HEADER TRANSCRIPTION, CELL CYCLE 31-AUG-04 1XBS TITLE CRYSTAL STRUCTURE OF HUMAN DIM2: A DIM1-LIKE PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIM1-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIM2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH5A; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX4T KEYWDS SPLICEOSOMAL PROTEIN, CELL CYCLE, THIOREDOXIN, SNRNP, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR F.SIMEONI,A.ARVAI,K.-P.HOPFNER,P.BELLO,C.GONDEAU,F.HEITZ,J.TAINER, AUTHOR 2 G.DIVITA REVDAT 6 14-FEB-24 1XBS 1 REMARK REVDAT 5 11-OCT-17 1XBS 1 REMARK REVDAT 4 24-FEB-09 1XBS 1 VERSN REVDAT 3 12-JUN-07 1XBS 1 REMARK REVDAT 2 13-SEP-05 1XBS 1 JRNL REVDAT 1 30-AUG-05 1XBS 0 JRNL AUTH F.SIMEONI,A.ARVAI,P.BELLO,C.GONDEAU,K.-P.HOPFNER,P.NEYROZ, JRNL AUTH 2 F.HEITZ,J.TAINER,G.DIVITA JRNL TITL BIOCHEMICAL CHARACTERIZATION AND CRYSTAL STRUCTURE OF A DIM1 JRNL TITL 2 FAMILY ASSOCIATED PROTEIN: DIM2 JRNL REF BIOCHEMISTRY V. 44 11997 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 16142897 JRNL DOI 10.1021/BI050427O REMARK 2 REMARK 2 RESOLUTION. 2.50 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : -3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 6538 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.305 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL 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 : 1089 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 21 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : NULL 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XBS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1000030178. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-00 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 7.2 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 : NULL REMARK 200 OPTICS : NULL 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 : 6538 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 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 <I/SIGMA(I)> 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 (%): 58.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, SODIUM CHLORIDE, REMARK 280 EDTA, TRIS-HCL, PH 7.2, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.16700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.08000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.08000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.08350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.08000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.08000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.25050 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.08000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.08000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 15.08350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.08000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.08000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 45.25050 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 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 30.16700 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 ASN A 138 REMARK 465 ILE A 139 REMARK 465 PRO A 140 REMARK 465 LYS A 141 REMARK 465 TYR A 142 REMARK 465 ASP A 143 REMARK 465 LEU A 144 REMARK 465 LEU A 145 REMARK 465 TYR A 146 REMARK 465 GLN A 147 REMARK 465 ASP A 148 REMARK 465 ILE A 149 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 109 CG CD CE NZ 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 PRO A 6 171.00 -57.92 REMARK 500 GLU A 23 -6.69 73.65 REMARK 500 SER A 53 -38.89 -39.13 REMARK 500 TYR A 94 -95.35 29.51 REMARK 500 ILE A 134 -150.19 -123.54 REMARK 500 PRO A 136 -122.30 -63.53 REMARK 500 REMARK 500 REMARK: NULL DBREF 1XBS A 1 149 GB 45594298 AAS68520 1 149 SEQRES 1 A 149 MET SER PHE LEU LEU PRO LYS LEU THR SER LYS LYS GLU SEQRES 2 A 149 VAL ASP GLN ALA ILE LYS SER THR ALA GLU LYS VAL LEU SEQRES 3 A 149 VAL LEU ARG PHE GLY ARG ASP GLU ASP PRO VAL CYS LEU SEQRES 4 A 149 GLN LEU ASP ASP ILE LEU SER LYS THR SER SER ASP LEU SEQRES 5 A 149 SER LYS MET ALA ALA ILE TYR LEU VAL ASP VAL ASP GLN SEQRES 6 A 149 THR ALA VAL TYR THR GLN TYR PHE ASP ILE SER TYR ILE SEQRES 7 A 149 PRO SER THR VAL PHE PHE PHE ASN GLY GLN HIS MET LYS SEQRES 8 A 149 VAL ASP TYR GLY SER PRO ASP HIS THR LYS PHE VAL GLY SEQRES 9 A 149 SER PHE LYS THR LYS GLN ASP PHE ILE ASP LEU ILE GLU SEQRES 10 A 149 VAL ILE TYR ARG GLY ALA MET ARG GLY LYS LEU ILE VAL SEQRES 11 A 149 GLN SER PRO ILE ASP PRO LYS ASN ILE PRO LYS TYR ASP SEQRES 12 A 149 LEU LEU TYR GLN ASP ILE FORMUL 2 HOH *21(H2 O) HELIX 1 1 SER A 10 THR A 21 1 12 HELIX 2 2 ASP A 35 SER A 53 1 19 HELIX 3 3 THR A 66 PHE A 73 1 8 HELIX 4 4 THR A 108 ARG A 125 1 18 SHEET 1 A 5 LYS A 7 LEU A 8 0 SHEET 2 A 5 ALA A 56 ASP A 62 1 O LEU A 60 N LEU A 8 SHEET 3 A 5 VAL A 25 GLY A 31 1 N GLY A 31 O VAL A 61 SHEET 4 A 5 SER A 80 PHE A 85 -1 O SER A 80 N PHE A 30 SHEET 5 A 5 PHE A 102 VAL A 103 -1 O PHE A 102 N THR A 81 SHEET 1 B 6 LYS A 7 LEU A 8 0 SHEET 2 B 6 ALA A 56 ASP A 62 1 O LEU A 60 N LEU A 8 SHEET 3 B 6 VAL A 25 GLY A 31 1 N GLY A 31 O VAL A 61 SHEET 4 B 6 SER A 80 PHE A 85 -1 O SER A 80 N PHE A 30 SHEET 5 B 6 GLN A 88 VAL A 92 -1 O MET A 90 N PHE A 83 SHEET 6 B 6 ILE A 129 VAL A 130 1 O VAL A 130 N LYS A 91 CISPEP 1 ILE A 78 PRO A 79 0 -0.02 CRYST1 78.160 78.160 60.334 90.00 90.00 90.00 P 41 21 2 8 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 0.012794 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012794 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016574 0.00000