HEADER PLANT SEED PROTEIN 31-JAN-97 1AB1 TITLE SI FORM CRAMBIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRAMBIN (SER22/ILE25); COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CRAMBE HISPANICA SUBSP. ABYSSINICA; SOURCE 3 ORGANISM_TAXID: 3721; SOURCE 4 STRAIN: SUBSP. ABYSSINICA KEYWDS THIONIN, PLANT SEED PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.M.TEETER,A.YAMANO REVDAT 4 19-OCT-16 1AB1 1 REMARK VERSN REVDAT 3 24-FEB-09 1AB1 1 VERSN REVDAT 2 10-MAY-00 1AB1 1 COMPND REVDAT 1 12-AUG-97 1AB1 0 JRNL AUTH A.YAMANO,N.H.HEO,M.M.TEETER JRNL TITL CRYSTAL STRUCTURE OF SER-22/ILE-25 FORM CRAMBIN CONFIRMS JRNL TITL 2 SOLVENT, SIDE CHAIN SUBSTATE CORRELATIONS. JRNL REF J.BIOL.CHEM. V. 272 9597 1997 JRNL REFN ISSN 0021-9258 JRNL PMID 9092482 JRNL DOI 10.1074/JBC.272.15.9597 REMARK 2 REMARK 2 RESOLUTION. 0.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.6 REMARK 3 NUMBER OF REFLECTIONS : 19803 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : DIFFERENCE DENSITY PEAKS REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : NULL 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 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 326 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 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) : 5.50 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) : 0.08 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 17.60 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.014 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.033 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.058 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : 0.010 ; 0.006 REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.010 ; 0.010 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.063 ; 0.050 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.158 ; 0.500 REMARK 3 MULTIPLE TORSION (A) : 0.160 ; 0.500 REMARK 3 H-BOND (X...Y) (A) : 0.158 ; 0.500 REMARK 3 H-BOND (X-H...Y) (A) : 0.000 ; 0.500 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : 0.000 ; 15.000 REMARK 3 PLANAR (DEGREES) : 5.100 ; 3.000 REMARK 3 STAGGERED (DEGREES) : 10.200; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 25.600; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.110 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.110 ; 1.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.136 ; 1.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 0.136 ; 1.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 OVERALL WEIGHT WAS 1/(SIGDEL) AND SIGDEL=8-10(SINTH/L-0.166667) REMARK 3 REMARK 3 THIS STRUCTURE ILLUSTRATES THE CONFIRMATION OF THE ABILITY REMARK 3 OF X-RAY DIFFRACTION TO DETECT SUBSTATES. HERE THE REMARK 3 SUBSTATES WERE PHYSICALLY SEPARATED (TWO SEQUENCE FORMS OF REMARK 3 CRAMBIN) AND SEPARATE STRUCTURES DETERMINED. FURTHER REMARK 3 SUBSTATES ARE EXTENDED FROM PROTEIN TO SURROUNDING SOLVENT. REMARK 4 REMARK 4 1AB1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : OCT-92 REMARK 200 TEMPERATURE (KELVIN) : 150 REMARK 200 PH : 7. 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 RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : LEHMANN-LARSEN REMARK 200 DATA SCALING SOFTWARE : TEXSAN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23165 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.890 REMARK 200 RESOLUTION RANGE LOW (A) : 17.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.8 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : 0.10000 REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.0 REMARK 200 DATA REDUNDANCY IN SHELL : 0.10 REMARK 200 R MERGE FOR SHELL (I) : 0.10000 REMARK 200 R SYM FOR SHELL (I) : 0.15000 REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: ALREADY SOLVED 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 (%): 30.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HPLC PURIFIED SI-CRAMBIN PROTEIN WAS REMARK 280 DISSOLVED AT 25 MG/ML IN 80% ETHANOL/WATER (V/V), AND REMARK 280 EQUILIBRATED AGAINS 60% ETHANOL. AFTER 10 DAYS, THE RESERVOIR WAS REMARK 280 LOWERED TO 50% AND MICROSEEDED BY THE STREAK SEEDING METHOD (CAT REMARK 280 WHISKER). AFTER LOWERING THE RESERVOIR TO 45%, GOOD CRYSTALS WERE REMARK 280 FORMED., PH 7., VAPOR DIFFUSION - HANGING DROP - MICROSEEDING REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 9.20200 REMARK 290 SMTRY3 2 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: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 23 CD GLU A 23 OE2 0.075 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 THR A 2 19.4 L L OUTSIDE RANGE 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 EOH A 66 DBREF 1AB1 A 1 46 UNP P01542 CRAM_CRAAB 1 46 SEQADV 1AB1 SER A 22 UNP P01542 PRO 22 CONFLICT SEQADV 1AB1 ILE A 25 UNP P01542 LEU 25 CONFLICT SEQRES 1 A 46 THR THR CYS CYS PRO SER ILE VAL ALA ARG SER ASN PHE SEQRES 2 A 46 ASN VAL CYS ARG LEU PRO GLY THR SER GLU ALA ILE CYS SEQRES 3 A 46 ALA THR TYR THR GLY CYS ILE ILE ILE PRO GLY ALA THR SEQRES 4 A 46 CYS PRO GLY ASP TYR ALA ASN HET EOH A 66 6 HETNAM EOH ETHANOL FORMUL 2 EOH C2 H6 O HELIX 1 1 ASN A 12 LEU A 18 1 7 HELIX 2 2 ALA A 27 THR A 30 1 4 SHEET 1 A 2 THR A 2 CYS A 3 0 SHEET 2 A 2 ILE A 33 ILE A 34 -1 N ILE A 33 O CYS A 3 SSBOND 1 CYS A 3 CYS A 40 1555 1555 2.03 SSBOND 2 CYS A 4 CYS A 32 1555 1555 2.04 SSBOND 3 CYS A 16 CYS A 26 1555 1555 2.03 SITE 1 AC1 2 ILE A 7 ASN A 46 CRYST1 40.759 18.404 22.273 90.00 90.70 90.00 P 1 21 1 2 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 0.024534 0.000000 0.000300 0.00000 SCALE2 0.000000 0.054336 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044901 0.00000