HEADER TRANSFERASE 15-APR-02 1GY0 TITLE CRYSTAL STRUCTURE OF THE EUCARYOTIC TITLE 2 MONO-ADP-RIBOSYLTRANSFERASE ART2.2; CRYSTAL FORM C (P3121) COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-CELL ECTO-ADP-RIBOSYLTRANSFERASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADP-RIBOSYLTRANSFERASE, T-CELL COMPND 5 NAD(P)(+)--ARGININE ADP-RIBOSYLTRANSFERASE 2, T-CELL COMPND 6 MONO(ADP-RIBOSYL)TRANSFERASE 2, ALLOANTIGEN RT6.2, T-CELL COMPND 7 SURFACE PROTEIN RT6.2; COMPND 8 EC: 2.4.2.31; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: NM522 KEYWDS TRANSFERASE, ADP-RIBOSYLTRANSFERASE, IMMUNO-REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR C.MUELLER-DIECKMANN,G.E.SCHULZ REVDAT 2 24-FEB-09 1GY0 1 VERSN REVDAT 1 26-SEP-02 1GY0 0 JRNL AUTH C.MUELLER-DIECKMANN,H.RITTER,F.HAAG,F.KOCH-NOLTE, JRNL AUTH 2 G.E.SCHULZ JRNL TITL STRUCTURE OF THE ECTO-ADP-RIBOSYL TRANSFERASE JRNL TITL 2 ART2.2 FROM RAT JRNL REF J.MOL.BIOL. V. 322 687 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12270706 JRNL DOI 10.1016/S0022-2836(02)00818-5 REMARK 2 REMARK 2 RESOLUTION. 2.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 17765 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) : 0.209 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.8 REMARK 3 FREE R VALUE TEST SET COUNT : 855 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2767 REMARK 3 BIN R VALUE (WORKING SET) : 0.232 REMARK 3 BIN FREE R VALUE : 0.298 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 146 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1822 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 145 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.1 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.4 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.14 REMARK 3 B22 (A**2) : -1.14 REMARK 3 B33 (A**2) : 2.27 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.16 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.5 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.3 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.86 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) : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 50.77 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 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GY0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-APR-02. REMARK 100 THE PDBE ID CODE IS EBI-9715. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.30 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 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 : 17787 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.080 REMARK 200 RESOLUTION RANGE LOW (A) : 36.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37000 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS PH8.3, REMARK 280 200 MM LI2SO4, 22 % PEG4000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.84533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.69067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 51.69067 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.84533 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 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 LEU A 1 REMARK 465 THR A 2 REMARK 465 GLY A 3 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 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 ASP A 8 -154.92 -152.95 REMARK 500 ASN A 40 81.16 -151.62 REMARK 500 ASN A 96 76.33 -169.56 REMARK 500 HIS A 101 50.60 -106.30 REMARK 500 TYR A 102 26.20 -141.27 REMARK 500 ASP A 120 130.28 -39.36 REMARK 500 GLU A 180 31.35 -80.13 REMARK 500 PHE A 181 -25.44 -147.42 REMARK 500 ASN A 207 28.80 -142.09 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GXY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE EUCARYOTIC MONO-ADP REMARK 900 -RIBOSYLTRANSFERASE ART2.2 REMARK 900 RELATED ID: 1GXZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE EUCARYOTIC MONO-ADP REMARK 900 -RIBOSYLTRANSFERASE ART2.2 DBREF 1GY0 A 1 226 UNP P20974 NRT2_RAT 21 246 SEQRES 1 A 226 LEU THR GLY PRO LEU MET LEU ASP THR ALA PRO ASN ALA SEQRES 2 A 226 PHE ASP ASP GLN TYR GLU GLY CYS VAL ASN LYS MET GLU SEQRES 3 A 226 GLU LYS ALA PRO LEU LEU LEU GLN GLU ASP PHE ASN MET SEQRES 4 A 226 ASN ALA LYS LEU LYS VAL ALA TRP GLU GLU ALA LYS LYS SEQRES 5 A 226 ARG TRP ASN ASN ILE LYS PRO SER ARG SER TYR PRO LYS SEQRES 6 A 226 GLY PHE ASN ASP PHE HIS GLY THR ALA LEU VAL ALA TYR SEQRES 7 A 226 THR GLY SER ILE ALA VAL ASP PHE ASN ARG ALA VAL ARG SEQRES 8 A 226 GLU PHE LYS GLU ASN PRO GLY GLN PHE HIS TYR LYS ALA SEQRES 9 A 226 PHE HIS TYR TYR LEU THR ARG ALA LEU GLN LEU LEU SER SEQRES 10 A 226 ASN GLY ASP CYS HIS SER VAL TYR ARG GLY THR LYS THR SEQRES 11 A 226 ARG PHE HIS TYR THR GLY ALA GLY SER VAL ARG PHE GLY SEQRES 12 A 226 GLN PHE THR SER SER SER LEU SER LYS LYS VAL ALA GLN SEQRES 13 A 226 SER GLN GLU PHE PHE SER ASP HIS GLY THR LEU PHE ILE SEQRES 14 A 226 ILE LYS THR CYS LEU GLY VAL TYR ILE LYS GLU PHE SER SEQRES 15 A 226 PHE ARG PRO ASP GLN GLU GLU VAL LEU ILE PRO GLY TYR SEQRES 16 A 226 GLU VAL TYR GLN LYS VAL ARG THR GLN GLY TYR ASN GLU SEQRES 17 A 226 ILE PHE LEU ASP SER PRO LYS ARG LYS LYS SER ASN TYR SEQRES 18 A 226 ASN CYS LEU TYR SER FORMUL 2 HOH *145(H2 O1) HELIX 1 1 VAL A 22 MET A 39 1 18 HELIX 2 2 ALA A 41 ILE A 57 1 17 HELIX 3 3 ASN A 68 THR A 79 1 12 HELIX 4 4 SER A 81 GLU A 92 1 12 HELIX 5 5 LYS A 103 LEU A 116 1 14 HELIX 6 6 LYS A 152 GLN A 156 1 5 SHEET 1 AA 3 LEU A 5 LEU A 7 0 SHEET 2 AA 3 ARG A 131 HIS A 133 1 N HIS A 133 O LEU A 5 SHEET 1 AB 7 HIS A 122 THR A 128 0 SHEET 2 AB 6 THR A 166 THR A 172 -1 O THR A 166 N THR A 128 SHEET 3 AB 9 GLU A 208 ARG A 216 1 O ILE A 209 N ILE A 169 SHEET 4 AB 9 GLU A 196 GLN A 204 -1 O VAL A 197 N LYS A 215 SHEET 5 AB 5 VAL A 140 ARG A 141 -1 O VAL A 140 N TYR A 198 SHEET 1 AC 2 VAL A 176 TYR A 177 0 SHEET 2 AC 4 GLU A 189 ILE A 192 -1 O LEU A 191 N VAL A 176 SHEET 3 AC 5 THR A 146 LEU A 150 -1 O SER A 148 N VAL A 190 SSBOND 1 CYS A 21 CYS A 223 1555 1555 2.04 SSBOND 2 CYS A 121 CYS A 173 1555 1555 2.03 CRYST1 81.466 81.466 77.536 90.00 90.00 120.00 P 31 2 1 6 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 0.012275 0.007087 0.000000 0.00000 SCALE2 0.000000 0.014174 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012897 0.00000