10 20 30 40 50 60 70 80 3KB5 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER MEMBRANE PROTEIN 20-OCT-09 3KB5
TITLE PRY-SPRY DOMAIN OF HUMAN TRIM72
COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIPARTITE MOTIF-CONTAINING PROTEIN 72; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PRY-SPRY DOMAIN, UNP RESIDUES 278-470; COMPND 5 SYNONYM: MITSUGUMIN-53, MG53; COMPND 6 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: PRY-SPRY; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID
KEYWDS B30.2, GUSTAVUS, SPRY, TRIM21, TRIPARTITE MOTIF, TRIM72, KEYWDS 2 PRY, HIGH RESOLUTION, MG53
EXPDTA X-RAY DIFFRACTION
AUTHOR E.Y.PARK,O.-B.KWON,B.-C.JEONG,H.K.SONG
REVDAT 1 22-DEC-09 3KB5 0
JRNL AUTH E.Y.PARK,O.-B.KWON,B.-C.JEONG,J.-S.YI,C.S.LEE, JRNL AUTH 2 Y.-G.KO,H.K.SONG JRNL TITL CRYSTAL STRUCTURE OF PRY-SPRY DOMAIN OF HUMAN JRNL TITL 2 TRIM72 JRNL REF PROTEINS 2009 JRNL REFN ESSN 1097-0134 JRNL PMID 19967786 JRNL DOI 10.1002/PROT.22647
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.50 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.9 REMARK 3 NUMBER OF REFLECTIONS : 26011 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1269 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1526 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.70100 REMARK 3 B22 (A**2) : 2.29100 REMARK 3 B33 (A**2) : -5.99200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.41400 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.765 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.080 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.364 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.593 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 58.37 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 3KB5 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-OCT-09. REMARK 100 THE RCSB ID CODE IS RCSB055772.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : PAL/PLS; PHOTON FACTORY REMARK 200 BEAMLINE : 4A; AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97951, 0.97967, 0.9600; 1.0 REMARK 200 MONOCHROMATOR : NULL; SI 111 CHANNEL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210; ADSC REMARK 200 QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26011 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, 20% (W/V) REMARK 280 POLYETHYLENE GLYCOL 3350, 0.2M POTASSIUM NITRATE, PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, 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 76.87350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.96850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 76.87350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.96850 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000
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 316 -86.41 -132.67 REMARK 500 ALA A 318 107.03 -50.94 REMARK 500 GLU A 387 16.29 57.01 REMARK 500 LYS A 389 -13.26 -146.10 REMARK 500 ASP A 433 52.41 -114.06 REMARK 500 CYS A 456 168.44 68.11 REMARK 500 REMARK 500 REMARK: NULL
DBREF 3KB5 A 278 470 UNP Q6ZMU5 TRI72_HUMAN 278 470
SEQRES 1 A 193 ARG LYS MET PHE ARG ALA LEU MET PRO ALA LEU GLU GLU SEQRES 2 A 193 LEU THR PHE ASP PRO SER SER ALA HIS PRO SER LEU VAL SEQRES 3 A 193 VAL SER SER SER GLY ARG ARG VAL GLU CYS SER GLU GLN SEQRES 4 A 193 LYS ALA PRO PRO ALA GLY GLU ASP PRO ARG GLN PHE ASP SEQRES 5 A 193 LYS ALA VAL ALA VAL VAL ALA HIS GLN GLN LEU SER GLU SEQRES 6 A 193 GLY GLU HIS TYR TRP GLU VAL ASP VAL GLY ASP LYS PRO SEQRES 7 A 193 ARG TRP ALA LEU GLY VAL ILE ALA ALA GLU ALA PRO ARG SEQRES 8 A 193 ARG GLY ARG LEU HIS ALA VAL PRO SER GLN GLY LEU TRP SEQRES 9 A 193 LEU LEU GLY LEU ARG GLU GLY LYS ILE LEU GLU ALA HIS SEQRES 10 A 193 VAL GLU ALA LYS GLU PRO ARG ALA LEU ARG SER PRO GLU SEQRES 11 A 193 ARG ARG PRO THR ARG ILE GLY LEU TYR LEU SER PHE GLY SEQRES 12 A 193 ASP GLY VAL LEU SER PHE TYR ASP ALA SER ASP ALA ASP SEQRES 13 A 193 ALA LEU VAL PRO LEU PHE ALA PHE HIS GLU ARG LEU PRO SEQRES 14 A 193 ARG PRO VAL TYR PRO PHE PHE ASP VAL CYS TRP HIS ASP SEQRES 15 A 193 LYS GLY LYS ASN ALA GLN PRO LEU LEU LEU VAL
FORMUL 2 HOH *160(H2 O)
HELIX 1 1 ARG A 278 MET A 285 1 8 HELIX 2 2 VAL A 375 GLN A 378 5 4
SHEET 1 A 7 LEU A 302 SER A 305 0 SHEET 2 A 7 ARG A 310 CYS A 313 -1 O ARG A 310 N SER A 305 SHEET 3 A 7 LEU A 467 LEU A 469 -1 O LEU A 467 N VAL A 311 SHEET 4 A 7 GLU A 344 ASP A 350 -1 N ASP A 350 O LEU A 468 SHEET 5 A 7 ARG A 412 SER A 418 -1 O LEU A 417 N HIS A 345 SHEET 6 A 7 VAL A 423 ASP A 428 -1 O SER A 425 N TYR A 416 SHEET 7 A 7 VAL A 436 PHE A 441 -1 O PHE A 439 N PHE A 426 SHEET 1 B 6 ALA A 333 VAL A 335 0 SHEET 2 B 6 VAL A 449 ASP A 454 -1 O PHE A 453 N VAL A 334 SHEET 3 B 6 TRP A 357 ALA A 363 -1 N ALA A 358 O ASP A 454 SHEET 4 B 6 LEU A 380 ARG A 386 -1 O LEU A 383 N LEU A 359 SHEET 5 B 6 ILE A 390 ALA A 393 -1 O ILE A 390 N ARG A 386 SHEET 6 B 6 ARG A 401 ALA A 402 -1 O ARG A 401 N ALA A 393
CISPEP 1 SER A 405 PRO A 406 0 -0.26 CISPEP 2 ARG A 447 PRO A 448 0 -0.02
CRYST1 153.747 35.937 33.200 90.00 99.87 90.00 C 1 2 1 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 0.006504 0.000000 0.001132 0.00000
SCALE2 0.000000 0.027826 0.000000 0.00000
SCALE3 0.000000 0.000000 0.030573 0.00000