HEADER PROTEIN TURNOVER/ENDOCYTOSIS 29-DEC-05 2FIF TITLE CRYSTAL STRUCTURE OF A BOVINE RABEX-5 FRAGMENT COMPLEXED WITH TITLE 2 UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A, C, E; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: RAB5 GDP/GTP EXCHANGE FACTOR; COMPND 6 CHAIN: B, D, F; COMPND 7 FRAGMENT: A20 ZINC FINGER AND INVERTED UBIQUITIN INTERACTING MOTIF COMPND 8 DOMAINS; COMPND 9 SYNONYM: RABEX-5; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 7 ORGANISM_COMMON: CATTLE; SOURCE 8 ORGANISM_TAXID: 9913; SOURCE 9 GENE: RABGEF1, RABEX5; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PARALLEL GST2 KEYWDS ZINC FINGER, HELIX, PROTEIN TURNOVER-ENDOCYTOSIS COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.LEE,J.H.HURLEY REVDAT 5 30-AUG-23 2FIF 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 2FIF 1 VERSN REVDAT 3 24-FEB-09 2FIF 1 VERSN REVDAT 2 21-MAR-06 2FIF 1 JRNL REVDAT 1 07-FEB-06 2FIF 0 JRNL AUTH S.LEE,Y.C.TSAI,R.MATTERA,W.J.SMITH,M.S.KOSTELANSKY, JRNL AUTH 2 A.M.WEISSMAN,J.S.BONIFACINO,J.H.HURLEY JRNL TITL STRUCTURAL BASIS FOR UBIQUITIN RECOGNITION AND JRNL TITL 2 AUTOUBIQUITINATION BY RABEX-5 JRNL REF NAT.STRUCT.MOL.BIOL. V. 13 264 2006 JRNL REFN ISSN 1545-9993 JRNL PMID 16462746 JRNL DOI 10.1038/NSMB1064 REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 90.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 18271 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 + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 985 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1137 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.3210 REMARK 3 BIN FREE R VALUE SET COUNT : 61 REMARK 3 BIN FREE R VALUE : 0.4680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3201 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 19 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.17000 REMARK 3 B22 (A**2) : 0.90000 REMARK 3 B33 (A**2) : 0.14000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.21000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.453 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.283 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.208 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.649 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3262 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4382 ; 0.991 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 386 ; 4.750 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;35.839 ;25.207 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 636 ;16.527 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;16.682 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 464 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2451 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1315 ; 0.178 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2194 ; 0.295 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 92 ; 0.132 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 61 ; 0.195 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.128 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2011 ; 0.245 