HEADER CHAPERONE 26-NOV-13 4CGW TITLE SECOND TPR OF SPAGHETTI (RPAP3) BOUND TO HSP90 PEPTIDE SRMEEVD COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA POLYMERASE II-ASSOCIATED PROTEIN 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SECOND TPR, RESIDUES 265-381; COMPND 5 SYNONYM: SPAGHETTI; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HEAT SHOCK PROTEIN HSP 90-ALPHA; COMPND 9 CHAIN: C, D; COMPND 10 FRAGMENT: C-TERMINAL PEPTIDE, RESIDUES 726-732; COMPND 11 SYNONYM: HEAT SHOCK 86 KDA, HSP 86, HSP86, RENAL CARCINOMA ANTIGEN COMPND 12 NY-REN-38, HSP90 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 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS CHAPERONE, R2TP, TAH1, PIH1 EXPDTA X-RAY DIFFRACTION AUTHOR S.M.ROE,M.PAL REVDAT 2 25-JUN-14 4CGW 1 JRNL REVDAT 1 14-MAY-14 4CGW 0 JRNL AUTH M.PAL,M.MORGAN,S.E.PHELPS,S.M.ROE,S.PARRY-MORRIS,J.A.DOWNS, JRNL AUTH 2 S.POLIER,L.H.PEARL,C.PRODROMOU JRNL TITL STRUCTURAL BASIS FOR PHOSPHORYLATION-DEPENDENT RECRUITMENT JRNL TITL 2 OF TEL2 TO HSP90 BY PIH1. JRNL REF STRUCTURE V. 22 805 2014 JRNL REFN ISSN 0969-2126 JRNL PMID 24794838 JRNL DOI 10.1016/J.STR.2014.04.001 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.001 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.255 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.35 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.16 REMARK 3 NUMBER OF REFLECTIONS : 6351 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.2437 REMARK 3 R VALUE (WORKING SET) : 0.2414 REMARK 3 FREE R VALUE : 0.2913 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.6 REMARK 3 FREE R VALUE TEST SET COUNT : 293 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 48.2612 - 3.7803 0.92 3062 144 0.2189 0.2566 REMARK 3 2 3.7803 - 3.0006 0.94 2996 149 0.2884 0.3555 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.30 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.75 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 61.46 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 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 : 0.003 1805 REMARK 3 ANGLE : 0.671 2421 REMARK 3 CHIRALITY : 0.048 262 REMARK 3 PLANARITY : 0.002 325 REMARK 3 DIHEDRAL : 14.084 670 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 4CGW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-NOV-13. REMARK 100 THE PDBE ID CODE IS EBI-59085. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9200 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL (PILATUS 2M) REMARK 200 DETECTOR MANUFACTURER : DECTRIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6373 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.00 REMARK 200 RESOLUTION RANGE LOW (A) : 48.26 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 3.3 REMARK 200 R MERGE (I) : 0.08 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.50 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.4 REMARK 200 R MERGE FOR SHELL (I) : 0.51 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: IN-HOUSE STRUCTURE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.9 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 31.78500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.04500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.25500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.04500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.78500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.25500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 SER A 265 REMARK 465 THR A 266 REMARK 465 SER B 265 REMARK 465 THR B 266 REMARK 465 GLU B 267 REMARK 465 GLY B 268 REMARK 465 GLU B 269 REMARK 465 ARG B 270 REMARK 465 LYS B 271 REMARK 465 GLN B 272 REMARK 465 PRO B 381 REMARK 465 SER D 1 REMARK 465 ARG D 2 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 A 267 CG CD OE1 OE2 REMARK 470 GLU A 269 CG CD OE1 OE2 REMARK 470 ARG A 270 CZ NH1 NH2 REMARK 470 LYS