HEADER PLANT PROTEIN 04-JUL-23 8JZ0 TITLE CRYSTAL STRUCTURE OF A SINGLE-CHAIN MONELLIN MUTANT C41A COMPND MOL_ID: 1; COMPND 2 MOLECULE: MONELLIN CHAIN B,MONELLIN CHAIN A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MONELLIN CHAIN II,MONELLIN CHAIN I; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DIOSCOREOPHYLLUM CUMMINSII; SOURCE 3 ORGANISM_COMMON: SERENDIPITY BERRY; SOURCE 4 ORGANISM_TAXID: 3457; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SWEET PROTEIN, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.YASUI,K.OHNUMA,A.YAMASHITA REVDAT 2 01-NOV-23 8JZ0 1 JRNL REVDAT 1 11-OCT-23 8JZ0 0 JRNL AUTH K.OHNUMA,A.YAMASHITA,N.YASUI JRNL TITL INVESTIGATING THE EFFECT OF SUBSTITUTING A SINGLE CYSTEINE JRNL TITL 2 RESIDUE ON THE THERMAL STABILITY OF AN ENGINEERED SWEET JRNL TITL 3 PROTEIN, SINGLE-CHAIN MONELLIN. JRNL REF PROTEIN J. V. 42 698 2023 JRNL REFN ISSN 1572-3887 JRNL PMID 37737932 JRNL DOI 10.1007/S10930-023-10154-0 REMARK 2 REMARK 2 RESOLUTION. 1.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.980 REMARK 3 COMPLETENESS FOR RANGE (%) : 78.7 REMARK 3 NUMBER OF REFLECTIONS : 84196 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 4263 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 35.6600 - 3.8172 0.83 2817 154 0.1863 0.1921 REMARK 3 2 3.8172 - 3.0303 0.92 3109 155 0.1778 0.1933 REMARK 3 3 3.0303 - 2.6474 0.94 3096 219 0.1937 0.2328 REMARK 3 4 2.6474 - 2.4054 0.93 3186 162 0.2031 0.2258 REMARK 3 5 2.4054 - 2.2330 0.92 3080 175 0.1993 0.2504 REMARK 3 6 2.2330 - 2.1014 0.93 3145 173 0.1962 0.2167 REMARK 3 7 2.1014 - 1.9961 0.92 3143 153 0.2112 0.2393 REMARK 3 8 1.9961 - 1.9093 0.92 3155 163 0.2160 0.2473 REMARK 3 9 1.9093 - 1.8358 0.92 3123 157 0.2248 0.2356 REMARK 3 10 1.8358 - 1.7724 0.91 3083 151 0.2420 0.3043 REMARK 3 11 1.7724 - 1.7170 0.92 3132 149 0.2411 0.2508 REMARK 3 12 1.7170 - 1.6679 0.92 3114 145 0.2348 0.2578 REMARK 3 13 1.6679 - 1.6240 0.92 3154 170 0.2377 0.2692 REMARK 3 14 1.6240 - 1.5844 0.91 3053 137 0.2623 0.3156 REMARK 3 15 1.5844 - 1.5484 0.91 3112 194 0.2453 0.3029 REMARK 3 16 1.5484 - 1.5154 0.91 3039 185 0.2493 0.2995 REMARK 3 17 1.5154 - 1.4851 0.90 3054 173 0.2630 0.3354 REMARK 3 18 1.4851 - 1.4571 0.91 3081 161 0.2827 0.3325 REMARK 3 19 1.4571 - 1.4311 0.90 3079 138 0.2825 0.3451 REMARK 3 20 1.4311 - 1.4068 0.90 3007 175 0.2830 0.2858 REMARK 3 21 1.4068 - 1.3841 0.88 2995 147 0.2953 0.2905 REMARK 3 22 1.3841 - 1.3628 0.86 2866 172 0.2890 0.3276 REMARK 3 23 1.3628 - 1.3428 0.80 2705 151 0.2883 0.3109 REMARK 3 24 1.3428 - 1.3239 0.62 2098 99 0.2869 0.3478 REMARK 3 25 1.3239 - 1.3060 0.52 1741 110 0.2987 0.3143 REMARK 3 26 1.3060 - 1.2890 0.44 1543 65 0.3099 0.3669 REMARK 3 27 1.2890 - 1.2729 0.40 1306 74 0.3163 0.3566 REMARK 3 28 1.2729 - 1.2575 0.34 1148 65 0.3182 0.3488 REMARK 3 29 1.2575 - 1.2429 0.28 936 47 0.3352 0.3798 REMARK 3 30 1.2429 - 1.2290 0.25 833 44 0.3311 0.3806 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.130 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 : 0.006 1541 REMARK 3 ANGLE : 0.917 2077 REMARK 3 CHIRALITY : 0.039 211 REMARK 3 PLANARITY : 0.005 269 REMARK 3 DIHEDRAL : 10.817 599 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 8JZ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039152. