HEADER PLANT PROTEIN 08-DEC-22 8HNR TITLE MOLECULAR STRUCTURE OF KUNITZ-TYPE TRYPSIN INHIBITOR FROM SEEDS OF TITLE 2 ALBIZIA PROCERA COMPND MOL_ID: 1; COMPND 2 MOLECULE: KUNITZ-TYPE TRYPSIN INHIBITOR; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALBIZIA PROCERA; SOURCE 3 ORGANISM_TAXID: 384949 KEYWDS TRYPSIN, INHIBITOR, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.MEHMOOD,S.S.THIRUP,A.SAEED,M.RAFIQ,B.KHALIQ,A.AKREM REVDAT 3 06-NOV-24 8HNR 1 REMARK REVDAT 2 18-SEP-24 8HNR 1 JRNL REVDAT 1 01-FEB-23 8HNR 0 JRNL AUTH S.MEHMOOD,S.S.THIRUP,S.AHMED,N.BASHIR,A.SAEED,M.RAFIQ, JRNL AUTH 2 Q.SAEED,M.NAJAM-UL-HAQ,B.KHALIQ,M.IBRAHIM,W.B.ALONAZI, JRNL AUTH 3 A.AKREM JRNL TITL CRYSTAL STRUCTURE OF KUNITZ-TYPE TRYPSIN INHIBITOR: JRNL TITL 2 ENTOMOTOXIC EFFECT OF NATIVE AND ENCAPSULATED PROTEIN JRNL TITL 3 TARGETING GUT TRYPSIN OF TRIBOLIUM CASTANEUM HERBST. JRNL REF COMPUT STRUCT BIOTECHNOL J V. 23 3132 2024 JRNL REFN ESSN 2001-0370 JRNL PMID 39229336 JRNL DOI 10.1016/J.CSBJ.2024.07.023 REMARK 2 REMARK 2 RESOLUTION. 1.42 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 32153 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1608 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 41.3000 - 3.1600 0.99 2902 153 0.1558 0.1747 REMARK 3 2 3.1600 - 2.5100 1.00 2829 149 0.1603 0.1711 REMARK 3 3 2.5100 - 2.1900 1.00 2851 150 0.1524 0.1757 REMARK 3 4 2.1900 - 1.9900 0.99 2797 147 0.1434 0.1543 REMARK 3 5 1.9900 - 1.8500 0.99 2771 146 0.1452 0.1970 REMARK 3 6 1.8500 - 1.7400 0.98 2761 146 0.1525 0.1852 REMARK 3 7 1.7400 - 1.6500 0.98 2757 145 0.1592 0.2087 REMARK 3 8 1.6500 - 1.5800 0.98 2760 146 0.1893 0.2375 REMARK 3 9 1.5800 - 1.5200 0.98 2726 142 0.2326 0.2671 REMARK 3 10 1.5200 - 1.4700 0.97 2720 143 0.2722 0.3087 REMARK 3 11 1.4700 - 1.4200 0.96 2671 141 0.2902 0.3245 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.430 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 1369 REMARK 3 ANGLE : 0.895 1853 REMARK 3 CHIRALITY : 0.072 197 REMARK 3 PLANARITY : 0.009 245 REMARK 3 DIHEDRAL : 7.324 189 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 8HNR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1300034007. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAY-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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 : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9724 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 1.12 REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32197 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 41.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.1700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 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 <I/SIGMA(I)> 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES MONOHYDRATE (PH: 6.0), PEG REMARK 280 400 (25%), PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 60.31350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.48350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 60.31350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.48350 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 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 205 LIES ON A SPECIAL POSITION. 