HEADER PLANT PROTEIN 22-NOV-02 1N98 OBSLTE 13-NOV-07 1N98 2Q33 TITLE CRYSTAL STRUCTURE OF ALL-D MONELLIN AT 1.8 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: MONELLIN CHAIN A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MONELLIN CHAIN I; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: MONELLIN CHAIN B; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: MONELLIN CHAIN II; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE ENANTIOMERIC PROTEIN WAS CHEMICALLY SOURCE 4 SYNTHESIZED WITH ALL D-AMINO ACIDS. THE SEQUENCE OF THE SOURCE 5 PROTEIN IS NATURALLY FOUND IN DIOSCOREOPHYLLUM CUMMINSII.; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 OTHER_DETAILS: THE ENANTIOMERIC PROTEIN WAS CHEMICALLY SOURCE 9 SYNTHESIZED WITH ALL D-AMINO ACIDS. THE SEQUENCE OF THE SOURCE 10 PROTEIN IS NATURALLY FOUND IN DIOSCOREOPHYLLUM CUMMINSII. KEYWDS ALPHA/BETA, ALL-D PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.-W.HUNG,M.KOHMURA,Y.ARIYOSHI,S.-H.KIM REVDAT 2 13-NOV-07 1N98 1 OBSLTE REVDAT 1 25-DEC-02 1N98 0 JRNL AUTH L.W.HUNG,M.KOHMURA,Y.ARIYOSHI,S.H.KIM JRNL TITL STRUCTURE OF AN ENANTIOMERIC PROTEIN, D-MONELLIN JRNL TITL 2 AT 1.8 A RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 54 494 1998 JRNL REFN ASTM ABCRE6 DK ISSN 0907-4449 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 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) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 735264.360 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.7 REMARK 3 NUMBER OF REFLECTIONS : 8665 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) : 0.175 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.600 REMARK 3 FREE R VALUE TEST SET COUNT : 919 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1040 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : 0.3230 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 118 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 754 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.67000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : 0.46000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.89000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.19 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) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.30 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) : 1.990 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.270 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.480 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.290 ; 2.500 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.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: THE PROTEIN WAS CHEMICALLY REMARK 3 SYNTHESIZED WITH ALL D-AMINO ACIDS. THIS STRUCTURE WAS REMARK 3 DETERMINED AND REFINED WITH L-AMINO ACID PARAMETERS. THE REMARK 3 ACTUAL ASYMMETRIC UNIT SHOULD CONTAIN THE ENANTIOMER OF THE REMARK 3 PROTEIN REPRESENTED BY THIS COORDINATE FILE. REMARK 4 REMARK 4 1N98 COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.101 (2007-05-29) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE RCSB ID CODE IS RCSB017676. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-1994 REMARK 200 TEMPERATURE (KELVIN) : 277.0 REMARK 200 PH : 7.20 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : SYNCHROTRON REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9511 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.0 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM SODIUM PHOSPHATE BUFFER, PH REMARK 280 7.2, 28% PEG 8000 , VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 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 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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH 214 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TYR A 61 N - CA - C ANGL. DEV. =-11.2 DEGREES REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 130 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH 135 DISTANCE = 10.00 ANGSTROMS DBREF 1N98 A 52 94 UNP P02881 MONA_DIOCU 3 45 DBREF 1N98 B 1 48 UNP P02882 MONB_DIOCU 1 48 SEQRES 1 A 43 GLU ILE LYS GLY TYR GLU TYR GLN LEU TYR VAL TYR ALA SEQRES 2 A 43 SER ASP LYS LEU PHE ARG ALA ASP ILE SER GLU ASP TYR SEQRES 3 A 43 LYS THR ARG GLY ARG LYS LEU LEU ARG PHE ASN GLY PRO SEQRES 4 A 43 VAL PRO PRO PRO SEQRES 1 B 48 GLY GLU TRP GLU ILE ILE ASP ILE GLY PRO PHE THR GLN SEQRES 2 B 48 ASN LEU GLY LYS PHE ALA VAL ASP GLU GLU ASN LYS ILE SEQRES 3 B 48 GLY GLN TYR GLY ARG LEU THR PHE ASN LYS VAL ILE ARG SEQRES 4 B 48 PRO CYS MET LYS LYS THR ILE TYR GLU FORMUL 3 HOH *82(H2 O) HELIX 1 1 GLY B 9 GLY B 27 1 19 SHEET 1 A 5 ARG A 82 ASN A 88 0 SHEET 2 A 5 LYS A 67 ASP A 76 -1 N ASP A 72 O LEU A 85 SHEET 3 A 5 ILE A 53 ALA A 64 -1 N LEU A 60 O ALA A 71 SHEET 4 A 5 PHE B 34 TYR B 47 -1 O LYS B 36 N TYR A 63 SHEET 5 A 5 GLU B 4 ILE B 6 -1 N ILE B 6 O CYS B 41 CISPEP 1 GLY A 89 PRO A 90 0 -0.24 CISPEP 2 ARG B 39 PRO B 40 0 -0.09 CRYST1 40.400 32.940 41.110 90.00 96.73 90.00 P 1 2 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 0.024752 0.000000 0.002921 0.00000 SCALE2 0.000000 0.030358 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024494 0.00000