 INHIBITOR E3AD_N19D HAS NOT BEEN DEPOSITED AT UNIPROT NOR GENBANK. COMPND 7 MUTANT N19D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SOLANUM TUBEROSUM; SOURCE 3 ORGANISM_COMMON: POTATO; SOURCE 4 ORGANISM_TAXID: 4113; SOURCE 5 VARIANT: ESTIMA; SOURCE 6 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS GS115; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 644223; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPICZALPHAC KEYWDS HYDROLASE, STI-KUNITZ INHIBITOR, ASPARTIC PROTEASES, SERINE KEYWDS 2 PROTEASES, PROTEASE INHIBITOR, BI-FUNCTIONAL PROTEASE INHIBITOR, KEYWDS 3 HYDROLASE INHIBITOR, KUNITZ-TYPE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR Y.GUERRA,E.RUDINO-PINERA REVDAT 3 10-JAN-24 5FNW 1 REMARK REVDAT 2 29-MAR-17 5FNW 1 JRNL REVDAT 1 06-JUL-16 5FNW 0 JRNL AUTH Y.GUERRA,P.A.VALIENTE,T.PONS,C.BERRY,E.RUDINO-PINERA JRNL TITL STRUCTURES OF A BI-FUNCTIONAL KUNITZ-TYPE STI FAMILY JRNL TITL 2 INHIBITOR OF SERINE AND ASPARTIC PROTEASES: COULD THE JRNL TITL 3 ASPARTIC PROTEASE INHIBITION HAVE EVOLVED FROM A CANONICAL JRNL TITL 4 SERINE PROTEASE-BINDING LOOP? JRNL REF J. STRUCT. BIOL. V. 195 259 2016 JRNL REFN ESSN 1095-8657 JRNL PMID 27329566 JRNL DOI 10.1016/J.JSB.2016.06.014 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10961 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 503 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 19.4981 - 3.8817 0.99 2738 130 0.1639 0.2179 REMARK 3 2 3.8817 - 3.0850 1.00 2600 122 0.2294 0.2844 REMARK 3 3 3.0850 - 2.6962 1.00 2560 135 0.2831 0.3360 REMARK 3 4 2.6962 - 2.4502 1.00 2560 116 0.3195 0.3559 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) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 58.19 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 : 0.010 1471 REMARK 3 ANGLE : 1.205 1995 REMARK 3 CHIRALITY : 0.045 227 REMARK 3 PLANARITY : 0.006 259 REMARK 3 DIHEDRAL : 14.139 551 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 5FNW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1290065560. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MICROBEAM REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10963 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 19.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 18.50 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.0100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.28 REMARK 200 R MERGE FOR SHELL (I) : 0.64000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.580 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: PDB ENTRY 3TC2 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTAL WAS CRYSTALLIZED FROM 15% REMARK 280 (W/V) PEG 20000, 0.1 M HEPES PH 7.0, 30 MM GLYCYL-GLYCYL-GLYCINE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 47.12000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 70.68000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 23.56000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 47.12000 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 23.56000 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 70.68000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.1 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -23.56000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLU A 1 REMARK 465 SER A 2 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 ASP A 123 O HOH A 2025 2.07 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 LEU A 71 42.91 -69.37 REMARK 500 SER A 72 154.98 55.66 REMARK 500 THR A 97 -22.93 -140.80 REMARK 500 ASP A 123 -138.73 -109.23 REMARK 500 LYS A 134 -87.86 -89.64 REMARK 500 PRO A 153 108.99 -52.