HEADER ISOMERASE 10-OCT-02 1MZW TITLE CRYSTAL STRUCTURE OF A U4/U6 SNRNP COMPLEX BETWEEN HUMAN SPLICEOSOMAL TITLE 2 CYCLOPHILIN H AND A U4/U6-60K PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: U-SNRNP-ASSOCIATED CYCLOPHILIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYCLOPHILIN H; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: U4/U6 SNRNP 60KDA PROTEIN; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: RESIDUES 107-137, INTERNAL DOMAIN; COMPND 10 SYNONYM: WD SPLICING FACTOR PRP4, HPRP4, U4/U6 SMALL NUCLEAR COMPND 11 RIBONUCLEO PROTEIN PRP4; COMPND 12 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-4T-2; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: PEPTIDE B106-B136 WAS CHEMICALLY SYNTHESIZED KEYWDS CYCLOPHILIN, PEPTIDYL-PROLYL-CIS/TRANS ISOMERASE, SPLICEOSOME, SNRNP, KEYWDS 2 U4/U6-60K PROTEIN, WD PROTEIN, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR U.REIDT,M.C.WAHL,D.S.HOROWITZ,R.LUEHRMANN,R.FICNER REVDAT 4 14-FEB-24 1MZW 1 SEQADV REVDAT 3 24-FEB-09 1MZW 1 VERSN REVDAT 2 02-SEP-03 1MZW 1 DBREF REVDAT 1 19-AUG-03 1MZW 0 JRNL AUTH U.REIDT,M.C.WAHL,D.FASSHAUER,D.S.HOROWITZ,R.LUEHRMANN, JRNL AUTH 2 R.FICNER JRNL TITL CRYSTAL STRUCTURE OF A COMPLEX BETWEEN HUMAN SPLICEOSOMAL JRNL TITL 2 CYCLOPHILIN H AND A U4/U6 SNRNP-60K PEPTIDE JRNL REF J.MOL.BIOL. V. 331 45 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12875835 JRNL DOI 10.1016/S0022-2836(03)00684-3 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 13458 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) : 0.195 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1344 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 : 1565 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 260 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) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.280 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 1MZW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-02. REMARK 100 THE DEPOSITION ID IS D_1000017344. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRROR REMARK 200 OPTICS : OSMIC MIRRORS 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 : 55492 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.23600 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1QOI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, MAGNESIUM ACETATE, HEPES, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294.0K 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 29.76300 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 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: DIMERIC 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 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 ALA A 2 REMARK 465 VAL A 3 REMARK 465 ALA A 4 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 GLU B 106 CG CD OE1 OE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASN A 5 N CB CG OD1 ND2 REMARK 480 SER A 7 OG REMARK 480 PRO A 8 CG REMARK 480 VAL A 17 CG2 REMARK 480 GLN A 22 CG CD OE1 NE2 REMARK 480 VAL A 24 CA REMARK 480 MET A 27 CG REMARK 480 LYS A 28 CA REMARK 480 LYS A 38 NZ REMARK 480 GLU A 50 CD OE2 REMARK 480 ARG A 52 CG CD NE CZ NH2 REMARK 480 LYS A 53 CD CE NZ REMARK 480 ASP A 54 CB REMARK 480 GLY A 55 CA REMARK 480 VAL A 