HEADER PLANT PROTEIN 30-JUN-04 1TW0 TITLE NATIVE CRYSTAL STRUCTURE OF SPE16 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PATHOGENESIS-RELATED CLASS 10 PROTEIN SPE-16; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PATHOGENESIS-RELATED PROTEIN CLASS 10, SPE16 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PACHYRHIZUS EROSUS; SOURCE 3 ORGANISM_TAXID: 109171 KEYWDS SEVEN ANTIPARALLEL BETA-SHEET, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.WU,Z.WEI,Z.ZHOU,W.GONG REVDAT 3 13-MAR-24 1TW0 1 SEQADV REVDAT 2 24-FEB-09 1TW0 1 VERSN REVDAT 1 11-OCT-05 1TW0 0 JRNL AUTH F.WU,Z.WEI,Z.ZHOU,W.GONG JRNL TITL NATIVE CRYSTAL STRUCTURE OF SPE16 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 312705.540 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 12358 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 SET) : 0.199 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1265 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1582 REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 188 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2254 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 124 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.89000 REMARK 3 B22 (A**2) : -5.34000 REMARK 3 B33 (A**2) : -3.55000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.25 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) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.33 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.650 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 61.92 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TW0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000022953. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 27.14650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.38550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.68050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.38550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.14650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.68050 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: DIMERIC 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 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 ARG A 6 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 33 CG1 CG2 CD1 REMARK 470 GLU A 59 CG CD OE1 OE2 REMARK 470 LYS A 62 CG CD CE NZ REMARK 470 ASN A 77 CG OD1 ND2 REMARK 470 LYS A 102 CG CD CE NZ REMARK 470 SER A 107 OG REMARK 470 LYS A 114 CG CD CE NZ REMARK 470 LYS A 122 CG CD CE NZ REMARK 470 ASP A 124 CG OD1 OD2 REMARK 470 ARG B 6 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 59 CG CD OE1 OE2 REMARK 470 ASP B 61 CG OD1 OD2 REMARK 470 LYS B 62 CG CD CE NZ REMARK 470 SER B 107 OG REMARK 470 LYS B 122 CG CD CE NZ 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 32 59.00 -115.42 REMARK 500 ILE A 33 117.06 -171.33 REMARK 500 GLU A 59 55.56 -109.74 REMARK 500 ASP B 61 -18.70 -142.32 REMARK 500 LYS B 122 -80.26 -53.01 REMARK 500 REMARK 500 REMARK: NULL DBREF 1TW0 A 1 147 UNP Q6T6J0 Q6T6J0_9FABA 2 148 DBREF 1TW0 B 1 147 UNP Q6T6J0 Q6T6J0_9FABA 2 148 SEQADV 1TW0 GLY A 148 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 TYR A 149 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 VAL A 150 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 LEU A 151 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 ALA A 152 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 ASN A 153 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 PRO A 154 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 ALA A 155 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 GLU A 156 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 