HEADER PLANT PROTEIN 08-SEP-17 5YCW TITLE DOUBLE DOMAIN SWAPPED DIMER OF ENGINEERED HAIRPIN LOOP1 AND LOOP3 TITLE 2 MUTANT IN SINGLE-CHAIN MONELLIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SINGLE CHAIN MONELLIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DIOSCOREOPHYLLUM CUMMINSII; SOURCE 3 ORGANISM_TAXID: 3457; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DOMAIN SWAPPED DIMER, SINGLE-CHAIN MONELLIN, LOOP MUTATION, QVVAG KEYWDS 2 MOTIF, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.SURANA,N.NANDWANI,J.B.UDGAONKAR,S.GOSAVI,R.DAS REVDAT 3 22-NOV-23 5YCW 1 REMARK REVDAT 2 13-FEB-19 5YCW 1 JRNL REVDAT 1 28-NOV-18 5YCW 0 JRNL AUTH N.NANDWANI,P.SURANA,H.NEGI,N.M.MASCARENHAS,J.B.UDGAONKAR, JRNL AUTH 2 R.DAS,S.GOSAVI JRNL TITL A FIVE-RESIDUE MOTIF FOR THE DESIGN OF DOMAIN SWAPPING IN JRNL TITL 2 PROTEINS. JRNL REF NAT COMMUN V. 10 452 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 30692525 JRNL DOI 10.1038/S41467-019-08295-X REMARK 2 REMARK 2 RESOLUTION. 2.29 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 6520 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.910 REMARK 3 FREE R VALUE TEST SET COUNT : 646 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 41.6714 - 3.9062 1.00 1291 136 0.1775 0.2073 REMARK 3 2 3.9062 - 3.1008 0.99 1198 140 0.2461 0.2932 REMARK 3 3 3.1008 - 2.7089 1.00 1182 127 0.3074 0.3882 REMARK 3 4 2.7089 - 2.4613 0.88 1038 116 0.3577 0.3824 REMARK 3 5 2.4613 - 2.2849 1.00 1165 127 0.3837 0.4302 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 71.49 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 : 0.006 737 REMARK 3 ANGLE : 1.047 996 REMARK 3 CHIRALITY : 0.040 105 REMARK 3 PLANARITY : 0.008 130 REMARK 3 DIHEDRAL : 14.575 279 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 2:23) REMARK 3 ORIGIN FOR THE GROUP (A): -3.2708 19.5334 -0.9586 REMARK 3 T TENSOR REMARK 3 T11: 0.4911 T22: 0.5804 REMARK 3 T33: 0.7136 T12: 0.0838 REMARK 3 T13: 0.0466 T23: 0.0015 REMARK 3 L TENSOR REMARK 3 L11: 0.8792 L22: 1.0839 REMARK 3 L33: 2.2506 L12: -0.4036 REMARK 3 L13: -0.2972 L23: -0.4133 REMARK 3 S TENSOR REMARK 3 S11: -0.1375 S12: 0.0563 S13: -0.4594 REMARK 3 S21: -0.0077 S22: 0.4033 S23: 0.3522 REMARK 3 S31: -0.2690 S32: -0.2086 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 24:31) REMARK 3 ORIGIN FOR THE GROUP (A): -0.5168 38.0568 -0.0660 REMARK 3 T TENSOR REMARK 3 T11: 1.2954 T22: 0.6229 REMARK 3 T33: 1.0090 T12: 0.1676 REMARK 3 T13: 0.1006 T23: 0.0644 REMARK 3 L TENSOR REMARK 3 L11: 0.1053 L22: 0.3433 REMARK 3 L33: -0.4193 L12: -0.1180 REMARK 3 L13: -0.4471 L23: 0.0987 REMARK 3 S TENSOR REMARK 3 S11: -0.8822 S12: -0.1037 S13: 0.5134 REMARK 3 S21: 0.5904 S22: 0.6124 S23: -0.1953 REMARK 3 S31: -0.5074 S32: -0.0919 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 32:52) REMARK 3 ORIGIN FOR THE GROUP (A): -0.7872 20.5726 0.8379 REMARK 3 T TENSOR REMARK 3 T11: 0.5984 T22: 0.6614 REMARK 3 T33: 0.5284 T12: 0.0971 REMARK 3 T13: -0.0147 T23: -0.0279 REMARK 3 L TENSOR REMARK 3 L11: 1.8579 L22: 1.3353 REMARK 3 L33: 0.9694 L12: -0.4471 REMARK 3 L13: -0.6914 L23: -0.8340 REMARK 3 S TENSOR REMARK 3 S11: 0.0148 S12: 0.0992 S13: 0.1526 REMARK 3 S21: 0.0934 S22: -0.0251 S23: -0.1503 REMARK 3 S31: -0.2077 S32: 0.0673 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 53:75) REMARK 3 ORIGIN FOR THE GROUP (A): -21.0754 11.1534 33.7663 REMARK 3 T TENSOR REMARK 3 T11: 0.5522 T22: 0.5182 REMARK 3 T33: 0.4519 T12: 0.0284 REMARK 3 T13: 0.0745 T23: 0.0187 REMARK 3 L TENSOR REMARK 3 L11: 2.4429 L22: 3.5193 REMARK 3 L33: 