A 271 CG CD CE NZ REMARK 470 GLN A 272 CG CD OE1 NE2 REMARK 470 GLN A 276 CG CD OE1 NE2 REMARK 470 GLN A 277 CG CD OE1 NE2 REMARK 470 LYS A 279 CE NZ REMARK 470 LYS A 294 CE NZ REMARK 470 GLU A 380 CG CD OE1 OE2 REMARK 470 PRO A 381 C O REMARK 470 ILE B 273 CG1 CG2 CD1 REMARK 470 GLU B 274 CG CD OE1 OE2 REMARK 470 GLN B 277 CG CD OE1 NE2 REMARK 470 ASN B 278 CG OD1 ND2 REMARK 470 LYS B 279 CE NZ REMARK 470 LYS B 294 CE NZ REMARK 470 LYS B 331 CE NZ REMARK 470 LYS B 351 CG CD CE NZ REMARK 470 GLU B 380 CG CD OE1 OE2 REMARK 470 SER C 1 OG REMARK 470 ARG C 2 CG CD NE CZ NH1 NH2 REMARK 470 MET D 3 CG SD CE 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 GLN A 276 -81.51 -63.02 REMARK 500 GLN A 277 -27.24 -36.57 REMARK 500 ASP A 312 111.73 64.43 REMARK 500 TYR A 332 -49.99 69.91 REMARK 500 LYS B 279 46.21 -84.51 REMARK 500 ALA B 311 -81.38 -90.56 REMARK 500 LYS B 331 74.78 -112.18 REMARK 500 LEU B 379 -83.75 -68.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4CGQ RELATED DB: PDB REMARK 900 FULL LENGTH TAH1 BOUND TO HSP90 PEPTIDE SRMEEVD REMARK 900 RELATED ID: 4CGU RELATED DB: PDB REMARK 900 FULL LENGTH TAH1 BOUND TO YEAST PIH1 AND HSP90 REMARK 900 PEPTIDE SRMEEVD REMARK 900 RELATED ID: 4CGV RELATED DB: PDB REMARK 900 FIRST TPR OF SPAGHETTI (RPAP3) BOUND TO HSP90 PEPTIDE REMARK 900 SRMEEVD REMARK 900 RELATED ID: 4CHH RELATED DB: PDB REMARK 900 N-TERMINAL DOMAIN OF YEAST PIH1P REMARK 900 RELATED ID: 4CKT RELATED DB: PDB REMARK 900 PIH1 N-TERMINAL DOMAIN REMARK 900 RELATED ID: 4CSE RELATED DB: PDB REMARK 900 PIH N-TERMINAL DOMAIN REMARK 900 RELATED ID: 4CV4 RELATED DB: PDB REMARK 900 PIH N-TERMINAL DOMAIN DBREF 4CGW A 265 381 UNP Q9H6T3 RPAP3_HUMAN 265 381 DBREF 4CGW B 265 381 UNP Q9H6T3 RPAP3_HUMAN 265 381 DBREF 4CGW C 1 7 UNP P07900 HS90A_HUMAN 726 732 DBREF 4CGW D 1 7 UNP P07900 HS90A_HUMAN 726 732 SEQRES 1 A 117 SER THR GLU GLY GLU ARG LYS GLN ILE GLU ALA GLN GLN SEQRES 2 A 117 ASN LYS GLN GLN ALA ILE SER GLU LYS ASP ARG GLY ASN SEQRES 3 A 117 GLY PHE PHE LYS GLU GLY LYS TYR GLU ARG ALA ILE GLU SEQRES 4 A 117 CYS TYR THR ARG GLY ILE ALA ALA ASP GLY ALA ASN ALA SEQRES 5 A 117 LEU LEU PRO ALA ASN ARG ALA MET ALA TYR LEU LYS ILE SEQRES 6 A 117 GLN LYS TYR GLU GLU ALA GLU LYS ASP CYS THR GLN ALA SEQRES 7 A 117 ILE LEU LEU ASP GLY SER TYR SER LYS ALA PHE ALA ARG SEQRES 8 A 117 ARG GLY THR ALA ARG THR PHE LEU GLY LYS LEU ASN GLU SEQRES 9 A 117 ALA LYS GLN ASP PHE GLU THR VAL LEU LEU LEU GLU PRO SEQRES 1 B 117 SER THR GLU GLY GLU ARG LYS GLN ILE GLU ALA GLN GLN SEQRES 2 B 117 ASN LYS GLN GLN ALA ILE SER GLU LYS ASP ARG GLY ASN SEQRES 3 B 117 GLY PHE PHE LYS GLU GLY LYS TYR GLU ARG ALA ILE GLU SEQRES 4 B 117 CYS TYR THR ARG GLY ILE ALA ALA ASP GLY ALA ASN ALA SEQRES 5 B 117 LEU LEU PRO ALA ASN ARG ALA MET ALA TYR LEU LYS ILE SEQRES 6 B 117 GLN LYS TYR GLU GLU ALA GLU LYS ASP CYS THR GLN ALA SEQRES 7 B 117 ILE LEU LEU ASP GLY SER TYR SER LYS ALA PHE ALA ARG SEQRES 8 B 117 ARG GLY THR ALA ARG THR PHE LEU GLY LYS LEU ASN GLU SEQRES 9 B 117 ALA LYS GLN ASP PHE GLU THR VAL LEU LEU LEU GLU PRO SEQRES 1 C 7 SER ARG MET GLU GLU VAL ASP SEQRES 1 D 7 SER ARG MET GLU GLU VAL ASP FORMUL 3 HOH *12(H2 O) HELIX 1 1 GLU A 267 ASN A 278 1 12 HELIX 2 2 GLN A 280 GLU A 295 1 16 HELIX 3 3 LYS A 297 ALA A 311 1 15 HELIX 4 4 ALA A 316 ILE A 329 1 14 HELIX 5 5 TYR A 332 ASP A 346 1 15 HELIX 6 6 TYR A 349 GLY A 364 1 16 HELIX 7 7 LYS A 365 GLU A 380 1 16 HELIX 8 8 GLN B 280 GLU B 295 1 16 HELIX 9 9 LYS B 297 ASP B 312 1 16 HELIX 10 10 ALA B 316 LYS B 328 1 13 HELIX 11 11 LYS B 331 ASP B 346 1 16 HELIX 12 12 TYR B 349 GLY B 364 1 16 HELIX 13 13 LYS B 365 GLU B 380 1 16 CISPEP 1 ASP A 312 GLY A 313 0 2.64 CRYST1 63.570 96.510 52.090 90.00 90.00 90.00 P 21 21 21 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 0.015731 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010362 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019198 0.00000