HEADER TRANSCRIPTION 06-MAY-99 1QGV TITLE HUMAN SPLICEOSOMAL PROTEIN U5-15KD COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPLICEOSOMAL PROTEIN U5-15KD; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FULL-LENGTH; 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 CELL_LINE: HELA; SOURCE 6 CELLULAR_LOCATION: NUCLEUS; SOURCE 7 GENE: U5-15KD; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: TAP106; SOURCE 11 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 12 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 13 EXPRESSION_SYSTEM_VECTOR: PXC35; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PXC35-15K; SOURCE 15 EXPRESSION_SYSTEM_GENE: U5-15KD KEYWDS SPLICEOSOMAL PROTEIN, SNRNP, THIOREDOXIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR K.REUTER,S.NOTTROTT,P.FABRIZIO,R.LUEHRMANN,R.FICNER REVDAT 5 27-DEC-23 1QGV 1 REMARK REVDAT 4 27-NOV-19 1QGV 1 JRNL REVDAT 3 24-FEB-09 1QGV 1 VERSN REVDAT 2 01-APR-03 1QGV 1 JRNL REVDAT 1 12-DEC-99 1QGV 0 JRNL AUTH K.REUTER,S.NOTTROTT,P.FABRIZIO,R.LUHRMANN,R.FICNER JRNL TITL IDENTIFICATION, CHARACTERIZATION AND CRYSTAL STRUCTURE JRNL TITL 2 ANALYSIS OF THE HUMAN SPLICEOSOMAL U5 SNRNP-SPECIFIC 15 KD JRNL TITL 3 PROTEIN. JRNL REF J.MOL.BIOL. V. 294 515 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10610776 JRNL DOI 10.1006/JMBI.1999.3258 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.REUTER,R.FICNER REMARK 1 TITL OVERPRODUCTION, PURIFICATION, CRYSTALLIZATION AND REMARK 1 TITL 2 PRELIMINARY X-RAY DIFFRACTION STUDIES OF THE HUMAN REMARK 1 TITL 3 SPLICEOSOMAL PROTEIN U5-15KD. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 55 888 1999 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 10089325 REMARK 1 DOI 10.1107/S0907444998016151 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 27623 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) : 0.216 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.570 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.46 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2997 REMARK 3 BIN R VALUE (WORKING SET) : 0.3240 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.84 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 138 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 : 1050 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 144 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.90 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) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.630 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.839 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) : 1.760 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.870 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.960 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.890 ; 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 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QGV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAY-99. REMARK 100 THE DEPOSITION ID IS D_1000001009. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-97 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8856 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28054 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 13.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.02900 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26500 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MLPHARE, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M AMMONIUM SULPHATE 0.2 M REMARK 280 HEPES/NAOH, PH 7.6 AT 294 K, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 30.61250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.54600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.61250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.54600 REMARK 290 SMTRY3 4 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 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 MET A 1 REMARK 465 THR A 96 REMARK 465 GLY A 97 REMARK 465 ASN A 98 REMARK 465 ASN A 99 REMARK 465 ASN A 100 REMARK 465 LYS A 101 REMARK 465 LYS A 139 REMARK 465 TYR A 140 REMARK 465 ARG A 141 REMARK 465 TYR A 142 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 SER A 2 OG REMARK 470 TYR A 3 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 74 CB CG CD OE1 OE2 REMARK 470 TYR A 76 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 76 OH REMARK 470 ASP A 77 CB CG OD1 OD2 REMARK 470 THR A 138 CA C O CB OG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 183 O HOH A 218 1.98 REMARK 500 O HOH A 158 O HOH A 254 2.13 REMARK 500 O ASP A 77 O HOH A 278 2.18 REMARK 500 O HOH A 158 O HOH A 192 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 148 O HOH A 244 2555 1.58 REMARK 500 REMARK 500 REMARK: NULL 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 TYR A 3 137.26 178.94 REMARK 500 TYR A 76 -63.09 -19.77 REMARK 500 ASP A 77 -74.74 129.88 REMARK 500 PRO A 133 90.64 -52.74 REMARK 500 ASP A 135 60.87 -108.32 REMARK 500 SER A 137 -32.21 144.66 REMARK 500 REMARK 500 REMARK: NULL DBREF 1QGV A 1 142 UNP P83876 TXN4A_HUMAN 1 142 SEQRES 1 A 142 MET SER TYR MET LEU PRO HIS LEU HIS ASN GLY TRP GLN SEQRES 2 A 142 VAL ASP GLN ALA ILE LEU SER GLU GLU ASP ARG VAL VAL SEQRES 3 A 142 VAL ILE ARG PHE GLY HIS ASP TRP ASP PRO THR CYS MET SEQRES 4 A 142 LYS MET ASP GLU VAL LEU TYR SER ILE ALA GLU LYS VAL SEQRES 5 A 142 LYS ASN PHE ALA VAL ILE TYR LEU VAL ASP ILE THR GLU SEQRES 6 A 142 VAL PRO ASP PHE ASN LYS MET TYR GLU LEU TYR ASP PRO SEQRES 7 A 142 CYS THR VAL MET PHE PHE PHE ARG ASN LYS HIS ILE MET SEQRES 8 A 142 ILE ASP LEU GLY THR GLY ASN ASN ASN LYS ILE ASN TRP SEQRES 9 A 142 ALA MET GLU ASP LYS GLN GLU MET VAL ASP ILE ILE GLU SEQRES 10 A 142 THR VAL TYR ARG GLY ALA ARG LYS GLY ARG GLY LEU VAL SEQRES 11 A 142 VAL SER PRO LYS ASP TYR SER THR LYS TYR ARG TYR FORMUL 2 HOH *144(H2 O) HELIX 1 1 GLY A 11 LEU A 19 1 9 HELIX 2 2 PRO A 36 ILE A 48 1 13 HELIX 3 3 LYS A 109 LYS A 125 1 17 SHEET 1 A 4 ALA A 56 ASP A 62 0 SHEET 2 A 4 VAL A 25 GLY A 31 1 N VAL A 25 O VAL A 57 SHEET 3 A 4 THR A 80 PHE A 85 -1 N PHE A 84 O VAL A 26 SHEET 4 A 4 LYS A 88 ILE A 90 -1 N ILE A 90 O PHE A 83 SHEET 1 B 2 MET A 91 ASP A 93 0 SHEET 2 B 2 LEU A 129 VAL A 131 1 N VAL A 130 O MET A 91 SSBOND 1 CYS A 38 CYS A 79 1555 1555 2.05 CRYST1 61.225 65.092 36.275 90.00 90.00 90.00 P 21 21 2 4 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 0.016333 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015363 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027567 0.00000