HEADER CELL CYCLE 16-OCT-16 5TO5 TITLE STRUCTURE OF THE TPR OLIGOMERIZATION DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN TPR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 2-142; COMPND 5 SYNONYM: MEGATOR,NPC-ASSOCIATED INTRANUCLEAR PROTEIN,TRANSLOCATED COMPND 6 PROMOTER REGION PROTEIN; 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: TPR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TPR OLIGOMERIZATION DOMAIN, RECEPTOR TYROSINE KINASE, MET, ONCOGENIC KEYWDS 2 FUSION KINASES, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR K.PAL,Q.XU,X.E.ZHOU,K.MELCHER,H.E.XU REVDAT 3 06-MAR-24 5TO5 1 REMARK REVDAT 2 01-MAY-19 5TO5 1 JRNL REVDAT 1 18-OCT-17 5TO5 0 JRNL AUTH K.PAL,A.BANDYOPADHYAY,X.E.ZHOU,Q.XU,D.P.MARCIANO, JRNL AUTH 2 J.S.BRUNZELLE,S.YERRUM,P.R.GRIFFIN,G.VANDE WOUDE,K.MELCHER, JRNL AUTH 3 H.E.XU JRNL TITL STRUCTURAL BASIS OF TPR-MEDIATED OLIGOMERIZATION AND JRNL TITL 2 ACTIVATION OF ONCOGENIC FUSION KINASES. JRNL REF STRUCTURE V. 25 867 2017 JRNL REFN ISSN 0969-2126 JRNL PMID 28528776 JRNL DOI 10.1016/J.STR.2017.04.015 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.940 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 11481 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 544 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 21.4123 - 3.9623 0.92 2670 129 0.2020 0.2572 REMARK 3 2 3.9623 - 3.1482 0.96 2734 138 0.2273 0.2731 REMARK 3 3 3.1482 - 2.7512 0.98 2790 137 0.2543 0.2981 REMARK 3 4 2.7512 - 2.5001 0.98 2743 140 0.2722 0.3450 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 1.00 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.55 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 2349 REMARK 3 ANGLE : 0.722 3135 REMARK 3 CHIRALITY : 0.026 355 REMARK 3 PLANARITY : 0.003 415 REMARK 3 DIHEDRAL : 17.522 973 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5TO5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1000223447. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.25 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07812 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17251 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 21.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG1.5K, 0.1M BISTRIS (6.25), PH REMARK 280 6.25, EVAPORATION, TEMPERATURE 295K 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 37.08850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.77550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 37.08850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.77550 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 263 LIES ON A SPECIAL POSITION. 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 ALA B 2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU B 80 CB - CG - CD1 ANGL. DEV. = -17.7 DEGREES 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 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 263 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH B 263 DISTANCE = 6.07 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TO6 RELATED DB: PDB REMARK 900 RELATED ID: 5TO7 RELATED DB: PDB DBREF 5TO5 A 2 142 UNP P12270 TPR_HUMAN 2 142 DBREF 5TO5 B 2 142 UNP P12270 TPR_HUMAN 2 142 SEQADV 5TO5 MET A 55 UNP P12270 PHE 55 ENGINEERED MUTATION SEQADV 5TO5 MET A 113 UNP P12270 PHE 113 ENGINEERED MUTATION SEQADV 5TO5 MET B 55 UNP P12270 PHE 55 ENGINEERED MUTATION SEQADV 5TO5 MET B 113 UNP P12270 PHE 113 ENGINEERED MUTATION SEQRES 1 A 141 ALA ALA VAL LEU GLN GLN VAL LEU GLU ARG THR GLU LEU SEQRES 2 A 141 ASN LYS LEU PRO LYS SER VAL GLN ASN LYS LEU GLU LYS SEQRES 3 A 141 PHE LEU ALA ASP GLN GLN SER GLU ILE ASP GLY LEU LYS SEQRES 4 A 141 GLY ARG HIS GLU LYS PHE LYS VAL GLU SER GLU GLN GLN SEQRES 5 A 141 TYR MET GLU ILE GLU LYS ARG LEU SER HIS SER GLN GLU SEQRES 6 A 141 ARG LEU VAL ASN GLU THR ARG GLU CYS GLN SER LEU ARG SEQRES 7 A 141 LEU GLU LEU GLU LYS LEU ASN ASN GLN LEU LYS ALA LEU SEQRES 8 A 141 THR GLU LYS ASN LYS GLU LEU GLU ILE ALA GLN ASP ARG SEQRES 9 A 141 ASN ILE ALA ILE GLN SER GLN MET THR ARG THR LYS GLU SEQRES 10 A 141 GLU LEU GLU ALA GLU LYS ARG ASP LEU ILE ARG THR ASN SEQRES 11 A 141 GLU ARG LEU SER GLN GLU LEU GLU TYR LEU THR SEQRES 1 B 141 ALA ALA VAL LEU GLN GLN VAL LEU GLU ARG THR GLU LEU SEQRES 2 B 141 ASN LYS LEU PRO LYS SER VAL GLN ASN LYS LEU GLU LYS SEQRES 3 B 141 PHE LEU ALA ASP GLN GLN SER GLU ILE ASP GLY LEU LYS SEQRES 4 B 141 GLY ARG HIS GLU LYS PHE LYS VAL GLU SER GLU GLN GLN SEQRES 5 B 141 TYR MET GLU ILE GLU LYS ARG LEU SER HIS SER GLN GLU SEQRES 6 B 141 ARG LEU VAL ASN GLU THR ARG GLU CYS GLN SER LEU ARG SEQRES 7 B 141 LEU GLU LEU GLU LYS LEU ASN ASN GLN LEU LYS ALA LEU SEQRES 8 B 141 THR GLU LYS ASN LYS GLU LEU GLU ILE ALA GLN ASP ARG SEQRES 9 B 141 ASN ILE ALA ILE GLN SER GLN MET THR ARG THR LYS GLU SEQRES 10 B 141 GLU LEU GLU ALA GLU LYS ARG ASP LEU ILE ARG THR ASN SEQRES 11 B 141 GLU ARG LEU SER GLN GLU LEU GLU TYR LEU THR FORMUL 3 HOH *126(H2 O) HELIX 1 AA1 VAL A 4 LEU A 9 1 6 HELIX 2 AA2 GLU A 10 ASN A 15 1 6 HELIX 3 AA3 PRO A 18 LEU A 141 1 124 HELIX 4 AA4 VAL B 4 LEU B 9 1 6 HELIX 5 AA5 GLU B 10 ASN B 15 1 6 HELIX 6 AA6 PRO B 18 THR B 142 1 125 CRYST1 74.177 51.551 94.980 90.00 107.83 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 0.013481 0.000000 0.004337 0.00000 SCALE2 0.000000 0.019398 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011060 0.00000