0.0323 L12: -2.0103 REMARK 3 L13: 0.4631 L23: -0.7002 REMARK 3 S TENSOR REMARK 3 S11: -0.0435 S12: 0.4039 S13: -0.2120 REMARK 3 S21: 0.2853 S22: -0.1707 S23: 0.1135 REMARK 3 S31: 0.0648 S32: -0.4134 S33: -0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 76:91) REMARK 3 ORIGIN FOR THE GROUP (A): 2.3372 26.6221 1.7848 REMARK 3 T TENSOR REMARK 3 T11: 0.8463 T22: 0.7788 REMARK 3 T33: 0.8707 T12: -0.0157 REMARK 3 T13: 0.0225 T23: -0.0693 REMARK 3 L TENSOR REMARK 3 L11: 1.5313 L22: 1.5200 REMARK 3 L33: 0.7590 L12: -2.2207 REMARK 3 L13: 1.5297 L23: -2.7869 REMARK 3 S TENSOR REMARK 3 S11: -0.1385 S12: 0.2884 S13: -0.1652 REMARK 3 S21: 0.5027 S22: -0.0315 S23: -0.6135 REMARK 3 S31: -0.4528 S32: -0.3010 S33: 0.0000 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 5YCW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300004231. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4-7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.966 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6521 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.285 REMARK 200 RESOLUTION RANGE LOW (A) : 41.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.03691 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.7600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.70520 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.460 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: 1IV7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8-12% (WT/VOL) PEG 8000, 50MM SODIUM REMARK 280 PHOSPHATE, PH 6.4-6.8, CRYSTALS GREW IN A WEEK, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.49667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 68.99333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 68.99333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 34.49667 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 34.49667 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 MET A 1 REMARK 465 SER A 92 REMARK 465 THR A 93 REMARK 465 PRO A 94 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 GLN A 29 33.17 -85.40 REMARK 500 ASP A 63 39.08 38.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE COMPLETE SEQUENCE OF SINGLE CHAIN MONELLIN HAS BEEN DEPOSITED REMARK 999 TO NCBI WITH ACCESSION CODE AFF58925. RESIDUES 48-57 YENEGFREIK REMARK 999 HAVE BEEN REPLACED WITH QVVA, RESIDUES 79-83 DYKTR HAVE BEEN REMARK 999 REPLACED WITH QVVAG IN THIS STRUCTURE. C-TERMINAL RESIDUES STP ARE REMARK 999 FROM EXPRESSION TAG. DBREF 5YCW A 1 94 PDB 5YCW 5YCW 1 94 SEQRES 1 A 94 MET GLY GLU TRP GLU ILE ILE ASP ILE GLY PRO PHE THR SEQRES 2 A 94 GLN ASN LEU GLY LYS PHE ALA VAL ASP GLU GLU ASN LYS SEQRES 3 A 94 ILE GLY GLN TYR GLY ARG LEU THR PHE ASN LYS VAL ILE SEQRES 4 A 94 ARG PRO CYS MET LYS LYS THR ILE GLN VAL VAL ALA GLY SEQRES 5 A 94 TYR GLU TYR GLN LEU TYR VAL TYR ALA SER ASP LYS LEU SEQRES 6 A 94 PHE ARG ALA ASP ILE SER GLU GLN VAL VAL ALA GLY GLY SEQRES 7 A 94 ARG LYS LEU LEU ARG PHE ASN GLY PRO VAL PRO PRO PRO SEQRES 8 A 94 SER THR PRO FORMUL 2 HOH *4(H2 O) HELIX 1 AA1 GLY A 10 LYS A 26 1 17 SHEET 1 AA1 2 GLU A 3 ILE A 7 0 SHEET 2 AA1 2 CYS A 42 THR A 46 -1 O THR A 46 N GLU A 3 SHEET 1 AA2 2 TYR A 53 ALA A 61 0 SHEET 2 AA2 2 LYS A 64 GLU A 72 -1 O GLU A 72 N TYR A 53 CISPEP 1 ARG A 40 PRO A 41 0 -3.31 CISPEP 2 GLY A 86 PRO A 87 0 -1.47 CRYST1 48.110 48.110 103.490 90.00 90.00 120.00 P 31 2 1 6 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 0.020786 0.012001 0.000000 0.00000 SCALE2 0.000000 0.024001 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009663 0.00000