56 CG2 REMARK 480 ILE A 58 CD1 REMARK 480 THR A 64 OG1 REMARK 480 LYS A 70 CD CE REMARK 480 ILE A 74 CG2 CD1 REMARK 480 GLN A 75 CG NE2 REMARK 480 ASP A 83 CB REMARK 480 THR A 85 CA REMARK 480 ARG A 92 CB CG CD NE CZ NH1 NH2 REMARK 480 GLY A 93 CA REMARK 480 LYS A 101 CD REMARK 480 ARG A 103 CD NE CZ NH1 REMARK 480 LYS A 130 CD CE NZ REMARK 480 CYS A 131 CB REMARK 480 ASP A 132 CB CG OD2 REMARK 480 LYS A 137 CE NZ REMARK 480 ILE A 144 CD1 REMARK 480 VAL A 150 CA REMARK 480 VAL A 157 CG1 REMARK 480 PRO A 161 CG REMARK 480 ASN A 162 ND2 REMARK 480 LYS A 166 CD REMARK 480 LEU A 167 CD2 REMARK 480 SER A 172 OG 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 SER A 6 42.17 -89.41 REMARK 500 VAL A 35 -42.27 -132.50 REMARK 500 PHE A 72 -69.81 -137.47 REMARK 500 ARG A 92 104.28 74.89 REMARK 500 HIS A 104 55.65 -90.85 REMARK 500 CYS A 131 65.76 -118.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QOI RELATED DB: PDB REMARK 900 U4/U6 SNRNP-SPECIFIC CYCLOPHILIN SNUCYP-20 DBREF 1MZW A 1 177 UNP O43447 PPIH_HUMAN 1 177 DBREF 1MZW B 106 136 UNP O43172 PRP4_HUMAN 107 137 SEQADV 1MZW SER B 110 UNP O43172 CYS 111 CONFLICT SEQRES 1 A 177 MET ALA VAL ALA ASN SER SER PRO VAL ASN PRO VAL VAL SEQRES 2 A 177 PHE PHE ASP VAL SER ILE GLY GLY GLN GLU VAL GLY ARG SEQRES 3 A 177 MET LYS ILE GLU LEU PHE ALA ASP VAL VAL PRO LYS THR SEQRES 4 A 177 ALA GLU ASN PHE ARG GLN PHE CYS THR GLY GLU PHE ARG SEQRES 5 A 177 LYS ASP GLY VAL PRO ILE GLY TYR LYS GLY SER THR PHE SEQRES 6 A 177 HIS ARG VAL ILE LYS ASP PHE MET ILE GLN GLY GLY ASP SEQRES 7 A 177 PHE VAL ASN GLY ASP GLY THR GLY VAL ALA SER ILE TYR SEQRES 8 A 177 ARG GLY PRO PHE ALA ASP GLU ASN PHE LYS LEU ARG HIS SEQRES 9 A 177 SER ALA PRO GLY LEU LEU SER MET ALA ASN SER GLY PRO SEQRES 10 A 177 SER THR ASN GLY CYS GLN PHE PHE ILE THR CYS SER LYS SEQRES 11 A 177 CYS ASP TRP LEU ASP GLY LYS HIS VAL VAL PHE GLY LYS SEQRES 12 A 177 ILE ILE ASP GLY LEU LEU VAL MET ARG LYS ILE GLU ASN SEQRES 13 A 177 VAL PRO THR GLY PRO ASN ASN LYS PRO LYS LEU PRO VAL SEQRES 14 A 177 VAL ILE SER GLN CYS GLY GLU MET SEQRES 1 B 31 GLU VAL LYS ALA SER LEU ARG ALA LEU GLY GLU PRO ILE SEQRES 2 B 31 THR LEU PHE GLY GLU GLY PRO ALA GLU ARG ARG GLU ARG SEQRES 3 B 31 LEU ARG ASN ILE LEU FORMUL 3 HOH *260(H2 O) HELIX 1 1 VAL A 36 GLY A 49 1 14 HELIX 2 2 CYS A 131 ASP A 135 5 5 HELIX 3 3 GLY A 147 ASN A 156 1 10 HELIX 4 4 GLY A 160 LYS A 164 5 5 HELIX 5 5 GLU B 106 LEU B 114 1 9 HELIX 6 6 GLY B 124 LEU B 136 1 13 SHEET 1 A 9 ARG A 67 ILE A 69 0 SHEET 2 A 9 MET A 73 GLY A 76 -1 O MET A 73 N ILE A 69 SHEET 3 A 9 PHE A 124 THR A 127 -1 O ILE A 126 N ILE A 74 SHEET 4 A 9 LEU A 109 MET A 112 -1 N SER A 111 O PHE A 125 SHEET 5 A 9 VAL A 140 ASP A 146 -1 O GLY A 142 N LEU A 110 SHEET 6 A 9 GLN A 22 LEU A 31 -1 N LYS A 28 O ASP A 146 SHEET 7 A 9 VAL A 12 ILE A 19 -1 N VAL A 13 O ILE A 29 SHEET 8 A 9 VAL A 169 GLU A 176 -1 O GLN A 173 N ASP A 16 SHEET 9 A 9 THR B 119 LEU B 120 -1 O THR B 119 N GLU A 176 SHEET 1 B 2 ARG A 52 LYS A 53 0 SHEET 2 B 2 VAL A 56 PRO A 57 -1 O VAL A 56 N LYS A 53 CRYST1 44.369 59.526 47.040 90.00 110.65 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 0.022538 0.000000 0.008494 0.00000 SCALE2 0.000000 0.016799 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022718 0.00000