10 20 30 40 50 60 70 80 2G5X - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 23-FEB-06 2G5X
TITLE CRYSTAL STRUCTURE OF LYCHNIN A TYPE 1 RIBOSOME INACTIVATING TITLE 2 PROTEIN (RIP)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOME-INACTIVATING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LYCHNIN; COMPND 5 EC: 3.2.2.22
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LYCHNIS CHALCEDONICA; SOURCE 3 ORGANISM_COMMON: SCARLET LYCHNIS; SOURCE 4 ORGANISM_TAXID: 39855; SOURCE 5 TISSUE: SEEDS
KEYWDS ALPHA-BETA PROTEIN, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.FERMANI,G.FALINI,G.TOSI,A.RIPAMONTI,L.POLITO,A.BOLOGNESI, AUTHOR 2 F.STIRPE
REVDAT 3 24-FEB-09 2G5X 1 VERSN REVDAT 2 13-MAR-07 2G5X 1 JRNL REVDAT 1 06-MAR-07 2G5X 0
JRNL AUTH S.FERMANI,G.FALINI,G.TOSI,A.RIPAMONTI,L.POLITO, JRNL AUTH 2 A.BOLOGNESI,F.STIRPE JRNL TITL CRYSTAL STRUCTURE OF LYCHNIN A TYPE 1 RIBOSOME JRNL TITL 2 INACTIVATING PROTEIN (RIP) JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.BOLOGNESI,L.BARBIERI,A.ABBONDANZA,A.I.FALASCA, REMARK 1 AUTH 2 D.CARNICELLI,M.G.BATTELLI,F.STIRPE REMARK 1 TITL PURIFICATION AND PROPERTIES OF NEW REMARK 1 TITL 2 RIBOSOME-INACTIVATING PROTEINS WITH RNA REMARK 1 TITL 3 N-GLYCOSIDASE ACTIVITY REMARK 1 REF BIOCHIM.BIOPHYS.ACTA V.1087 293 1990 REMARK 1 REFN ISSN 0006-3002 REMARK 1 PMID 2248976 REMARK 1 DOI 10.1016/0167-4781(90)90002-J REMARK 1 REFERENCE 2 REMARK 1 AUTH S.FERMANI,G.FALINI,A.RIPAMONTI,A.BOLOGNESI, REMARK 1 AUTH 2 L.POLITO,F.STIRPE REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION REMARK 1 TITL 2 ANALYSIS OF TWO RIBOSOME-INACTIVATING PROTEINS: REMARK 1 TITL 3 LYCHNIN AND DIANTHIN 30 REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 59 1227 2003 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 12832768 REMARK 1 DOI 10.1107/S0907444903010680
REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 948638.520 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 21878 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) : 0.162 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2170 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2875 REMARK 3 BIN R VALUE (WORKING SET) : 0.1920 REMARK 3 BIN FREE R VALUE : 0.2290 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 305 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1863 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 364 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.65000 REMARK 3 B22 (A**2) : -0.50000 REMARK 3 B33 (A**2) : -1.15000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.14000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.15 REMARK 3 ESD FROM SIGMAA (A) : 0.06 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) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.09 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.64 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) : 0.980 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.350 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.900 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.680 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.46 REMARK 3 BSOL : 80.47 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 2G5X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-MAR-06. REMARK 100 THE RCSB ID CODE IS RCSB036728.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21895 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 29.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 51.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 39.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.08400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 14.200 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: PDB ENTRY 1WUC REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 8000, 0.1M SODIUM REMARK 280 PHOSPHATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K
