HEADER HYDROLASE 15-FEB-25 9NCC TITLE SERIAL SYNCHROTRON X-RAY DIFFRACTION STRUCTURE OF THE APO FORM OF TITLE 2 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 ENZYME, SERIAL, PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.W.VLAHAKIS,J.A.SUMMERS,S.WAKATSUKI,J.A.RODRIGUEZ REVDAT 2 13-AUG-25 9NCC 1 JRNL REVDAT 1 18-JUN-25 9NCC 0 JRNL AUTH N.W.VLAHAKIS,C.W.FLOWERS,M.LIU,M.P.AGDANOWSKI,S.JOHNSON, JRNL AUTH 2 J.A.SUMMERS,L.M.C.JACOBS,C.KEYSER,P.RUSSELL,S.L.ROSE, JRNL AUTH 3 J.ORLANS,N.ADHAMI,Y.CHEN,M.R.SAWAYA,S.BASU,D.DE SANCTIS, JRNL AUTH 4 Y.CHEN,S.WAKATSUKI,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-SMALL MOLECULE COMPLEXES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 122 80122 2025 JRNL REFN ESSN 1091-6490 JRNL PMID 40720654 JRNL DOI 10.1073/PNAS.2503780122 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20282 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) : 0.198 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1015 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 44.0500 - 3.4400 1.00 2910 154 0.1694 0.2031 REMARK 3 2 3.4400 - 2.7300 1.00 2775 146 0.1844 0.2064 REMARK 3 3 2.7300 - 2.3900 1.00 2743 144 0.2069 0.2491 REMARK 3 4 2.3900 - 2.1700 1.00 2734 144 0.2026 0.2487 REMARK 3 5 2.1700 - 2.0100 1.00 2697 142 0.2338 0.2811 REMARK 3 6 2.0100 - 1.9000 1.00 2717 143 0.2809 0.3298 REMARK 3 7 1.8900 - 1.8000 1.00 2691 142 0.3232 0.3464 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.570 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 : 0.008 1764 REMARK 3 ANGLE : 0.983 2405 REMARK 3 CHIRALITY : 0.067 239 REMARK 3 PLANARITY : 0.011 318 REMARK 3 DIHEDRAL : 5.490 256 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 9NCC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1000293049. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-24 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.072 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI JUNGFRAU 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20289 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 44.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 84.25 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 58.54 REMARK 200 R MERGE FOR SHELL (I) : 2.12700 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 889 MM SODIUM CHLORIDE, 59% METHANOL REMARK 280 IN RESERVOIR, 66% METHANOL IN SITTING DROP, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K 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 21.25000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.75000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.45000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.75000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.25000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.45000 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9220 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: 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 ARG A 93 -152.76 -122.11 REMARK 500 ARG A 93 -151.12 -122.11 REMARK 500 GLN A 128 159.99 179.65 REMARK 500 ASP A 158 4.51 -153.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9NAG RELATED DB: PDB REMARK 900 MICROED STRUCTURE OF THE APO FORM OF PAPAIN REMARK 900 RELATED ID: 9NBN RELATED DB: PDB REMARK 900 SSX STRUCTURE OF PAPAIN SOAKED WITH A MIXTURE OF E-64, E-64C, AND E- REMARK 900 64D DBREF 9NCC 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 *59(H2 O) HELIX 1 AA1 SER A 24 GLY A 43 1 20 HELIX 2 AA2 SER A 49 ASP A 57 1 9 HELIX 3 AA3 TYR A 61 GLY A 65 5 5 HELIX 4 AA4 TYR A 67 TYR A 78 1 12 HELIX 5 AA5 SER A 97 GLY A 101 5 5 HELIX 6 AA6 ASN A 117 GLN A 128 1 12 HELIX 7 AA7 GLY A 138 LEU A 143 1 6 HELIX 8 AA8 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 132 O VAL A 161 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 2.01 SSBOND 2 CYS A 56 CYS A 95 1555 1555 2.06 SSBOND 3 CYS A 153 CYS A 200 1555 1555 2.04 CISPEP 1 GLY A 151 PRO A 152 0 0.20 CRYST1 42.500 48.900 101.500 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 0.023529 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020450 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009852 0.00000 CONECT 179 499 CONECT 441 798 CONECT 499 179 CONECT 798 441 CONECT 1252 1614 CONECT 1614 1252 MASTER 227 0 0 8 10 0 0 6 1714 1 6 17 END