HEADER CHAPERONE 28-SEP-16 5LYP TITLE CRYSTAL STRUCTURE OF THE TPR DOMAIN OF SGT2. COMPND MOL_ID: 1; COMPND 2 MOLECULE: SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT-CONTAINING COMPND 3 PROTEIN 2; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: SGT/UBP,VIRAL PROTEIN U-BINDING PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: SGT2, YOR007C, UNF346; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28 KEYWDS CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR E.M.KRYSZTOFINSKA,R.M.L.MORGAN,A.THAPALIYA,N.J.EVANS,J.W.MURRAY, AUTHOR 2 S.MARTINEZ-LUMBRERAS,R.L.ISAACSON REVDAT 3 17-JAN-24 5LYP 1 JRNL REVDAT 2 08-NOV-17 5LYP 1 JRNL REVDAT 1 25-OCT-17 5LYP 0 JRNL AUTH E.M.KRYSZTOFINSKA,N.J.EVANS,A.THAPALIYA,J.W.MURRAY, JRNL AUTH 2 R.M.L.MORGAN,S.MARTINEZ-LUMBRERAS,R.L.ISAACSON JRNL TITL STRUCTURE AND INTERACTIONS OF THE TPR DOMAIN OF SGT2 WITH JRNL TITL 2 YEAST CHAPERONES AND YBR137WP. JRNL REF FRONT MOL BIOSCI V. 4 68 2017 JRNL REFN ESSN 2296-889X JRNL PMID 29075633 JRNL DOI 10.3389/FMOLB.2017.00068 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 18909 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 937 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 33.5660 - 2.9645 1.00 2704 147 0.1908 0.2092 REMARK 3 2 2.9645 - 2.3532 1.00 2592 133 0.2092 0.2418 REMARK 3 3 2.3532 - 2.0558 1.00 2561 128 0.1923 0.2168 REMARK 3 4 2.0558 - 1.8679 1.00 2526 139 0.1978 0.2263 REMARK 3 5 1.8679 - 1.7340 1.00 2546 125 0.1964 0.2157 REMARK 3 6 1.7340 - 1.6318 1.00 2512 138 0.1761 0.1961 REMARK 3 7 1.6318 - 1.5500 1.00 2531 127 0.1736 0.2178 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.98 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.02 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 : 0.005 1081 REMARK 3 ANGLE : 0.619 1453 REMARK 3 CHIRALITY : 0.037 156 REMARK 3 PLANARITY : 0.005 189 REMARK 3 DIHEDRAL : 17.554 673 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 5LYP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1200001574. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 298.15 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.920 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18957 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 36.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : 0.13600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.40 REMARK 200 R MERGE FOR SHELL (I) : 0.56200 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: PHASER REMARK 200 STARTING MODEL: 2VYI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SPG, PH 6.0, 25 % W/V PEG 1500, REMARK 280 BATCH MODE, TEMPERATURE 293.15K 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 18.43050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.55800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.38000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.55800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.43050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.38000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 GLY A 90 REMARK 465 SER A 91 REMARK 465 VAL A 229 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 MET A 92 CG SD CE REMARK 470 GLU A 93 CG CD OE1 OE2 REMARK 470 ASP A 94 CG OD1 OD2 REMARK 470 LYS A 99 CG CD CE NZ REMARK 470 ASN A 203 CG OD1 ND2 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 LYS A 185 64.26 -117.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BO4 A 301 DBREF 5LYP A 93 229 UNP Q12118 SGT2_YEAST 93 229 SEQADV 5LYP GLY A 90 UNP Q12118 EXPRESSION TAG SEQADV 5LYP SER A 91 UNP Q12118 EXPRESSION TAG SEQADV 5LYP MET A 92 UNP Q12118 EXPRESSION TAG SEQRES 1 A 140 GLY SER MET GLU ASP ASP ALA GLU THR LYS ALA LYS ALA SEQRES 2 A 140 GLU ASP LEU LYS MET GLN GLY ASN LYS ALA MET ALA ASN SEQRES 3 A 140 LYS ASP TYR GLU LEU ALA ILE ASN LYS TYR THR GLU ALA SEQRES 4 A 140 ILE LYS VAL LEU PRO THR ASN ALA ILE TYR TYR ALA ASN SEQRES 5 A 140 ARG ALA ALA ALA HIS SER SER LEU LYS GLU TYR ASP GLN SEQRES 6 A 140 ALA VAL LYS ASP ALA GLU SER ALA ILE SER ILE ASP PRO SEQRES 7 A 140 SER TYR PHE ARG GLY TYR SER ARG LEU GLY PHE ALA LYS SEQRES 8 A 140 TYR ALA GLN GLY LYS PRO GLU GLU ALA LEU GLU ALA TYR SEQRES 9 A 140 LYS LYS VAL LEU ASP ILE GLU GLY ASP ASN ALA THR GLU SEQRES 10 A 140 ALA MET LYS ARG ASP TYR GLU SER ALA LYS LYS LYS VAL SEQRES 11 A 140 GLU GLN SER LEU ASN LEU GLU LYS THR VAL HET BO4 A 301 9 HETNAM BO4 BORATE ION FORMUL 2 BO4 B H4 O4 1- FORMUL 3 HOH *90(H2 O) HELIX 1 AA1 ASP A 95 ASN A 115 1 21 HELIX 2 AA2 ASP A 117 LEU A 132 1 16 HELIX 3 AA3 ASN A 135 LEU A 149 1 15 HELIX 4 AA4 GLU A 151 ASP A 166 1 16 HELIX 5 AA5 TYR A 169 GLN A 183 1 15 HELIX 6 AA6 LYS A 185 GLY A 201 1 17 HELIX 7 AA7 ASP A 202 ALA A 204 5 3 HELIX 8 AA8 THR A 205 LEU A 225 1 21 SITE 1 AC1 5 ASP A 153 GLN A 183 LYS A 185 ARG A 210 SITE 2 AC1 5 HOH A 403 CRYST1 36.861 50.760 67.116 90.00 90.00 90.00 P 21 21 21 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 0.027129 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019701 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014900 0.00000