HEADER RNA BINDING PROTEIN 30-MAR-10 3MDF TITLE CRYSTAL STRUCTURE OF THE RRM DOMAIN OF CYCLOPHILIN 33 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RNA-RECOGNITION MOTIF (UNP RESIDUES:1-83); COMPND 5 SYNONYM: PPIASE E, ROTAMASE E, CYCLOPHILIN E, CYCLOPHILIN-33; COMPND 6 EC: 5.2.1.8; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PPIE, CYP33; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2 DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28 LIC KEYWDS RRM DOMAIN, PHD FINGER, CYP33, MLL, RNA BINDING PROTEIN, ISOMERASE, KEYWDS 2 MRNA PROCESSING, MRNA SPLICING, NUCLEUS, RNA-BINDING, ROTAMASE, KEYWDS 3 SPLICEOSOME EXPDTA X-RAY DIFFRACTION AUTHOR R.A.HOM,P.Y.CHANG,S.ROY,C.A.MUSSLEMAN,K.C.GLASS,A.I.SELEZNEVIA, AUTHOR 2 O.GOZANI,R.F.ISMAGILOV,M.L.CLEARY,T.G.KUTATELADZE REVDAT 3 06-SEP-23 3MDF 1 SEQADV REVDAT 2 10-OCT-12 3MDF 1 JRNL VERSN REVDAT 1 12-MAY-10 3MDF 0 JRNL AUTH R.A.HOM,P.Y.CHANG,S.ROY,C.A.MUSSELMAN,K.C.GLASS, JRNL AUTH 2 A.I.SELEZNEVA,O.GOZANI,R.F.ISMAGILOV,M.L.CLEARY, JRNL AUTH 3 T.G.KUTATELADZE JRNL TITL MOLECULAR MECHANISM OF MLL PHD3 AND RNA RECOGNITION BY THE JRNL TITL 2 CYP33 RRM DOMAIN. JRNL REF J.MOL.BIOL. V. 400 145 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20460131 JRNL DOI 10.1016/J.JMB.2010.04.067 REMARK 2 REMARK 2 RESOLUTION. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.100 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 15587 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) : 0.210 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2895 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.92 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.05 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2767 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 331 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 : 1304 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) : 26.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.41600 REMARK 3 B22 (A**2) : -7.00500 REMARK 3 B33 (A**2) : 3.58900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 8.91700 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.23 REMARK 3 LOW RESOLUTION CUTOFF (A) : 1.85 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.25 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.340 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.14 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.830 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 3MDF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000058408. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NOIR1 REMARK 200 DETECTOR MANUFACTURER : MBC DETECTOR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15587 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 26.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.760 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.41 REMARK 200 R MERGE FOR SHELL (I) : 0.23200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: PDB ENTRY 1CVJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES AND 1.0 M TRI-SODIUM REMARK 280 DEHYDRATE CITRATE PH 7.6, MICROCAPILLARY, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 42.92000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.26000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.92000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.26000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 GLY B -1 REMARK 465 SER B 0 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 ASN B 80 CB REMARK 470 ALA B 82 CB 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 GLU A 44 10.64 80.73 REMARK 500 ALA B 2 123.92 -32.35 REMARK 500 REMARK 500 REMARK: NULL DBREF 3MDF A 1 83 UNP Q9UNP9 PPIE_HUMAN 1 83 DBREF 3MDF B 1 83 UNP Q9UNP9 PPIE_HUMAN 1 83 SEQADV 3MDF GLY A -1 UNP Q9UNP9 EXPRESSION TAG SEQADV 3MDF SER A 0 UNP Q9UNP9 EXPRESSION TAG SEQADV 3MDF GLY B -1 UNP Q9UNP9 EXPRESSION TAG SEQADV 3MDF SER B 0 UNP Q9UNP9 EXPRESSION TAG SEQRES 1 A 85 GLY SER MET ALA THR THR LYS ARG VAL LEU TYR VAL GLY SEQRES 2 A 85 GLY LEU ALA GLU GLU VAL ASP ASP LYS VAL LEU HIS ALA SEQRES 3 A 85 ALA PHE ILE PRO PHE GLY ASP ILE THR ASP ILE GLN ILE SEQRES 4 A 85 PRO LEU ASP TYR GLU THR GLU LYS HIS ARG GLY PHE ALA SEQRES 5 A 85 PHE VAL GLU PHE GLU LEU ALA GLU ASP ALA ALA ALA ALA SEQRES 6 A 85 ILE ASP ASN MET ASN GLU SER GLU LEU PHE GLY ARG THR SEQRES 7 A 85 ILE ARG VAL ASN LEU ALA LYS SEQRES 1 B 85 GLY SER MET ALA THR THR LYS ARG VAL LEU TYR VAL GLY SEQRES 2 B 85 GLY LEU ALA GLU GLU VAL ASP ASP LYS VAL LEU HIS ALA SEQRES 3 B 85 ALA PHE ILE PRO PHE GLY ASP ILE THR ASP ILE GLN ILE SEQRES 4 B 85 PRO LEU ASP TYR GLU THR GLU LYS HIS ARG GLY PHE ALA SEQRES 5 B 85 PHE VAL GLU PHE GLU LEU ALA GLU ASP ALA ALA ALA ALA SEQRES 6 B 85 ILE ASP ASN MET ASN GLU SER GLU LEU PHE GLY ARG THR SEQRES 7 B 85 ILE ARG VAL ASN LEU ALA LYS FORMUL 3 HOH *144(H2 O) HELIX 1 1 ASP A 18 ILE A 27 1 10 HELIX 2 2 PRO A 28 GLY A 30 5 3 HELIX 3 3 LEU A 56 ASN A 68 1 13 HELIX 4 4 ASP B 18 ILE B 27 1 10 HELIX 5 5 PRO B 28 GLY B 30 5 3 HELIX 6 6 LEU B 56 ASN B 68 1 13 SHEET 1 A 4 ILE A 32 GLN A 36 0 SHEET 2 A 4 PHE A 49 PHE A 54 -1 O GLU A 53 N ASP A 34 SHEET 3 A 4 VAL A 7 GLY A 11 -1 N LEU A 8 O VAL A 52 SHEET 4 A 4 ARG A 78 LEU A 81 -1 O ASN A 80 N TYR A 9 SHEET 1 B 2 GLU A 71 LEU A 72 0 SHEET 2 B 2 ARG A 75 THR A 76 -1 O ARG A 75 N LEU A 72 SHEET 1 C 4 ILE B 32 GLN B 36 0 SHEET 2 C 4 PHE B 49 PHE B 54 -1 O GLU B 53 N ASP B 34 SHEET 3 C 4 VAL B 7 GLY B 11 -1 N LEU B 8 O VAL B 52 SHEET 4 C 4 ARG B 78 LEU B 81 -1 O ASN B 80 N TYR B 9 SHEET 1 D 2 GLU B 71 LEU B 72 0 SHEET 2 D 2 ARG B 75 THR B 76 -1 O ARG B 75 N LEU B 72 CRYST1 85.840 40.520 65.660 90.00 127.06 90.00 C 1 2 1 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 0.011650 0.000000 0.008798 0.00000 SCALE2 0.000000 0.024679 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019085 0.00000