HEADER PLANT SEED STORAGE PROTEIN (VICILIN) 21-MAR-90 1PHS TITLE THE THREE-DIMENSIONAL STRUCTURE OF THE SEED STORAGE PROTEIN PHASEOLIN TITLE 2 AT 3 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHASEOLIN, BETA-TYPE PRECURSOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHASEOLUS VULGARIS; SOURCE 3 ORGANISM_TAXID: 3885 KEYWDS PLANT SEED STORAGE PROTEIN (VICILIN) EXPDTA X-RAY DIFFRACTION MDLTYP CA ATOMS ONLY, CHAIN A AUTHOR M.C.LAWRENCE,E.SUZUKI,J.N.VARGHESE,P.C.DAVIS,A.VANDONKELAAR, AUTHOR 2 P.A.TULLOCH,P.M.COLMAN REVDAT 4 27-SEP-23 1PHS 1 REMARK SCALE MTRIX ATOM REVDAT 3 24-FEB-09 1PHS 1 VERSN REVDAT 2 01-APR-03 1PHS 1 JRNL REVDAT 1 15-OCT-90 1PHS 0 JRNL AUTH M.C.LAWRENCE,E.SUZUKI,J.N.VARGHESE,P.C.DAVIS, JRNL AUTH 2 A.VAN DONKELAAR,P.A.TULLOCH,P.M.COLMAN JRNL TITL THE THREE-DIMENSIONAL STRUCTURE OF THE SEED STORAGE PROTEIN JRNL TITL 2 PHASEOLIN AT 3 A RESOLUTION. JRNL REF EMBO J. V. 9 9 1990 JRNL REFN ISSN 0261-4189 JRNL PMID 2295315 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.SUZUKI,A.VANDONKELAAR,J.N.VARGHESE,G.G.LILLEY, REMARK 1 AUTH 2 R.J.BLAGROVE,P.M.COLMAN REMARK 1 TITL CRYSTALLIZATION OF PHASEOLIN FROM PHASEOLUS VULGARIS REMARK 1 REF J.BIOL.CHEM. V. 258 2634 1983 REMARK 1 REFN ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 34024 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 364 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 3.730 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 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 1PHS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175685. 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) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 63.40000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 67.25000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 63.40000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 67.25000 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: 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: TRIMERIC 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 0.240153 -0.061545 -0.968815 90.99927 REMARK 350 BIOMT2 2 0.938499 -0.240084 0.247750 14.00179 REMARK 350 BIOMT3 2 -0.247869 -0.968863 -0.000070 120.80507 REMARK 350 BIOMT1 3 0.240053 0.938645 -0.247845 -5.04645 REMARK 350 BIOMT2 3 -0.061344 -0.240156 -0.968730 125.97244 REMARK 350 BIOMT3 3 -0.968786 0.247930 0.000103 84.67497 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 THR A 1 REMARK 465 SER A 2 REMARK 465 LEU A 3 REMARK 465 ARG A 4 REMARK 465 GLU A 5 REMARK 465 GLU A 6 REMARK 465 GLU A 7 REMARK 465 GLU A 8 REMARK 465 SER A 9 REMARK 465 GLN A 10 REMARK 465 LYS A 213 REMARK 465 SER A 214 REMARK 465 LEU A 215 REMARK 465 SER A 216 REMARK 465 LYS A 217 REMARK 465 GLN A 218 REMARK 465 ASP A 219 REMARK 465 HIS A 382 REMARK 465 HIS A 383 REMARK 465 GLN A 384 REMARK 465 GLN A 385 REMARK 465 GLU A 386 REMARK 465 GLN A 387 REMARK 465 GLN A 388 REMARK 465 LYS A 389 REMARK 465 GLY A 390 REMARK 465 ARG A 391 REMARK 465 LYS A 392 REMARK 465 GLY A 393 REMARK 465 ALA A 394 REMARK 465 PHE A 395 REMARK 465 VAL A 396 REMARK 465 TYR A 397 DBREF 1PHS A 1 397 UNP P02853 