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3124 ; 0.426 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1432 ; 0.688 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1258 ; 1.077 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 73 REMARK 3 ORIGIN FOR THE GROUP (A): 143.6409 6.3544 10.4229 REMARK 3 T TENSOR REMARK 3 T11: -0.2448 T22: -0.3859 REMARK 3 T33: -0.2660 T12: -0.0014 REMARK 3 T13: -0.0039 T23: -0.0354 REMARK 3 L TENSOR REMARK 3 L11: 3.0870 L22: 6.3617 REMARK 3 L33: 6.5466 L12: 1.6437 REMARK 3 L13: -0.1583 L23: -2.0602 REMARK 3 S TENSOR REMARK 3 S11: 0.1104 S12: -0.2968 S13: 0.1097 REMARK 3 S21: 0.4605 S22: -0.0275 S23: 0.0607 REMARK 3 S31: -0.1676 S32: 0.1288 S33: -0.0829 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 73 REMARK 3 ORIGIN FOR THE GROUP (A): 117.1598 -3.2328 15.9929 REMARK 3 T TENSOR REMARK 3 T11: -0.1540 T22: 0.0422 REMARK 3 T33: 0.0239 T12: 0.0461 REMARK 3 T13: 0.0182 T23: 0.0405 REMARK 3 L TENSOR REMARK 3 L11: 15.6228 L22: 7.0593 REMARK 3 L33: 8.5124 L12: -2.4764 REMARK 3 L13: -7.5349 L23: -1.2880 REMARK 3 S TENSOR REMARK 3 S11: -0.0292 S12: -0.2359 S13: 0.8121 REMARK 3 S21: -0.1707 S22: 0.4635 S23: 0.8744 REMARK 3 S31: -0.2533 S32: -0.7520 S33: -0.4343 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 1 E 73 REMARK 3 ORIGIN FOR THE GROUP (A): 176.7764 -16.8890 20.1920 REMARK 3 T TENSOR REMARK 3 T11: -0.0432 T22: 0.4272 REMARK 3 T33: 0.0214 T12: -0.0929 REMARK 3 T13: -0.1563 T23: 0.1144 REMARK 3 L TENSOR REMARK 3 L11: 16.1285 L22: 5.5651 REMARK 3 L33: 7.2807 L12: -0.6302 REMARK 3 L13: 1.6985 L23: -0.5606 REMARK 3 S TENSOR REMARK 3 S11: -0.3371 S12: 0.4914 S13: 0.9778 REMARK 3 S21: -0.5195 S22: -0.1505 S23: -0.2088 REMARK 3 S31: -0.6052 S32: 1.5821 S33: 0.4876 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 15 B 37 REMARK 3 ORIGIN FOR THE GROUP (A): 158.0977 -23.2462 18.7878 REMARK 3 T TENSOR REMARK 3 T11: -0.1454 T22: -0.0350 REMARK 3 T33: -0.0561 T12: 0.0117 REMARK 3 T13: -0.1849 T23: -0.0137 REMARK 3 L TENSOR REMARK 3 L11: 15.4757 L22: 18.8896 REMARK 3 L33: 20.8544 L12: 1.4213 REMARK 3 L13: 7.8601 L23: 4.7584 REMARK 3 S TENSOR REMARK 3 S11: 0.5584 S12: -1.1516 S13: -0.6161 REMARK 3 S21: 1.0565 S22: -0.2998 S23: -0.4159 REMARK 3 S31: 1.0063 S32: -0.4503 S33: -0.2587 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 16 D 37 REMARK 3 ORIGIN FOR THE GROUP (A): 124.7377 -25.2335 37.9852 REMARK 3 T TENSOR REMARK 3 T11: 0.1322 T22: -0.0067 REMARK 3 T33: -0.2141 T12: 0.0893 REMARK 3 T13: 0.0012 T23: -0.1199 REMARK 3 L TENSOR REMARK 3 L11: 16.0741 L22: 14.6495 REMARK 3 L33: 23.8676 L12: -8.9729 REMARK 3 L13: -7.1212 L23: 1.3584 REMARK 3 S TENSOR REMARK 3 S11: 0.4279 S12: 1.9552 S13: -0.6855 REMARK 3 S21: -0.7162 S22: -0.8946 S23: 0.3395 REMARK 3 S31: 1.1757 S32: -0.8173 S33: 0.4667 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 17 F 37 REMARK 3 ORIGIN FOR THE GROUP (A): 160.1725 -37.3515 38.5014 REMARK 3 T TENSOR REMARK 3 T11: 0.1609 T22: 0.7328 REMARK 3 T33: 0.4996 T12: -0.0583 REMARK 3 T13: 0.3613 T23: -0.4671 REMARK 3 L TENSOR REMARK 3 L11: 15.9956 L22: 18.3449 REMARK 3 L33: 7.1637 L12: 0.3561 REMARK 3 L13: -2.6207 L23: -6.6173 