HEADER HYDROLASE INHIBITOR 19-NOV-12 3ZC8 TITLE CRYSTAL STRUCTURE OF MURRAYA KOENIGII MIRACULIN-LIKE PROTEIN AT 2.2 A TITLE 2 RESOLUTION AT PH 7.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPSIN INHIBITOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MIRACULIN-LIKE PROTEIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MURRAYA KOENIGII; SOURCE 3 ORGANISM_COMMON: CURRY LEAF; SOURCE 4 ORGANISM_TAXID: 311449; SOURCE 5 ORGAN: SEEDS KEYWDS HYDROLASE INHIBITOR, BETA-TREFOIL FOLD, KUNITZ SUPER-FAMILY EXPDTA X-RAY DIFFRACTION AUTHOR P.SELVAKUMAR,N.SHARMA,P.P.S.TOMAR,P.KUMAR,A.K.SHARMA REVDAT 3 20-DEC-23 3ZC8 1 REMARK REVDAT 2 23-APR-14 3ZC8 1 JRNL REVDAT 1 04-DEC-13 3ZC8 0 JRNL AUTH P.SELVAKUMAR,N.SHARMA,P.P.S.TOMAR,P.KUMAR,A.K.SHARMA JRNL TITL STRUCTURAL INSIGHTS INTO THE AGGREGATION BEHAVIOR OF MURRAYA JRNL TITL 2 KOENIGII MIRACULIN-LIKE PROTEIN BELOW PH 7.5. JRNL REF PROTEINS V. 82 830 2014 JRNL REFN ISSN 0887-3585 JRNL PMID 24265134 JRNL DOI 10.1002/PROT.24461 REMARK 2 REMARK 2 RESOLUTION. 2.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 8240 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 409 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.24 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.30 REMARK 3 REFLECTION IN BIN (WORKING SET) : 585 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE SET COUNT : 28 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1409 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.54000 REMARK 3 B22 (A**2) : 0.63000 REMARK 3 B33 (A**2) : -0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.59000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.354 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.234 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.161 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.374 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.922 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.872 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1442 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1965 ; 1.174 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 181 ; 6.427 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 68 ;33.916 ;23.529 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 224 ;14.879 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;16.967 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 219 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1114 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 727 ; 0.840 ; 1.633 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 907 ; 1.558 ; 2.447 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 715 ; 0.582 ; 1.653 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. RESIDUES 183-190 ARE DISORDERED REMARK 4 REMARK 4 3ZC8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1290054405. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8649 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.240 REMARK 200 RESOLUTION RANGE LOW (A) : 50.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.27000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3IIR REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4M AMMONIUM ACETATE, 0.1M BIS-TRIS REMARK 280 PROPANE, PH 7.0 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 50.75500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.84500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.75500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.84500 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 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 183 REMARK 465 GLY A 184 REMARK 465 SER A 185 REMARK 465 ALA A 186 REMARK 465 SER A 187 REMARK 465 CYS A 188 REMARK 465 VAL A 189 REMARK 465 SER A 190 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 GLU A 39 -3.97 -147.12 REMARK 500 LEU A 40 -75.41 -127.71 REMARK 500 SER A 80 49.50 -85.47 REMARK 500 CYS A 140 68.23 -154.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZC9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURRAYA KOENIGII MIRACULIN-LIKE PROTEIN AT 2.2 REMARK 900 A RESOLUTION AT PH 4.6 DBREF 3ZC8 A 1 190 UNP D2YW43 D2YW43_9ROSI 1 190 SEQRES 1 A 190 ASP PRO LEU LEU ASP ILE ASN GLY ASN VAL VAL GLU ALA SEQRES 2 A 190 SER ARG ASP TYR TYR LEU VAL SER VAL ILE GLY GLY ALA SEQRES 3 A 190 GLY GLY GLY GLY LEU THR LEU TYR ARG GLY ARG ASN GLU SEQRES 4 A 190 LEU CYS PRO LEU ASP VAL ILE GLN LEU SER PRO ASP LEU SEQRES 5 A 190 HIS LYS GLY THR ARG LEU ARG PHE ALA ALA TYR ASN ASN SEQRES 6 A 190 THR SER ILE ILE HIS GLU ALA VAL ASP LEU ASN VAL LYS SEQRES 7 A 190 PHE SER THR GLU THR SER CYS ASN GLU PRO THR VAL TRP SEQRES 8 A 190 ARG VAL ASP ASN TYR ASP PRO SER ARG GLY LYS TRP PHE SEQRES 9 A 190 ILE THR THR GLY GLY VAL GLU GLY ASN PRO GLY ALA GLN SEQRES 10 A 190 THR LEU LYS ASN TRP PHE LYS LEU GLU ARG VAL GLY THR SEQRES 11 A 190 ASP GLN GLY THR TYR GLU ILE VAL HIS CYS PRO SER VAL SEQRES 12 A 190 CYS LYS SER CYS VAL PHE LEU CYS ASN ASP VAL GLY VAL SEQRES 13 A 190 SER TYR ASP TYR ARG ARG ARG LEU ALA LEU THR ALA GLY SEQRES 14 A 190 ASN GLU ARG VAL PHE GLY VAL VAL ILE VAL PRO ALA ASN SEQRES 15 A 190 GLU GLY SER ALA SER CYS VAL SER FORMUL 2 HOH *76(H2 O) HELIX 1 1 GLY A 115 TRP A 122 5 8 HELIX 2 2 TYR A 158 ARG A 161 5 4 SHEET 1 AA 2 TYR A 17 ILE A 23 0 SHEET 2 AA 2 GLY A 175 PRO A 180 -1 O GLY A 175 N VAL A 22 SHEET 1 AB 2 LEU A 31 TYR A 34 0 SHEET 2 AB 2 ASP A 44 GLN A 47 -1 O ASP A 44 N TYR A 34 SHEET 1 AC 2 LEU A 58 ALA A 62 0 SHEET 2 AC 2 LEU A 75 PHE A 79 -1 O ASN A 76 N ALA A 61 SHEET 1 AD 2 VAL A 90 VAL A 93 0 SHEET 2 AD 2 ILE A 105 GLY A 109 -1 O THR A 106 N ARG A 92 SHEET 1 AE 4 LYS A 124 ARG A 127 0 SHEET 2 AE 4 TYR A 135 HIS A 139 -1 O GLU A 136 N GLU A 126 SHEET 3 AE 4 ASN A 152 VAL A 156 -1 O ASN A 152 N HIS A 139 SHEET 4 AE 4 LEU A 164 THR A 167 -1 O ALA A 165 N GLY A 155 SSBOND 1 CYS A 41 CYS A 85 1555 1555 2.03 SSBOND 2 CYS A 140 CYS A 151 1555 1555 2.04 SSBOND 3 CYS A 144 CYS A 147 1555 1555 2.04 CISPEP 1 ASN A 38 GLU A 39 0 0.77 CISPEP 2 CYS A 41 PRO A 42 0 -0.77 CRYST1 101.510 45.690 38.780 90.00 95.02 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 0.009851 0.000000 0.000865 0.00000 SCALE2 0.000000 0.021887 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025886 0.00000