PHSB_PHAVU 25 421 SEQRES 1 A 397 THR SER LEU ARG GLU GLU GLU GLU SER GLN ASP ASN PRO SEQRES 2 A 397 PHE TYR PHE ASN SER ASP ASN SER TRP ASN THR LEU PHE SEQRES 3 A 397 LYS ASN GLN TYR GLY HIS ILE ARG VAL LEU GLN ARG PHE SEQRES 4 A 397 ASP GLN GLN SER LYS ARG LEU GLN ASN LEU GLU ASP TYR SEQRES 5 A 397 ARG LEU VAL GLU PHE ARG SER LYS PRO GLU THR LEU LEU SEQRES 6 A 397 LEU PRO GLN GLN ALA ASP ALA GLU LEU LEU LEU VAL VAL SEQRES 7 A 397 ARG SER GLY SER ALA ILE LEU VAL LEU VAL LYS PRO ASP SEQRES 8 A 397 ASP ARG ARG GLU TYR PHE PHE LEU THR SER ASP ASN PRO SEQRES 9 A 397 ILE PHE SER ASP HIS GLN LYS ILE PRO ALA GLY THR ILE SEQRES 10 A 397 PHE TYR LEU VAL ASN PRO ASP PRO LYS GLU ASP LEU ARG SEQRES 11 A 397 ILE ILE GLN LEU ALA MET PRO VAL ASN ASN PRO GLN ILE SEQRES 12 A 397 HIS GLU PHE PHE LEU SER SER THR GLU ALA GLN GLN SER SEQRES 13 A 397 TYR LEU GLN GLU PHE SER LYS HIS ILE LEU GLU ALA SER SEQRES 14 A 397 PHE ASN SER LYS PHE GLU GLU ILE ASN ARG VAL LEU PHE SEQRES 15 A 397 GLU GLU GLU GLY GLN GLN GLU GLY VAL ILE VAL ASN ILE SEQRES 16 A 397 ASP SER GLU GLN ILE LYS GLU LEU SER LYS HIS ALA LYS SEQRES 17 A 397 SER SER SER ARG LYS SER LEU SER LYS GLN ASP ASN THR SEQRES 18 A 397 ILE GLY ASN GLU PHE GLY ASN LEU THR GLU ARG THR ASP SEQRES 19 A 397 ASN SER LEU ASN VAL LEU ILE SER SER ILE GLU MET GLU SEQRES 20 A 397 GLU GLY ALA LEU PHE VAL PRO HIS TYR TYR SER LYS ALA SEQRES 21 A 397 ILE VAL ILE LEU VAL VAL ASN GLU GLY GLU ALA HIS VAL SEQRES 22 A 397 GLU LEU VAL GLY PRO LYS GLY ASN LYS GLU THR LEU GLU SEQRES 23 A 397 TYR GLU SER TYR ARG ALA GLU LEU SER LYS ASP ASP VAL SEQRES 24 A 397 PHE VAL ILE PRO ALA ALA TYR PRO VAL ALA ILE LYS ALA SEQRES 25 A 397 THR SER ASN VAL ASN PHE THR GLY PHE GLY ILE ASN ALA SEQRES 26 A 397 ASN ASN ASN ASN ARG ASN LEU LEU ALA GLY LYS THR ASP SEQRES 27 A 397 ASN VAL ILE SER SER ILE GLY ARG ALA LEU ASP GLY LYS SEQRES 28 A 397 ASP VAL LEU GLY LEU THR PHE SER GLY SER GLY ASP GLU SEQRES 29 A 397 VAL MET LYS LEU ILE ASN LYS GLN SER GLY SER TYR PHE SEQRES 30 A 397 VAL ASP ALA HIS HIS HIS GLN GLN GLU GLN GLN LYS GLY SEQRES 31 A 397 ARG LYS GLY ALA PHE VAL TYR CRYST1 126.800 134.500 161.600 90.00 90.00 90.00 P 21 21 2 24 ORIGX1 -0.193172 0.892279 0.408276 -64.06165 ORIGX2 -0.702380 -0.416197 0.577323 49.46682 ORIGX3 0.684999 -0.175234 0.707047 -59.87779 SCALE1 0.007886 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007435 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006188 0.00000 MTRIX1 1 0.240153 -0.061545 -0.968815 90.99927 MTRIX2 1 0.938499 -0.240084 0.247750 14.00179 MTRIX3 1 -0.247869 -0.968863 -0.000070 120.80507 MTRIX1 2 0.240053 0.938645 -0.247845 -5.04645 MTRIX2 2 -0.061344 -0.240156 -0.968730 125.97244 MTRIX3 2 -0.968786 0.247930 0.000103 84.67497 MTRIX1 3 -0.877146 0.480335 0.000019 86.70777 MTRIX2 3 0.480110 0.877146 0.000075 -22.18006 MTRIX3 3 -0.000032 -0.000126 -1.000000 79.87325 MTRIX1 4 0.240140 -0.061355 0.968797 13.61587 MTRIX2 4 0.938483 -0.240209 -0.247824 33.80023 MTRIX3 4 0.247743 0.968894 0.000069 -40.93646 MTRIX1 5 -0.240046 -0.938679 -0.247919 151.64488 MTRIX2 5 0.061371 0.240019 -0.968711 85.89973 MTRIX3 5 0.968786 -0.247931 0.000027 -4.81743