REMARK 3 S TENSOR REMARK 3 S11: -1.2519 S12: 1.6056 S13: -2.1040 REMARK 3 S21: -0.0577 S22: 1.2807 S23: -0.5289 REMARK 3 S31: 0.9171 S32: 0.4716 S33: -0.0288 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 38 B 73 REMARK 3 ORIGIN FOR THE GROUP (A): 139.5021 -3.8315 3.3567 REMARK 3 T TENSOR REMARK 3 T11: -0.2649 T22: -0.4077 REMARK 3 T33: -0.2158 T12: -0.0576 REMARK 3 T13: 0.0098 T23: -0.0350 REMARK 3 L TENSOR REMARK 3 L11: 17.8673 L22: 18.0771 REMARK 3 L33: 8.5511 L12: -14.7196 REMARK 3 L13: 8.8024 L23: -9.3934 REMARK 3 S TENSOR REMARK 3 S11: -0.1858 S12: -0.5745 S13: 0.5482 REMARK 3 S21: 0.1340 S22: 0.3494 S23: 0.0844 REMARK 3 S31: -0.1105 S32: -0.5258 S33: -0.1636 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 38 D 73 REMARK 3 ORIGIN FOR THE GROUP (A): 124.7656 -13.0281 11.3079 REMARK 3 T TENSOR REMARK 3 T11: 0.0429 T22: 0.0057 REMARK 3 T33: 0.0013 T12: -0.0003 REMARK 3 T13: 0.0831 T23: 0.0409 REMARK 3 L TENSOR REMARK 3 L11: 6.5677 L22: 13.4252 REMARK 3 L33: 64.5651 L12: -4.5810 REMARK 3 L13: 9.4178 L23: -22.1607 REMARK 3 S TENSOR REMARK 3 S11: -0.3375 S12: 0.2018 S13: -0.2116 REMARK 3 S21: -0.7706 S22: 0.0530 S23: 0.3996 REMARK 3 S31: 0.8045 S32: -0.3795 S33: 0.2845 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 38 F 72 REMARK 3 ORIGIN FOR THE GROUP (A): 181.4065 -29.3983 22.5921 REMARK 3 T TENSOR REMARK 3 T11: -0.0991 T22: 0.6228 REMARK 3 T33: 0.2160 T12: 0.2099 REMARK 3 T13: -0.0447 T23: 0.0535 REMARK 3 L TENSOR REMARK 3 L11: 20.8595 L22: 5.1876 REMARK 3 L33: 25.5132 L12: 5.0953 REMARK 3 L13: -19.2186 L23: -3.3632 REMARK 3 S TENSOR REMARK 3 S11: -0.3138 S12: -0.0267 S13: -0.6368 REMARK 3 S21: -0.4569 S22: -0.4226 S23: -0.1877 REMARK 3 S31: 0.1902 S32: 1.4255 S33: 0.7364 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FIF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000035914. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-SEP-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2820 REMARK 200 MONOCHROMATOR : SILICON REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19257 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 REMARK 200 RESOLUTION RANGE LOW (A) : 90.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 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 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2FID REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-25% PEG 4000, 0.2M LITHIUM SULFATE REMARK 280 , PH 5.6, 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 96.10000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.21000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 96.10000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.21000 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 THE BIOLOGICAL ASSEMBLY IS RABEX-5 COMPLEXED WITH TWO REMARK 300 UBIQUITIN MOLECULES. THIS CORRESPONDIS TO CHAIN B REMARK 300 WITH CHAINS A AND E IN THE ASYMMETRIC UNIT. