HEADER PLANT PROTEIN 19-JUN-06 2DS2 TITLE CRYSTAL STRUCTURE OF MABINLIN II COMPND MOL_ID: 1; COMPND 2 MOLECULE: SWEET PROTEIN MABINLIN-2 CHAIN A; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: MABINLIN II, MAB II; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SWEET PROTEIN MABINLIN-2 CHAIN B; COMPND 7 CHAIN: B, D; COMPND 8 SYNONYM: MABINLIN II, MAB II SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAPPARIS MASAIKAI; SOURCE 3 ORGANISM_TAXID: 13395; SOURCE 4 TISSUE: SEED; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: CAPPARIS MASAIKAI; SOURCE 7 ORGANISM_TAXID: 13395; SOURCE 8 TISSUE: SEED KEYWDS PLANT PROTEIN, SEED STORAGE PROTEIN, SWEET PROTEIN, CRYSTAL KEYWDS 2 STRUCTURE EXPDTA X-RAY DIFFRACTION AUTHOR D.F.LI,D.Y.ZHU,D.C.WANG REVDAT 2 04-NOV-08 2DS2 1 JRNL VERSN REVDAT 1 12-JUN-07 2DS2 0 JRNL AUTH D.F.LI,P.JIANG,D.Y.ZHU,Y.HU,M.MAX,D.C.WANG JRNL TITL CRYSTAL STRUCTURE OF MABINLIN II: A NOVEL JRNL TITL 2 STRUCTURAL TYPE OF SWEET PROTEINS AND THE MAIN JRNL TITL 3 STRUCTURAL BASIS FOR ITS SWEETNESS. JRNL REF J.STRUCT.BIOL. V. 162 50 2008 JRNL REFN ISSN 1047-8477 JRNL PMID 18308584 JRNL DOI 10.1016/J.JSB.2007.12.007 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 16657 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1641 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3740 REMARK 3 BIN FREE R VALUE : 0.4340 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 230 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1547 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.70 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.14 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.97 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DS2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUN-06. REMARK 100 THE RCSB ID CODE IS RCSB025775. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 83.0 REMARK 200 PH : 4.60 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 : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : CON-FOCUSE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17686 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : 0.05300 REMARK 200 FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.26600 REMARK 200 R SYM FOR SHELL (I) : 0.26600 REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 24.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM MALONATE, SODIUM ACETATE , REMARK 280 PH 4.60, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 310K 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 40.05500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.54000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.05500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.54000 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 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: 2420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 GLN A 1 REMARK 465 LEU A 2 REMARK 465 TRP A 3 REMARK 465 GLY A 30 REMARK 465 GLN A 31 REMARK 465 PRO A 32 REMARK 465 ASP A 33 REMARK 465 GLN