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FNX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURAL AT PH 9.0 OF A POTATO STI- KUNITZ BI-FUNCTIONAL REMARK 900 INHIBITOR OF SERINE AND ASPARTIC PROTEASES REMARK 999 REMARK 999 SEQUENCE REMARK 999 WHEN POTATO STI-KUNITZ BI-FUNCTIONAL INHIBITOR E3AD_N19D REMARK 999 WAS SEQUENCED RESIDUES 19 AND 177 WERE N AND E REMARK 999 RESPECTIVELY. HOWEVER, ELECTRON DENSITY MAPS CLEARLY REMARK 999 SUPPORTS A CHANGE IN POSITIONS 19 AND 177 TO D AND K REMARK 999 RESPECTIVELY DBREF 5FNW A 1 187 PDB 5FNW 5FNW 1 187 SEQRES 1 A 187 GLU SER PRO LEU PRO LYS PRO VAL LEU ASP THR ASN GLY SEQRES 2 A 187 LYS GLU LEU ASN PRO ASP SER SER TYR ARG ILE ILE SER SEQRES 3 A 187 ILE GLY ARG GLY ALA LEU GLY GLY ASP VAL TYR LEU GLY SEQRES 4 A 187 LYS SER PRO ASN SER ASP ALA PRO CYS PRO ASP GLY VAL SEQRES 5 A 187 PHE ARG TYR ASN SER ASP VAL GLY PRO SER GLY THR PRO SEQRES 6 A 187 VAL ARG PHE ILE PRO LEU SER THR ASN ILE PHE GLU ASP SEQRES 7 A 187 GLN LEU LEU ASN ILE GLN PHE ASN ILE PRO THR VAL LYS SEQRES 8 A 187 LEU CYS VAL SER TYR THR ILE TRP LYS VAL GLY ASN LEU SEQRES 9 A 187 ASN ALA TYR PHE ARG THR MET LEU LEU GLU THR GLY GLY SEQRES 10 A 187 THR ILE GLY GLN ALA ASP ASN SER TYR PHE LYS ILE VAL SEQRES 11 A 187 LYS SER SER LYS ILE GLY TYR ASN LEU LEU SER CYS PRO SEQRES 12 A 187 PHE THR SER ILE ILE CYS LEU ARG CYS PRO GLU ASP GLN SEQRES 13 A 187 PHE CYS ALA LYS VAL GLY VAL VAL ILE GLN ASN GLY LYS SEQRES 14 A 187 ARG ARG LEU ALA LEU VAL ASN LYS ASN PRO LEU ASP VAL SEQRES 15 A 187 LEU PHE GLN GLU VAL FORMUL 2 HOH *33(H2 O) HELIX 1 1 ARG A 29 GLY A 33 5 5 HELIX 2 2 LYS A 91 TYR A 96 5 6 HELIX 3 3 CYS A 152 GLN A 156 5 5 SHEET 1 AA 2 TYR A 22 SER A 26 0 SHEET 2 AA 2 VAL A 182 GLU A 186 -1 O LEU A 183 N ILE A 25 SHEET 1 AB 6 VAL A 36 GLY A 39 0 SHEET 2 AB 6 GLY A 51 ARG A 54 -1 O GLY A 51 N GLY A 39 SHEET 3 AB 6 LYS A 169 VAL A 175 -1 O ARG A 170 N ARG A 54 SHEET 4 AB 6 ALA A 159 GLN A 166 -1 O LYS A 160 N VAL A 175 SHEET 5 AB 6 TYR A 137 SER A 141 -1 O LEU A 139 N VAL A 161 SHEET 6 AB 6 PHE A 127 LYS A 131 -1 O LYS A 128 N LEU A 140 SHEET 1 AC 2 VAL A 66 PRO A 70 0 SHEET 2 AC 2 LEU A 81 PHE A 85 -1 O ASN A 82 N ILE A 69 SHEET 1 AD 2 TRP A 99 ASN A 105 0 SHEET 2 AD 2 THR A 110 THR A 115 -1 O THR A 110 N ASN A 105 SSBOND 1 CYS A 48 CYS A 93 1555 1555 2.05 SSBOND 2 CYS A 142 CYS A 158 1555 1555 2.04 SSBOND 3 CYS A 149 CYS A 152 1555 1555 2.05 CISPEP 1 SER A 72 THR A 73 0 -13.22 CRYST1 77.220 77.220 94.240 90.00 90.00 90.00 P 43 2 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 0.012950 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012950 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010611 0.00000