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 ARG A 74 REMARK 465 GLY A 75 REMARK 465 GLY A 76 REMARK 465 GLY B 4 REMARK 465 ALA B 5 REMARK 465 MET B 6 REMARK 465 GLY B 7 REMARK 465 SER B 8 REMARK 465 GLY B 9 REMARK 465 ILE B 10 REMARK 465 HIS B 11 REMARK 465 VAL B 12 REMARK 465 ASP B 13 REMARK 465 GLN B 14 REMARK 465 ARG C 74 REMARK 465 GLY C 75 REMARK 465 GLY C 76 REMARK 465 GLY D 4 REMARK 465 ALA D 5 REMARK 465 MET D 6 REMARK 465 GLY D 7 REMARK 465 SER D 8 REMARK 465 GLY D 9 REMARK 465 ILE D 10 REMARK 465 HIS D 11 REMARK 465 VAL D 12 REMARK 465 ASP D 13 REMARK 465 GLN D 14 REMARK 465 SER D 15 REMARK 465 ARG E 74 REMARK 465 GLY E 75 REMARK 465 GLY E 76 REMARK 465 GLY F 4 REMARK 465 ALA F 5 REMARK 465 MET F 6 REMARK 465 GLY F 7 REMARK 465 SER F 8 REMARK 465 GLY F 9 REMARK 465 ILE F 10 REMARK 465 HIS F 11 REMARK 465 VAL F 12 REMARK 465 ASP F 13 REMARK 465 GLN F 14 REMARK 465 SER F 15 REMARK 465 GLU F 16 REMARK 465 GLN F 73 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLN B 50 O HOH B 907 1.97 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 TRP B 31 36.01 -99.07 REMARK 500 SER B 72 -83.80 -118.37 REMARK 500 SER D 71 32.25 -65.69 REMARK 500 LEU F 18 -71.54 -86.90 REMARK 500 TRP F 31 41.87 -106.74 REMARK 500 SER F 71 -39.05 -154.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 19 SG REMARK 620 2 CYS B 23 SG 113.1 REMARK 620 3 CYS B 35 SG 107.8 106.3 REMARK 620 4 CYS B 38 SG 105.4 123.9 98.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 19 SG REMARK 620 2 CYS D 23 SG 117.5 REMARK 620 3 CYS D 35 SG 110.8 102.7 REMARK 620 4 CYS D 38 SG 112.4 112.6 98.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN F 903 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS F 19 SG REMARK 620 2 CYS F 23 SG 111.4 REMARK 620 3 CYS F 35 SG 125.4 85.3 REMARK 620 4 CYS F 38 SG 149.3 81.1 82.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN F 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 101 DBREF 2FIF A 1 76 UNP P62990 UBIQ_BOVIN 1 76 DBREF 2FIF C 1 76 UNP P62990 UBIQ_BOVIN 1 76 DBREF 2FIF E 1 76 UNP P62990 UBIQ_BOVIN 1 76 DBREF 2FIF B 9 73 UNP O18973 RABX5_BOVIN 9 73 DBREF 2FIF D 9 73 UNP O18973 RABX5_BOVIN 9 73 DBREF 2FIF F 9 73 UNP O18973 RABX5_BOVIN 9 73 SEQADV 2FIF GLY B 4 UNP O18973 INSERTION SEQADV 2FIF ALA B 5 UNP O18973 INSERTION SEQADV 2FIF MET B 6 UNP O18973 INSERTION SEQADV 2FIF GLY B 7 UNP O18973 INSERTION SEQADV 2FIF SER B 8 UNP O18973 INSERTION SEQADV 2FIF GLY D 4 UNP O18973 INSERTION SEQADV 2FIF ALA D 5 UNP O18973 INSERTION SEQADV 2FIF MET D 6 UNP O18973 INSERTION SEQADV 2FIF GLY D 7 UNP O18973 INSERTION SEQADV 2FIF SER D 8 UNP O18973 INSERTION SEQADV 2FIF GLY F 4 UNP O18973 INSERTION SEQADV 2FIF ALA F 5 UNP O18973 INSERTION SEQADV 2FIF MET F 6 UNP O18973 INSERTION SEQADV 2FIF GLY F 7 UNP O18973 INSERTION SEQADV 2FIF SER F 8 UNP O18973 INSERTION SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 B 70 GLY ALA MET GLY SER GLY ILE HIS VAL ASP GLN SER GLU SEQRES 2 B 70 LEU LEU CYS LYS LYS GLY CYS GLY TYR TYR GLY ASN PRO SEQRES 3 B 70 ALA TRP GLN GLY PHE CYS SER LYS CYS TRP ARG GLU GLU SEQRES 4 B 70 TYR HIS LYS ALA ARG GLN LYS GLN ILE GLN GLU ASP TRP SEQRES 5 B 70 GLU LEU ALA GLU ARG LEU GLN ARG GLU GLU GLU GLU ALA SEQRES 6 B 70 PHE ALA SER SER GLN SEQRES 1 C 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 D 70 GLY ALA MET GLY SER GLY ILE HIS VAL ASP GLN