B 1 REMARK 465 PRO B 2 REMARK 465 ARG B 3 REMARK 465 ARG B 4 REMARK 465 TRP B 72 REMARK 465 GLN C 1 REMARK 465 GLY C 30 REMARK 465 GLN C 31 REMARK 465 PRO C 32 REMARK 465 ASP C 33 REMARK 465 GLN D 1 REMARK 465 PRO D 2 REMARK 465 ARG D 3 REMARK 465 TRP D 72 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 GLN C 6 CG CD OE1 NE2 REMARK 470 ARG D 8 CG CD NE CZ NH1 NH2 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 PRO B 62 -102.55 -19.83 REMARK 500 HIS C 12 43.67 -104.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY D 1001 DBREF 2DS2 A 1 33 UNP P30233 2SS2_CAPMA 36 68 DBREF 2DS2 C 1 33 UNP P30233 2SS2_CAPMA 36 68 DBREF 2DS2 B 1 72 UNP P30233 2SS2_CAPMA 83 154 DBREF 2DS2 D 1 72 UNP P30233 2SS2_CAPMA 83 154 SEQRES 1 A 33 GLN LEU TRP ARG CYS GLN ARG GLN PHE LEU GLN HIS GLN SEQRES 2 A 33 ARG LEU ARG ALA CYS GLN ARG PHE ILE HIS ARG ARG ALA SEQRES 3 A 33 GLN PHE GLY GLY GLN PRO ASP SEQRES 1 B 72 GLN PRO ARG ARG PRO ALA LEU ARG GLN CYS CYS ASN GLN SEQRES 2 B 72 LEU ARG GLN VAL ASP ARG PRO CYS VAL CYS PRO VAL LEU SEQRES 3 B 72 ARG GLN ALA ALA GLN GLN VAL LEU GLN ARG GLN ILE ILE SEQRES 4 B 72 GLN GLY PRO GLN GLN LEU ARG ARG LEU PHE ASP ALA ALA SEQRES 5 B 72 ARG ASN LEU PRO ASN ILE CYS ASN ILE PRO ASN ILE GLY SEQRES 6 B 72 ALA CYS PRO PHE ARG ALA TRP SEQRES 1 C 33 GLN LEU TRP ARG CYS GLN ARG GLN PHE LEU GLN HIS GLN SEQRES 2 C 33 ARG LEU ARG ALA CYS GLN ARG PHE ILE HIS ARG ARG ALA SEQRES 3 C 33 GLN PHE GLY GLY GLN PRO ASP SEQRES 1 D 72 GLN PRO ARG ARG PRO ALA LEU ARG GLN CYS CYS ASN GLN SEQRES 2 D 72 LEU ARG GLN VAL ASP ARG PRO CYS VAL CYS PRO VAL LEU SEQRES 3 D 72 ARG GLN ALA ALA GLN GLN VAL LEU GLN ARG GLN ILE ILE SEQRES 4 D 72 GLN GLY PRO GLN GLN LEU ARG ARG LEU PHE ASP ALA ALA SEQRES 5 D 72 ARG ASN LEU PRO ASN ILE CYS ASN ILE PRO ASN ILE GLY SEQRES 6 D 72 ALA CYS PRO PHE ARG ALA TRP HET ACY D1001 4 HETNAM ACY ACETIC ACID FORMUL 5 ACY C2 H4 O2 FORMUL 6 HOH *125(H2 O) HELIX 1 1 ARG A 4 HIS A 12 1 9 HELIX 2 2 LEU A 15 PHE A 28 1 14 HELIX 3 3 PRO B 5 ARG B 15 1 11 HELIX 4 4 GLN B 16 VAL B 17 5 2 HELIX 5 5 ASP B 18 PRO B 20 5 3 HELIX 6 6 CYS B 21 GLN B 37 1 17 HELIX 7 7 GLY B 41 CYS B 59 1 19 HELIX 8 8 LEU C 2 HIS C 12 1 11 HELIX 9 9 LEU C 15 GLY C 29 1 15 HELIX 10 10 ARG D 4 ARG D 15 1 12 HELIX 11 11 GLN D 16 VAL D 17 5 2 HELIX 12 12 ASP D 18 PRO D 20 5 3 HELIX 13 13 CYS D 21 GLN D 37 1 17 HELIX 14 14 GLY D 41 CYS D 59 1 19 SSBOND 1 CYS A 5 CYS B 21 1555 1555 2.03 SSBOND 2 CYS A 18 CYS B 10 1555 1555 2.04 SSBOND 3 CYS B 11 CYS B 59 1555 1555 2.03 SSBOND 4 CYS B 23 CYS B 67 1555 1555 2.03 SSBOND 5 CYS C 5 CYS D 21 1555 1555 2.03 SSBOND 6 CYS C 18 CYS D 10 1555 1555 2.02 SSBOND 7 CYS D 11 CYS D 59 1555 1555 2.03 SSBOND 8 CYS D 23 CYS D 67 1555 1555 2.04 SITE 1 AC1 5 ARG C 24 ARG D 27 PHE D 49 PHE D 69 SITE 2 AC1 5 ARG D 70 CRYST1 80.110 51.080 47.340 90.00 122.77 90.00 C 1 2 1 8 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 0.012483 0.000000 0.008035 0.00000 SCALE2 0.000000 0.019577 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025122 0.00000