TYR A 157 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 GLY B 148 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 TYR B 149 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 VAL B 150 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 LEU B 151 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 ALA B 152 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 ASN B 153 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 PRO B 154 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 ALA B 155 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 GLU B 156 UNP Q6T6J0 CLONING ARTIFACT SEQADV 1TW0 TYR B 157 UNP Q6T6J0 CLONING ARTIFACT SEQRES 1 A 157 GLY VAL PHE VAL PHE ARG ASP GLU THR SER SER SER VAL SEQRES 2 A 157 ALA PRO ALA LYS LEU TYR LYS ALA LEU THR LYS ASP SER SEQRES 3 A 157 ASP THR ILE ALA GLN LYS ILE ASP GLY PRO ILE GLN SER SEQRES 4 A 157 ILE GLU LEU VAL GLU GLY ASN GLY GLY VAL GLY THR ILE SEQRES 5 A 157 LYS LYS ILE THR ALA ASN GLU GLY ASP LYS THR SER PHE SEQRES 6 A 157 VAL LEU GLN LYS VAL ASP ALA ILE ASP GLU ALA ASN LEU SEQRES 7 A 157 GLY TYR ASP TYR SER ILE VAL GLY GLY THR GLY LEU PRO SEQRES 8 A 157 GLU SER LEU GLU LYS LEU SER PHE GLU THR LYS VAL VAL SEQRES 9 A 157 ALA GLY SER GLY GLY GLY SER ILE SER LYS VAL THR LEU SEQRES 10 A 157 LYS PHE HIS THR LYS GLY ASP ALA PRO LEU SER ASP ALA SEQRES 11 A 157 VAL ARG ASP ASP ALA LEU ALA LYS GLY ALA GLY PHE PHE SEQRES 12 A 157 LYS ALA ILE GLU GLY TYR VAL LEU ALA ASN PRO ALA GLU SEQRES 13 A 157 TYR SEQRES 1 B 157 GLY VAL PHE VAL PHE ARG ASP GLU THR SER SER SER VAL SEQRES 2 B 157 ALA PRO ALA LYS LEU TYR LYS ALA LEU THR LYS ASP SER SEQRES 3 B 157 ASP THR ILE ALA GLN LYS ILE ASP GLY PRO ILE GLN SER SEQRES 4 B 157 ILE GLU LEU VAL GLU GLY ASN GLY GLY VAL GLY THR ILE SEQRES 5 B 157 LYS LYS ILE THR ALA ASN GLU GLY ASP LYS THR SER PHE SEQRES 6 B 157 VAL LEU GLN LYS VAL ASP ALA ILE ASP GLU ALA ASN LEU SEQRES 7 B 157 GLY TYR ASP TYR SER ILE VAL GLY GLY THR GLY LEU PRO SEQRES 8 B 157 GLU SER LEU GLU LYS LEU SER PHE GLU THR LYS VAL VAL SEQRES 9 B 157 ALA GLY SER GLY GLY GLY SER ILE SER LYS VAL THR LEU SEQRES 10 B 157 LYS PHE HIS THR LYS GLY ASP ALA PRO LEU SER ASP ALA SEQRES 11 B 157 VAL ARG ASP ASP ALA LEU ALA LYS GLY ALA GLY PHE PHE SEQRES 12 B 157 LYS ALA ILE GLU GLY TYR VAL LEU ALA ASN PRO ALA GLU SEQRES 13 B 157 TYR FORMUL 3 HOH *124(H2 O) HELIX 1 1 ALA A 14 ASP A 25 1 12 HELIX 2 2 SER A 26 ILE A 33 5 8 HELIX 3 3 SER A 128 ASN A 153 1 26 HELIX 4 4 PRO A 154 TYR A 157 5 4 HELIX 5 5 ALA B 14 LYS B 24 1 11 HELIX 6 6 ASP B 25 ILE B 33 1 9 HELIX 7 7 GLU B 75 ASN B 77 5 3 HELIX 8 8 SER B 128 ASN B 153 1 26 HELIX 9 9 PRO B 154 TYR B 157 5 4 SHEET 1 A 7 VAL A 2 SER A 11 0 SHEET 2 A 7 SER A 111 THR A 121 -1 O VAL A 115 N ASP A 7 SHEET 3 A 7 LEU A 94 ALA A 105 -1 N GLU A 95 O HIS A 120 SHEET 4 A 7 GLY A 79 GLY A 86 -1 N TYR A 82 O PHE A 99 SHEET 5 A 7 LYS A 62 ASP A 74 -1 N ALA A 72 O ASP A 81 SHEET 6 A 7 ILE A 52 GLU A 59 -1 N LYS A 53 O GLN A 68 SHEET 7 A 7 ILE A 37 GLU A 44 -1 N GLU A 44 O ILE A 52 SHEET 1 B 7 VAL B 2 SER B 11 0 SHEET 2 B 7 SER B 111 THR B 121 -1 O SER B 113 N THR B 9 SHEET 3 B 7 LEU B 94 ALA B 105 -1 N LYS B 102 O LYS B 114 SHEET 4 B 7 GLY B 79 GLY B 86 -1 N TYR B 82 O PHE B 99 SHEET 5 B 7 LYS B 62 ASP B 74 -1 N LYS B 69 O SER B 83 SHEET 6 B 7 ILE B 52 GLU B 59 -1 N ILE B 55 O VAL B 66 SHEET 7 B 7 ILE B 37 GLU B 44 -1 N GLU B 41 O LYS B 54 CRYST1 54.293 63.361 72.771 90.00 90.00 90.00 P 21 21 21 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 0.018419 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015783 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013742 0.00000