PDB Short entry for 1LB4 HEADER SIGNALING PROTEIN 02-APR-02 1LB4 TITLE TRAF6 APO STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TNF RECEPTOR-ASSOCIATED FACTOR 6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 348-504; COMPND 5 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: TRAF6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS APO FORM, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.YE,J.R.ARRON,B.LAMOTHE,M.CIRILLI,T.KOBAYASHI,N.K.SHEVDE,D.SEGAL, AUTHOR 2 O.DZIVENU,M.VOLOGODSKAIA,M.YIM,K.DU,S.SINGH,J.W.PIKE,B.G.DARNAY, AUTHOR 3 Y.CHOI,H.WU REVDAT 6 03-APR-24 1LB4 1 REMARK REVDAT 5 14-FEB-24 1LB4 1 SEQADV REVDAT 4 11-OCT-17 1LB4 1 REMARK REVDAT 3 24-FEB-09 1LB4 1 VERSN REVDAT 2 01-APR-03 1LB4 1 JRNL REVDAT 1 31-JUL-02 1LB4 0 JRNL AUTH H.YE,J.R.ARRON,B.LAMOTHE,M.CIRILLI,T.KOBAYASHI,N.K.SHEVDE, JRNL AUTH 2 D.SEGAL,O.K.DZIVENU,M.VOLOGODSKAIA,M.YIM,K.DU,S.SINGH, JRNL AUTH 3 J.W.PIKE,B.G.DARNAY,Y.CHOI,H.WU JRNL TITL DISTINCT MOLECULAR MECHANISM FOR INITIATING TRAF6 JRNL TITL 2 SIGNALLING. JRNL REF NATURE V. 418 443 2002 JRNL REFN ISSN 0028-0836 JRNL PMID 12140561 JRNL DOI 10.1038/NATURE00888 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 10.6 REMARK 3 NUMBER OF REFLECTIONS : 6283 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) : 0.204 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 666 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 : 1269 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.00 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.30 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) : 0.44 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.840 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1LB4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-APR-02. REMARK 100 THE DEPOSITION ID IS D_1000015804. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7809 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09200 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) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REPLACE REMARK 200 STARTING MODEL: TRAF2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, TRIS, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 27.79050 REMARK 290 SMTRY3 2 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 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 PRO A 465 REMARK 465 ARG A 466 REMARK 465 ASN A 467 REMARK 465 PRO A 468 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 PRO A 385 C - N - CA ANGL. DEV. = -9.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 350 -92.80 -73.96 REMARK 500 ASN A 359 26.69 47.89 REMARK 500 GLU A 369 30.23 -95.64 REMARK 500 LYS A 384 -80.55 -46.84 REMARK 500 LEU A 457 2.89 -67.06 REMARK 500 THR A 463 -34.14 -140.55 REMARK 500 THR A 475 52.67 -113.58 REMARK 500 THR A 486 59.66 -97.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LB5 RELATED DB: PDB REMARK 900 TRAF6-RANK COMPLEX REMARK 900 RELATED ID: 1LB6 RELATED DB: PDB REMARK 900 TRAF6-CD40 COMPLEX DBREF 1LB4 A 348 504 UNP Q9Y4K3 TRAF6_HUMAN 348 504 SEQADV 1LB4 LEU A 505 UNP Q9Y4K3 CLONING ARTIFACT SEQADV 1LB4 GLU A 506 UNP Q9Y4K3 CLONING ARTIFACT SEQRES 1 A 159 GLN CYS ASN GLY ILE TYR ILE TRP LYS ILE GLY ASN PHE SEQRES 2 A 159 GLY MET HIS LEU LYS CYS GLN GLU GLU GLU LYS PRO VAL SEQRES 3 A 159 VAL ILE HIS SER PRO GLY PHE TYR THR GLY LYS PRO GLY SEQRES 4 A 159 TYR LYS LEU CYS MET ARG LEU HIS LEU GLN LEU PRO THR SEQRES 5 A 159 ALA GLN ARG CYS ALA ASN TYR ILE SER LEU PHE VAL HIS SEQRES 6 A 159 THR MET GLN GLY GLU TYR ASP SER HIS LEU PRO TRP PRO SEQRES 7 A 159 PHE GLN GLY THR ILE ARG LEU THR ILE LEU ASP GLN SER SEQRES 8 A 159 GLU ALA PRO VAL ARG GLN ASN HIS GLU GLU ILE MET ASP SEQRES 9 A 159 ALA LYS PRO GLU LEU LEU ALA PHE GLN ARG PRO THR ILE SEQRES 10 A 159 PRO ARG ASN PRO LYS GLY PHE GLY TYR VAL THR PHE MET SEQRES 11 A 159 HIS LEU GLU ALA LEU ARG GLN ARG THR PHE ILE LYS ASP SEQRES 12 A 159 ASP THR LEU LEU VAL ARG CYS GLU VAL SER THR ARG PHE SEQRES 13 A 159 ASP LEU GLU FORMUL 2 HOH *45(H2 O) HELIX 1 1 ASN A 359 GLU A 369 1 11 HELIX 2 2 TYR A 418 LEU A 422 5 5 HELIX 3 3 GLU A 439 ARG A 443 5 5 HELIX 4 4 GLU A 480 ARG A 485 5 6 SHEET 1 A 4 ILE A 352 ILE A 357 0 SHEET 2 A 4 LEU A 493 THR A 501 -1 O CYS A 497 N TYR A 353 SHEET 3 A 4 GLY A 428 ILE A 434 -1 N THR A 433 O ARG A 496 SHEET 4 A 4 HIS A 446 ASP A 451 -1 O MET A 450 N ILE A 430 SHEET 1 B 4 PHE A 471 HIS A 478 0 SHEET 2 B 4 TYR A 406 THR A 413 -1 N ILE A 407 O MET A 477 SHEET 3 B 4 LYS A 388 LEU A 395 -1 N HIS A 394 O SER A 408 SHEET 4 B 4 VAL A 373 HIS A 376 -1 N ILE A 375 O LEU A 393 SHEET 1 C 4 PHE A 471 HIS A 478 0 SHEET 2 C 4 TYR A 406 THR A 413 -1 N ILE A 407 O MET A 477 SHEET 3 C 4 LYS A 388 LEU A 395 -1 N HIS A 394 O SER A 408 SHEET 4 C 4 PHE A 380 TYR A 381 -1 N PHE A 380 O LEU A 389 CISPEP 1 TRP A 424 PRO A 425 0 -0.14 CRYST1 32.183 55.581 47.709 90.00 100.97 90.00 P 1 21 1 2 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 0.031072 0.000000 0.006023 0.00000 SCALE2 0.000000 0.017992 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021351 0.00000