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 28.66650 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 300 REMARK: THE PROTEIN IS A MONOMER. THE ASYMMETRIC UNIT CONTAIN REMARK 300 ONE MONOMER
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: 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 VAL A 6 95.48 -59.16 REMARK 500 ASN A 41 31.57 -91.26 REMARK 500 ASP A 75 -157.71 -137.52 REMARK 500 PRO A 114 23.10 -73.26 REMARK 500 VAL A 168 -62.04 -108.42 REMARK 500 LYS A 227 99.00 -66.96 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 593 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH A 595 DISTANCE = 7.98 ANGSTROMS
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RL0 RELATED DB: PDB REMARK 900 STRUCTURE OF DIANTHIN 30 REMARK 900 RELATED ID: 1WUC RELATED DB: PDB REMARK 900 STRUCTURE OF BOUGANIN
DBREF 2G5X A 1 234 PDB 2G5X 2G5X 1 234
SEQRES 1 A 234 ARG PRO SER TRP THR VAL ASP SER ASP SER ALA LYS TYR SEQRES 2 A 234 SER SER PHE LEU ASP SER LEU ARG GLU GLU PHE GLY ARG SEQRES 3 A 234 GLY THR PRO LYS VAL CYS ASN ILE PRO VAL THR LYS LYS SEQRES 4 A 234 ALA ASN ASN ASP LYS PHE VAL LEU VAL ASN LEU VAL LEU SEQRES 5 A 234 PRO PHE ASN ARG ASN THR ILE THR LEU ALA PHE ARG ALA SEQRES 6 A 234 SER ASP ALA TYR LEU VAL GLY PHE GLN ASP ARG ASP SER SEQRES 7 A 234 LYS THR ASN LYS LEU ARG ALA ASN PHE PHE SER ASP GLU SEQRES 8 A 234 TYR ARG ALA LEU SER GLY LYS TYR LYS SER ILE PHE THR SEQRES 9 A 234 ASP ALA GLU VAL LEU ALA PRO ALA LEU PRO CYS ALA SER SEQRES 10 A 234 THR TYR THR ASP LEU GLN ASN LYS ALA GLY VAL SER ARG SEQRES 11 A 234 GLU LYS LEU SER LEU GLY VAL SER SER LEU GLN THR ALA SEQRES 12 A 234 PHE THR ALA VAL TYR GLY LYS VAL PHE THR GLY LYS ASN SEQRES 13 A 234 VAL ALA LYS PHE ALA LEU ILE SER ILE GLN MET VAL ALA SEQRES 14 A 234 GLU ALA ALA ARG PHE LYS TYR ILE GLU ASP GLN VAL ILE SEQRES 15 A 234 ASN ARG GLY MET TYR SER SER PHE GLU ALA GLY ALA ARG SEQRES 16 A 234 ILE THR LEU LEU GLU ASN ASN TRP SER LYS ILE SER GLU SEQRES 17 A 234 GLN TYR HIS LYS SER CYS LYS LEU GLY GLY GLY GLN PHE SEQRES 18 A 234 THR GLU GLU GLU MET LYS LEU GLY LEU LEU LEU TYR ASN
FORMUL 2 HOH *364(H2 O)
HELIX 1 1 ASP A 9 ARG A 26 1 18 HELIX 2 2 ALA A 40 ASP A 43 5 4 HELIX 3 3 GLU A 91 SER A 96 1 6 HELIX 4 4 LYS A 98 PHE A 103 1 6 HELIX 5 5 THR A 118 GLY A 127 1 10 HELIX 6 6 GLY A 136 ALA A 146 1 11 HELIX 7 7 THR A 153 VAL A 168 1 16 HELIX 8 8 VAL A 168 PHE A 174 1 7 HELIX 9 9 PHE A 174 GLY A 185 1 12 HELIX 10 10 ALA A 192 ASN A 202 1 11 HELIX 11 11 ASN A 202 HIS A 211 1 10
SHEET 1 A 6 SER A 3 THR A 5 0 SHEET 2 A 6 PHE A 45 VAL A 51 1 O ASN A 49 N TRP A 4 SHEET 3 A 6 THR A 58 ARG A 64 -1 O LEU A 61 N VAL A 48 SHEET 4 A 6 TYR A 69 ARG A 76 -1 O TYR A 69 N ARG A 64 SHEET 5 A 6 LEU A 83 PHE A 87 -1 O ARG A 84 N ASP A 75 SHEET 6 A 6 VAL A 108 LEU A 109 1 O VAL A 108 N ALA A 85
SSBOND 1 CYS A 32 CYS A 214 1555 1555 2.03
CRYST1 35.247 57.333 53.230 90.00 106.25 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 0.028371 0.000000 0.008271 0.00000
SCALE2 0.000000 0.017442 0.000000 0.00000
SCALE3 0.000000 0.000000 0.019568 0.00000