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 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 REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84210 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.229 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 78.5 REMARK 200 DATA REDUNDANCY : 1.785 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.30 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 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: 1MOL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, PH 5.0, AND 35% REMARK 280 (W/V) PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 GLU A 48 REMARK 465 ASN A 49 REMARK 465 GLU A 50 REMARK 465 ARG A 51 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 GLU B 48 REMARK 465 ASN B 49 REMARK 465 GLU B 50 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 GLU B 52 CG CD OE1 OE2 REMARK 470 LYS B 83 CG CD CE NZ 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 OE1 GLN B 59 NH1 ARG B 70 2.15 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 ASN A 35 -65.54 -104.08 REMARK 500 ASN B 35 -60.35 -107.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 197 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A 198 DISTANCE = 7.16 ANGSTROMS DBREF 8JZ0 A 1 48 UNP P02882 MONB_DIOCU 1 48 DBREF 8JZ0 A 51 94 UNP P02881 MONA_DIOCU 2 45 DBREF 8JZ0 B 1 48 UNP P02882 MONB_DIOCU 1 48 DBREF 8JZ0 B 51 94 UNP P02881 MONA_DIOCU 2 45 SEQADV 8JZ0 GLY A -1 UNP P02882 EXPRESSION TAG SEQADV 8JZ0 SER A 0 UNP P02882 EXPRESSION TAG SEQADV 8JZ0 ALA A 41 UNP P02882 CYS 41 ENGINEERED MUTATION SEQADV 8JZ0 ASN A 49 UNP P02882 LINKER SEQADV 8JZ0 GLU A 50 UNP P02882 LINKER SEQADV 8JZ0 GLY B -1 UNP P02882 EXPRESSION TAG SEQADV 8JZ0 SER B 0 UNP P02882 EXPRESSION TAG SEQADV 8JZ0 ALA B 41 UNP P02882 CYS 41 ENGINEERED MUTATION SEQADV 8JZ0 ASN B 49 UNP P02882 LINKER SEQADV 8JZ0 GLU B 50 UNP P02882 LINKER SEQRES 1 A 96 GLY SER GLY GLU TRP GLU ILE ILE ASP ILE GLY PRO PHE SEQRES 2 A 96 THR GLN ASN LEU GLY LYS PHE ALA VAL ASP GLU GLU ASN SEQRES 3 A 96 LYS ILE GLY GLN TYR GLY ARG LEU THR PHE ASN LYS VAL SEQRES 4 A 96 ILE ARG PRO ALA MET LYS LYS THR ILE TYR GLU ASN GLU SEQRES 5 A 96 ARG GLU ILE LYS GLY TYR GLU TYR GLN LEU TYR VAL TYR SEQRES 6 A 96 ALA SER ASP LYS LEU PHE ARG ALA ASP ILE SER GLU ASP SEQRES 7 A 96 TYR LYS THR ARG GLY ARG LYS LEU LEU ARG PHE ASN GLY SEQRES 8 A 96 PRO VAL PRO PRO PRO SEQRES 1 B 96 GLY SER GLY GLU TRP GLU ILE ILE ASP ILE GLY PRO PHE SEQRES 2 B 96 THR GLN ASN LEU GLY LYS PHE ALA VAL ASP GLU GLU ASN SEQRES 3 B 96 LYS ILE GLY GLN TYR GLY ARG LEU THR PHE ASN LYS VAL SEQRES 4 B 96 ILE ARG PRO ALA MET LYS LYS THR ILE TYR GLU ASN GLU SEQRES 5 B 96 ARG GLU ILE LYS GLY TYR GLU TYR GLN LEU TYR VAL TYR SEQRES 6 B 96 ALA SER ASP LYS LEU PHE ARG ALA ASP ILE SER GLU ASP SEQRES 7 B 96 TYR LYS THR ARG GLY ARG LYS LEU LEU ARG PHE ASN GLY SEQRES 8 B 96 PRO VAL PRO PRO PRO FORMUL 3 HOH *186(H2 O) HELIX 1 AA1 GLY A 9 GLY A 27 1 19 HELIX 2 AA2 GLY B 9 GLY B 27 1 19 SHEET 1 AA1 5 GLU A 2 ILE A 6 0 SHEET 2 AA1 5 PHE A 34 ILE A 46 -1 O LYS A 43 N GLU A 4 SHEET 3 AA1 5 GLY A 55 ALA A 64 -1 O GLU A 57 N LYS A 44 SHEET 4 AA1 5 LYS A 67 ASP A 76 -1 O ALA A 71 N LEU A 60 SHEET 5 AA1 5 ARG A 82 ASN A 88 -1 O ASN A 88 N ARG A 70 SHEET 1 AA2 5 GLU B 2 ILE B 6 0 SHEET 2 AA2 5 PHE B 34 ILE B 46 -1 O LYS B 43 N GLU B 4 SHEET 3 AA2 5 GLY B 55 ALA B 64 -1 O TYR B 63 N LYS B 36 SHEET 4 AA2 5 LYS B 67 ASP B 76 -1 O ILE B 73 N TYR B 58 SHEET 5 AA2 5 ARG B 82 ASN B 88 -1 O LEU B 85 N ASP B 72 CISPEP 1 ARG A 39 PRO A 40 0 -2.35 CISPEP 2 GLY A 89 PRO A 90 0 0.69 CISPEP 3 ARG B 39 PRO B 40 0 -1.75 CISPEP 4 GLY B 89 PRO B 90 0 -1.91 CRYST1 31.695 39.748 44.410 106.22 109.25 103.35 P 1 2 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 0.031551 0.007488 0.015095 0.00000 SCALE2 0.000000 0.025857 0.010853 0.00000 SCALE3 0.000000 0.000000 0.025867 0.00000