HEADER SEED STORAGE PROTEIN 19-JUN-96 1WBA TITLE WINGED BEAN ALBUMIN 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: WINGED BEAN ALBUMIN 1; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSOPHOCARPUS TETRAGONOLOBUS; SOURCE 3 ORGANISM_COMMON: WINGED BEAN; SOURCE 4 ORGANISM_TAXID: 3891 KEYWDS SEED STORAGE PROTEIN, ALBUMIN EXPDTA X-RAY DIFFRACTION AUTHOR A.J.MCCOY REVDAT 3 03-APR-24 1WBA 1 REMARK REVDAT 2 24-FEB-09 1WBA 1 VERSN REVDAT 1 11-JAN-97 1WBA 0 JRNL AUTH S.M.DAYAN,A.VAN DONKELAAR,A.A.KORTT JRNL TITL CRYSTALLIZATION AND PRELIMINARY CRYSTALLOGRAPHIC DATA OF THE JRNL TITL 2 MAJOR ALBUMIN FROM PSOPHOCARPUS TETRAGONOLOBUS (L.) DC. JRNL REF J.BIOL.CHEM. V. 262 10287 1987 JRNL REFN ISSN 0021-9258 JRNL PMID 3611061 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 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) (%) : 80.0 REMARK 3 NUMBER OF REFLECTIONS : 15159 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) : 0.190 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 43.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2156 REMARK 3 BIN R VALUE (WORKING SET) : 0.2210 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 : 1308 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 87 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.50000 REMARK 3 B22 (A**2) : 9.50000 REMARK 3 B33 (A**2) : 9.50000 REMARK 3 B12 (A**2) : 9.50000 REMARK 3 B13 (A**2) : 9.50000 REMARK 3 B23 (A**2) : 9.50000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.531 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.87 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.207 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WBA 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_1000177171. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : DEC-94 REMARK 200 TEMPERATURE (KELVIN) : 286 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.04 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : WEISSENBERG REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AGROVATA, WEIS REMARK 200 DATA SCALING SOFTWARE : AGROVATA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12039 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.0 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.2000 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: MULTIPLE ISOMORPHOUS REMARK 200 REPLACEMENT AND MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: SOYBEAN TRYPSIN INHIBITOR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION FROM PROTEIN AT 5MG/ML REMARK 280 IN 0.1M SUCCINATE BUFFER PH 5.5 EQUILIBRATED AGAINST 30% REMARK 280 ETHANOL., VAPOR DIFFUSION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 47.80000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 47.80000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 47.80000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.50000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 47.80000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 64.50000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 47.80000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 64.50000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.80000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.50000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 47.80000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 47.80000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 43.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 47.80000 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 47.80000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 43.00000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 47.80000 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 64.50000 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 47.80000 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 21.50000 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 47.80000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 21.50000 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 47.80000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 64.50000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 47.80000 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 47.80000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 43.00000 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: 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 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 ALA A 1 REMARK 465 GLU A 173 REMARK 465 PRO A 174 REMARK 465 GLU A 175 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 LYS A 18 CD CE NZ REMARK 470 LYS A 64 CE NZ REMARK 470 ARG A 70 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 115 CD CE NZ REMARK 470 GLN A 161 CG CD OE1 NE2 REMARK 470 ARG A 171 CD NE CZ NH1 NH2 DBREF 1WBA A 1 175 UNP P15465 ALB1_PSOTE 1 175 SEQRES 1 A 175 ALA ASP ASP PRO VAL TYR ASP ALA GLU GLY ASN LYS LEU SEQRES 2 A 175 VAL ASN ARG GLY LYS TYR THR ILE VAL SER PHE SER ASP SEQRES 3 A 175 GLY ALA GLY ILE ASP VAL VAL ALA THR GLY ASN GLU ASN SEQRES 4 A 175 PRO GLU ASP PRO LEU SER ILE VAL LYS SER THR ARG ASN SEQRES 5 A 175 ILE MET TYR ALA THR SER ILE SER SER GLU ASP LYS THR SEQRES 6 A 175 PRO PRO GLN PRO ARG ASN ILE LEU GLU ASN MET ARG LEU SEQRES 7 A 175 LYS ILE ASN PHE ALA THR ASP PRO HIS LYS GLY ASP VAL SEQRES 8 A 175 TRP SER VAL VAL ASP PHE GLN PRO ASP GLY GLN GLN LEU SEQRES 9 A 175 LYS LEU ALA GLY ARG TYR PRO ASN GLN VAL LYS GLY ALA SEQRES 10 A 175 PHE THR ILE GLN LYS GLY SER ASN THR PRO ARG THR TYR SEQRES 11 A 175 LYS LEU LEU PHE CYS PRO VAL GLY SER PRO CYS LYS ASN SEQRES 12 A 175 ILE GLY ILE SER THR ASP PRO GLU GLY LYS LYS ARG LEU SEQRES 13 A 175 VAL VAL SER TYR GLN SER ASP PRO LEU VAL VAL LYS PHE SEQRES 14 A 175 HIS ARG HIS GLU PRO GLU FORMUL 2 HOH *87(H2 O) SHEET 1 A 4 VAL A 167 ARG A 171 0 SHEET 2 A 4 GLY A 17 SER A 23 -1 N VAL A 22 O LYS A 168 SHEET 3 A 4 ALA A 56 SER A 61 -1 N ILE A 59 O GLY A 17 SHEET 4 A 4 LEU A 78 PHE A 82 -1 N ASN A 81 O SER A 58 SHEET 1 B 2 ILE A 30 VAL A 33 0 SHEET 2 B 2 SER A 45 LYS A 48 -1 N VAL A 47 O ASP A 31 SHEET 1 C 2 TRP A 92 PHE A 97 0 SHEET 2 C 2 GLY A 101 LEU A 106 -1 N LYS A 105 O SER A 93 SHEET 1 D 2 GLY A 116 LYS A 122 0 SHEET 2 D 2 TYR A 130 PRO A 136 -1 N CYS A 135 O ALA A 117 SHEET 1 E 2 ASN A 143 THR A 148 0 SHEET 2 E 2 LYS A 154 SER A 159 -1 N SER A 159 O ASN A 143 SSBOND 1 CYS A 135 CYS A 141 1555 1555 2.02 CISPEP 1 PRO A 66 PRO A 67 0 -0.33 CISPEP 2 ASP A 85 PRO A 86 0 0.30 CISPEP 3 GLN A 98 PRO A 99 0 0.77 CRYST1 95.600 95.600 86.000 90.00 90.00 90.00 I 41 2 2 16 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 0.010460 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010460 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011628 0.00000