HEADER CHAPERONE 24-JUL-08 2VYI TITLE CRYSTAL STRUCTURE OF THE TPR DOMAIN OF HUMAN SGT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SGTA PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: TETRATRICOPEPTIDE REPEAT, RESIDUES 84-210; COMPND 5 SYNONYM: SMALL GLUTAMINE RICH PROTEIN WITH TETRATRICOPEPTIDE REPEAT COMPND 6 1, SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT (TPR)-CONTAINING, COMPND 7 ALPHA, ISOFORM CRA_A; COMPND 8 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX6P1 KEYWDS SGT, CHAPERONE, TPR REPEAT, PHOSPHOPROTEIN, TETRATRICOPEPTIDE REPEAT KEYWDS 2 PROTEIN, HOST-VIRUS INTERACTION EXPDTA X-RAY DIFFRACTION AUTHOR S.DUTTA,Y.J.TAN REVDAT 4 13-DEC-23 2VYI 1 REMARK REVDAT 3 24-FEB-09 2VYI 1 VERSN REVDAT 2 23-SEP-08 2VYI 1 JRNL REMARK REVDAT 1 12-AUG-08 2VYI 0 JRNL AUTH S.DUTTA,Y.J.TAN JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF HUMAN SGT AND JRNL TITL 2 ITS INTERACTION WITH VPU OF THE HUMAN IMMUNODEFICIENCY VIRUS JRNL TITL 3 TYPE 1. JRNL REF BIOCHEMISTRY V. 47 10123 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18759457 JRNL DOI 10.1021/BI800758A REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1088998.470 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 12690 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) : 0.187 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 651 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1970 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE : 0.3510 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 99 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.035 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1957 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.30000 REMARK 3 B22 (A**2) : 2.29000 REMARK 3 B33 (A**2) : 3.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.26 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.42 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 17.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 4.890 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 6.510 ; 8.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 10.410; 8.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 12.460; 12.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 46.73 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2VYI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1290036970. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12726 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.22000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 1WAO REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4M SODIUM FORMATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 33.91150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.96950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.91150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.96950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 83 REMARK 465 SER A 84 REMARK 465 GLU A 85 REMARK 465 GLY B 80 REMARK 465 PRO B 81 REMARK 465 LEU B 82 REMARK 465 GLY B 83 REMARK 465 SER B 84 REMARK 465 GLU B 85 REMARK 465 PRO B 210 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 ALA B 209 CA C O 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 ASN A 192 107.93 -34.89 REMARK 500 ARG B 207 39.77 -76.86 REMARK 500 GLU B 208 55.47 -147.03 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 A2047 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A2050 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A2052 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH B2045 DISTANCE = 5.96 ANGSTROMS DBREF 2VYI A 80 83 PDB 2VYI 2VYI 80 83 DBREF 2VYI A 84 210 UNP Q6FIA9 Q6FIA9_HUMAN 84 210 DBREF 2VYI B 80 83 PDB 2VYI 2VYI 80 83 DBREF 2VYI B 84 210 UNP Q6FIA9 Q6FIA9_HUMAN 84 210 SEQRES 1 A 131 GLY PRO LEU GLY SER GLU GLU ASP SER ALA GLU ALA GLU SEQRES 2 A 131 ARG LEU LYS THR GLU GLY ASN GLU GLN MET LYS VAL GLU SEQRES 3 A 131 ASN PHE GLU ALA ALA VAL HIS PHE TYR GLY LYS ALA ILE SEQRES 4 A 131 GLU LEU ASN PRO ALA ASN ALA VAL TYR PHE CYS ASN ARG SEQRES 5 A 131 ALA ALA ALA TYR SER LYS LEU GLY ASN TYR ALA GLY ALA SEQRES 6 A 131 VAL GLN ASP CYS GLU ARG ALA ILE CYS ILE ASP PRO ALA SEQRES 7 A 131 TYR SER LYS ALA TYR GLY ARG MET GLY LEU ALA LEU SER SEQRES 8 A 131 SER LEU ASN LYS HIS VAL GLU ALA VAL ALA TYR TYR LYS SEQRES 9 A 131 LYS ALA LEU GLU LEU ASP PRO ASP ASN GLU THR TYR LYS SEQRES 10 A 131 SER ASN LEU LYS ILE ALA GLU LEU LYS LEU ARG GLU ALA SEQRES 11 A 131 PRO SEQRES 1 B 131 GLY PRO LEU GLY SER GLU GLU ASP SER ALA GLU ALA GLU SEQRES 2 B 131 ARG LEU LYS THR GLU GLY ASN GLU GLN MET LYS VAL GLU SEQRES 3 B 131 ASN PHE GLU ALA ALA VAL HIS PHE TYR GLY LYS ALA ILE SEQRES 4 B 131 GLU LEU ASN PRO ALA ASN ALA VAL TYR PHE CYS ASN ARG SEQRES 5 B 131 ALA ALA ALA TYR SER LYS LEU GLY ASN TYR ALA GLY ALA SEQRES 6 B 131 VAL GLN ASP CYS GLU ARG ALA ILE CYS ILE ASP PRO ALA SEQRES 7 B 131 TYR SER LYS ALA TYR GLY ARG MET GLY LEU ALA LEU SER SEQRES 8 B 131 SER LEU ASN LYS HIS VAL GLU ALA VAL ALA TYR TYR LYS SEQRES 9 B 131 LYS ALA LEU GLU LEU ASP PRO ASP ASN GLU THR TYR LYS SEQRES 10 B 131 SER ASN LEU LYS ILE ALA GLU LEU LYS LEU ARG GLU ALA SEQRES 11 B 131 PRO FORMUL 3 HOH *180(H2 O) HELIX 1 1 GLU A 86 VAL A 104 1 19 HELIX 2 2 ASN A 106 ASN A 121 1 16 HELIX 3 3 ASN A 124 LEU A 138 1 15 HELIX 4 4 ASN A 140 ASP A 155 1 16 HELIX 5 5 TYR A 158 LEU A 172 1 15 HELIX 6 6 LYS A 174 ASP A 189 1 16 HELIX 7 7 ASN A 192 ARG A 207 1 16 HELIX 8 8 GLU B 86 VAL B 104 1 19 HELIX 9 9 ASN B 106 ASN B 121 1 16 HELIX 10 10 ASN B 124 LEU B 138 1 15 HELIX 11 11 ASN B 140 ASP B 155 1 16 HELIX 12 12 TYR B 158 LEU B 172 1 15 HELIX 13 13 LYS B 174 ASP B 189 1 16 HELIX 14 14 ASN B 192 ARG B 207 1 16 SSBOND 1 CYS A 153 CYS B 153 1555 3556 2.70 CRYST1 67.823 81.939 55.923 90.00 90.00 90.00 P 21 21 2 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 0.014744 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012204 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017882 0.00000