HEADER HYDROLASE 12-FEB-25 9NAG TITLE MICROED STRUCTURE OF THE APO-FORM OF PAPAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAPAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PAPAYA PROTEINASE I,PPI; COMPND 5 EC: 3.4.22.2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CARICA PAPAYA; SOURCE 3 ORGANISM_COMMON: PAPAYA; SOURCE 4 ORGANISM_TAXID: 3649 KEYWDS INHIBITOR, COMPLEX, MICROED, PROTEASE, HYDROLASE EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR N.VLAHAKIS,J.A.RODRIGUEZ REVDAT 1 26-MAR-25 9NAG 0 JRNL AUTH N.W.VLAHAKIS,C.W.FLOWERS,M.LIU,M.AGDANOWSKI,S.JOHNSON, JRNL AUTH 2 J.A.SUMMERS,C.KEYSER,P.RUSSELL,S.ROSE,J.ORLANS,N.ADHAMI, JRNL AUTH 3 Y.CHEN,M.R.SAWAYA,S.BASU,D.DE SANCTIS,S.WAKATSUKI, JRNL AUTH 4 H.M.NELSON,J.A.LOO,Y.TANG,J.A.RODRIGUEZ JRNL TITL COMBINING MICROED AND NATIVE MASS SPECTROMETRY FOR JRNL TITL 2 STRUCTURAL DISCOVERY OF ENZYME-BIOSYNTHETIC INHIBITOR JRNL TITL 3 COMPLEXES. JRNL REF BIORXIV 2025 JRNL REFN ISSN 2692-8205 JRNL PMID 40060639 JRNL DOI 10.1101/2025.02.20.638743 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 6898 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 690 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 50.0800 - 4.2800 0.87 1263 141 0.1619 0.1764 REMARK 3 2 4.2700 - 3.3900 0.90 1242 137 0.1681 0.2181 REMARK 3 3 3.3900 - 2.9600 0.92 1238 138 0.2263 0.2669 REMARK 3 4 2.9600 - 2.6900 0.93 1239 138 0.2753 0.3234 REMARK 3 5 2.6900 - 2.5000 0.92 1226 136 0.2937 0.3280 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.510 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 : 0.007 1774 REMARK 3 ANGLE : 0.999 2421 REMARK 3 CHIRALITY : 0.063 239 REMARK 3 PLANARITY : 0.009 321 REMARK 3 DIHEDRAL : 5.156 259 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 9NAG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1000292886. 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 : TFS TALOS F200C REMARK 240 DETECTOR TYPE : DIRECT ELECTRON APOLLO (4K X REMARK 240 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 : XSCALE 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: MOLECULAR REPLACEMENT REMARK 240 SOFTWARE USED : PHASER REMARK 240 STARTING MODEL : NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 20.99500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.07500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.54500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.07500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.99500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.54500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 139 CD CE NZ 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 TYR A 78 -69.49 -121.45 REMARK 500 ASP A 158 8.05 -153.