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 GLY A 133A REMARK 465 ASN A 133B REMARK 465 SER A 133C REMARK 465 ASP A 133D REMARK 465 ASP A 133E REMARK 465 GLU A 133F 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 HZ3 LYS A 26 O HOH A 201 1.13 REMARK 500 HZ1 LYS A 26 O HOH A 201 1.56 REMARK 500 O HOH A 355 O HOH A 365 1.83 REMARK 500 O HOH A 282 O HOH A 344 1.89 REMARK 500 NZ LYS A 26 O HOH A 201 1.92 REMARK 500 NZ LYS A 26 O HOH A 201 1.94 REMARK 500 O HOH A 210 O HOH A 268 2.08 REMARK 500 O HOH A 281 O HOH A 353 2.16 REMARK 500 O SER A 165 O HOH A 202 2.18 REMARK 500 O HOH A 351 O HOH A 361 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 364 O HOH A 366 4455 2.19 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 LYS A 26 54.45 -141.39 REMARK 500 LYS A 26 57.93 -140.02 REMARK 500 LEU A 93 74.51 -104.00 REMARK 500 LEU A 93 74.51 -103.29 REMARK 500 ARG A 124 -120.87 50.30 REMARK 500 ASP A 126 -137.65 -141.24 REMARK 500 LYS A 153 71.66 -153.79 REMARK 500 REMARK 500 REMARK: NULL DBREF 8HNR A 1 166 PDB 8HNR 8HNR 1 166 SEQRES 1 A 172 LYS GLU LEU LEU ASP ALA ASP GLY ASP ILE LEU ARG ASN SEQRES 2 A 172 GLY GLY THR TYR TYR ILE VAL PRO ALA PHE ARG GLY LYS SEQRES 3 A 172 GLY GLY GLY LEU THR LEU ALA LYS ILE GLY ASP GLU SER SEQRES 4 A 172 CYS PRO LEU ASN VAL VAL GLN ALA GLU SER GLU THR LYS SEQRES 5 A 172 ARG GLY LEU PRO ALA MET ILE TRP THR PRO PRO ARG ILE SEQRES 6 A 172 ALA ILE LEU THR PRO ALA PHE TYR LEU ASN ILE GLU PHE SEQRES 7 A 172 GLN PRO ARG ASP PRO PRO ALA CYS LEU GLN LYS TYR GLY SEQRES 8 A 172 ARG LEU SER TRP LYS VAL GLU GLY GLU SER GLN GLU VAL SEQRES 9 A 172 LYS ILE ALA PRO ALA SER GLU GLN HIS LEU PHE GLY SER SEQRES 10 A 172 PHE LYS ILE GLU PRO TYR ARG ASP ASP TYR LYS LEU VAL SEQRES 11 A 172 TYR CYS GLU GLY ASN SER ASP ASP GLU SER CYS LYS ASP SEQRES 12 A 172 LEU GLY ILE SER ILE ASP ASP GLU ASN ASN ARG LEU LEU SEQRES 13 A 172 VAL VAL LYS ASP GLY ASP PRO LEU ALA VAL ARG PHE GLU SEQRES 14 A 172 LYS SER LYS FORMUL 2 HOH *170(H2 O) HELIX 1 AA1 PRO A 84 GLN A 88 5 5 HELIX 2 AA2 PRO A 108 GLN A 112 5 5 SHEET 1 AA1 6 VAL A 104 ILE A 106 0 SHEET 2 AA1 6 LEU A 93 VAL A 97 -1 N LYS A 96 O LYS A 105 SHEET 3 AA1 6 ASN A 75 PHE A 78 -1 N ILE A 76 O TRP A 95 SHEET 4 AA1 6 ALA A 57 TRP A 60 -1 N MET A 58 O GLU A 77 SHEET 5 AA1 6 GLY A 15 PRO A 21 -1 N TYR A 17 O ALA A 57 SHEET 6 AA1 6 VAL A 160 LYS A 164 -1 O GLU A 163 N TYR A 18 SHEET 1 AA2 6 LEU A 30 ALA A 33 0 SHEET 2 AA2 6 ASN A 43 GLN A 46 -1 O VAL A 45 N THR A 31 SHEET 3 AA2 6 ARG A 148 VAL A 152 -1 O LEU A 150 N VAL A 44 SHEET 4 AA2 6 LYS A 136 ILE A 142 -1 N GLY A 139 O VAL A 151 SHEET 5 AA2 6 ASP A 126 TYR A 131 -1 N TYR A 131 O LYS A 136 SHEET 6 AA2 6 PHE A 118 TYR A 123 -1 N TYR A 123 O ASP A 126 SSBOND 1 CYS A 40 CYS A 86 1555 1555 2.05 SSBOND 2 CYS A 132 CYS A 135 1555 1555 2.05 CRYST1 120.627 34.967 42.703 90.00 104.74 90.00 C 1 2 1 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 0.008290 0.000000 0.002181 0.00000 SCALE2 0.000000 0.028598 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024214 0.00000