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9N9D RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH A LIGAND REMARK 900 RELATED ID: 9NAE RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH A LIGAND DBREF 9NAG A 1 212 UNP P00784 PAPA1_CARPA 134 345 SEQRES 1 A 212 ILE PRO GLU TYR VAL ASP TRP ARG GLN LYS GLY ALA VAL SEQRES 2 A 212 THR PRO VAL LYS ASN GLN GLY SER CYS GLY SER CYS TRP SEQRES 3 A 212 ALA PHE SER ALA VAL VAL THR ILE GLU GLY ILE ILE LYS SEQRES 4 A 212 ILE ARG THR GLY ASN LEU ASN GLU TYR SER GLU GLN GLU SEQRES 5 A 212 LEU LEU ASP CYS ASP ARG ARG SER TYR GLY CYS ASN GLY SEQRES 6 A 212 GLY TYR PRO TRP SER ALA LEU GLN LEU VAL ALA GLN TYR SEQRES 7 A 212 GLY ILE HIS TYR ARG ASN THR TYR PRO TYR GLU GLY VAL SEQRES 8 A 212 GLN ARG TYR CYS ARG SER ARG GLU LYS GLY PRO TYR ALA SEQRES 9 A 212 ALA LYS THR ASP GLY VAL ARG GLN VAL GLN PRO TYR ASN SEQRES 10 A 212 GLU GLY ALA LEU LEU TYR SER ILE ALA ASN GLN PRO VAL SEQRES 11 A 212 SER VAL VAL LEU GLU ALA ALA GLY LYS ASP PHE GLN LEU SEQRES 12 A 212 TYR ARG GLY GLY ILE PHE VAL GLY PRO CYS GLY ASN LYS SEQRES 13 A 212 VAL ASP HIS ALA VAL ALA ALA VAL GLY TYR GLY PRO ASN SEQRES 14 A 212 TYR ILE LEU ILE LYS ASN SER TRP GLY THR GLY TRP GLY SEQRES 15 A 212 GLU ASN GLY TYR ILE ARG ILE LYS ARG GLY THR GLY ASN SEQRES 16 A 212 SER TYR GLY VAL CYS GLY LEU TYR THR SER SER PHE TYR SEQRES 17 A 212 PRO VAL LYS ASN FORMUL 2 HOH *13(H2 O) HELIX 1 AA1 ARG A 8 GLY A 11 5 4 HELIX 2 AA2 SER A 24 GLY A 43 1 20 HELIX 3 AA3 SER A 49 ASP A 57 1 9 HELIX 4 AA4 TYR A 61 GLY A 65 5 5 HELIX 5 AA5 TYR A 67 TYR A 78 1 12 HELIX 6 AA6 SER A 97 GLY A 101 5 5 HELIX 7 AA7 ASN A 117 GLN A 128 1 12 HELIX 8 AA8 GLY A 138 LEU A 143 1 6 HELIX 9 AA9 GLY A 198 LEU A 202 5 5 SHEET 1 AA1 3 VAL A 5 ASP A 6 0 SHEET 2 AA1 3 HIS A 159 GLY A 167 -1 O TYR A 166 N VAL A 5 SHEET 3 AA1 3 VAL A 130 LEU A 134 -1 N VAL A 130 O ALA A 163 SHEET 1 AA2 5 VAL A 5 ASP A 6 0 SHEET 2 AA2 5 HIS A 159 GLY A 167 -1 O TYR A 166 N VAL A 5 SHEET 3 AA2 5 TYR A 170 LYS A 174 -1 O LYS A 174 N ALA A 162 SHEET 4 AA2 5 TYR A 186 LYS A 190 -1 O ILE A 187 N ILE A 173 SHEET 5 AA2 5 ILE A 148 PHE A 149 1 N PHE A 149 O ARG A 188 SHEET 1 AA3 2 GLY A 109 GLN A 112 0 SHEET 2 AA3 2 PHE A 207 VAL A 210 -1 O VAL A 210 N GLY A 109 SSBOND 1 CYS A 22 CYS A 63 1555 1555 2.05 SSBOND 2 CYS A 56 CYS A 95 1555 1555 2.05 SSBOND 3 CYS A 153 CYS A 200 1555 1555 2.06 CISPEP 1 GLY A 151 PRO A 152 0 3.86 CRYST1 41.990 49.090 100.150 90.00 90.00 90.00 P 21 21 21 4 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 0.023815 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020371 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009985 0.00000 TER 1721 ASN A 212 HETATM 1722 O HOH A 301 21.834 16.084 23.056 1.00 7.93 O HETATM 1723 O HOH A 302 20.257 17.511 8.221 1.00 25.57 O HETATM 1724 O HOH A 303 12.917 13.124 9.841 1.00 0.00 O HETATM 1725 O HOH A 304 8.938 3.950 23.301 1.00 10.92 O HETATM 1726 O HOH A 305 -2.310 -0.623 -2.374 1.00 13.85 O HETATM 1727 O HOH A 306 17.245 20.129 11.330 1.00 19.64 O HETATM 1728 O HOH A 307 16.975 -5.207 29.995 1.00 10.29 O HETATM 1729 O HOH A 308 17.559 6.196 26.400 1.00 11.55 O HETATM 1730 O HOH A 309 -0.097 7.826 2.962 1.00 11.92 O HETATM 1731 O HOH A 310 11.635 15.822 2.875 1.00 6.98 O HETATM 1732 O HOH A 311 2.066 4.105 21.378 1.00 9.75 O HETATM 1733 O HOH A 312 4.516 17.184 14.673 1.00 5.70 O HETATM 1734 O HOH A 313 -20.280 -5.225 -1.336 1.00 8.32 O CONECT 173 504 CONECT 435 805 CONECT 504 173 CONECT 805 435 CONECT 1268 1622 CONECT 1622 1268 MASTER 198 0 0 9 10 0 0 6 1665 1 6 17 END