SER GLU SEQRES 2 D 70 LEU LEU CYS LYS LYS GLY CYS GLY TYR TYR GLY ASN PRO SEQRES 3 D 70 ALA TRP GLN GLY PHE CYS SER LYS CYS TRP ARG GLU GLU SEQRES 4 D 70 TYR HIS LYS ALA ARG GLN LYS GLN ILE GLN GLU ASP TRP SEQRES 5 D 70 GLU LEU ALA GLU ARG LEU GLN ARG GLU GLU GLU GLU ALA SEQRES 6 D 70 PHE ALA SER SER GLN SEQRES 1 E 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 E 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 E 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 E 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 E 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 E 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 F 70 GLY ALA MET GLY SER GLY ILE HIS VAL ASP GLN SER GLU SEQRES 2 F 70 LEU LEU CYS LYS LYS GLY CYS GLY TYR TYR GLY ASN PRO SEQRES 3 F 70 ALA TRP GLN GLY PHE CYS SER LYS CYS TRP ARG GLU GLU SEQRES 4 F 70 TYR HIS LYS ALA ARG GLN LYS GLN ILE GLN GLU ASP TRP SEQRES 5 F 70 GLU LEU ALA GLU ARG LEU GLN ARG GLU GLU GLU GLU ALA SEQRES 6 F 70 PHE ALA SER SER GLN HET SO4 A 101 5 HET ZN B 901 1 HET ZN D 902 1 HET ZN F 903 1 HETNAM SO4 SULFATE ION HETNAM ZN ZINC ION FORMUL 7 SO4 O4 S 2- FORMUL 8 ZN 3(ZN 2+) FORMUL 11 HOH *19(H2 O) HELIX 1 1 THR A 22 GLY A 35 1 14 HELIX 2 2 PRO A 37 ASP A 39 5 3 HELIX 3 3 THR A 55 ASN A 60 5 6 HELIX 4 4 ASN B 28 GLN B 32 5 5 HELIX 5 5 CYS B 35 SER B 71 1 37 HELIX 6 6 THR C 22 GLY C 35 1 14 HELIX 7 7 PRO C 37 ASP C 39 5 3 HELIX 8 8 LEU C 56 ASN C 60 5 5 HELIX 9 9 ASN D 28 GLN D 32 5 5 HELIX 10 10 CYS D 35 ALA D 70 1 36 HELIX 11 11 THR E 22 ASP E 32 1 11 HELIX 12 12 PRO E 37 ASP E 39 5 3 HELIX 13 13 THR E 55 ASN E 60 5 6 HELIX 14 14 CYS F 35 ALA F 70 1 36 SHEET 1 A 5 THR A 12 GLU A 16 0 SHEET 2 A 5 GLN A 2 THR A 7 -1 N VAL A 5 O ILE A 13 SHEET 3 A 5 THR A 66 LEU A 71 1 O LEU A 67 N PHE A 4 SHEET 4 A 5 GLN A 41 PHE A 45 -1 N ARG A 42 O VAL A 70 SHEET 5 A 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 SHEET 1 B 5 THR C 12 GLU C 16 0 SHEET 2 B 5 GLN C 2 THR C 7 -1 N VAL C 5 O ILE C 13 SHEET 3 B 5 THR C 66 LEU C 71 1 O LEU C 67 N PHE C 4 SHEET 4 B 5 GLN C 41 PHE C 45 -1 N ARG C 42 O VAL C 70 SHEET 5 B 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 SHEET 1 C 5 THR E 12 GLU E 16 0 SHEET 2 C 5 GLN E 2 THR E 7 -1 N VAL E 5 O ILE E 13 SHEET 3 C 5 THR E 66 LEU E 71 1 O LEU E 67 N PHE E 4 SHEET 4 C 5 GLN E 41 PHE E 45 -1 N ILE E 44 O HIS E 68 SHEET 5 C 5 LYS E 48 GLN E 49 -1 O LYS E 48 N PHE E 45 LINK SG CYS B 19 ZN ZN B 901 1555 1555 2.33 LINK SG CYS B 23 ZN ZN B 901 1555 1555 2.29 LINK SG CYS B 35 ZN ZN B 901 1555 1555 2.33 LINK SG CYS B 38 ZN ZN B 901 1555 1555 2.38 LINK SG CYS D 19 ZN ZN D 902 1555 1555 2.42 LINK SG CYS D 23 ZN ZN D 902 1555 1555 2.37 LINK SG CYS D 35 ZN ZN D 902 1555 1555 2.53 LINK SG CYS D 38 ZN ZN D 902 1555 1555 2.31 LINK SG CYS F 19 ZN ZN F 903 1555 1555 2.88 LINK SG CYS F 23 ZN ZN F 903 1555 1555 2.88 LINK SG CYS F 35 ZN ZN F 903 1555 1555 2.55 LINK SG CYS F 38 ZN ZN F 903 1555 1555 2.86 SITE 1 AC1 4 CYS B 19 CYS B 23 CYS B 35 CYS B 38 SITE 1 AC2 4 CYS D 19 CYS D 23 CYS D 35 CYS D 38 SITE 1 AC3 4 CYS F 19 CYS F 23 CYS F 35 CYS F 38 SITE 1 AC4 4 ARG A 42 ARG A 72 LYS C 11 GLU C 34 CRYST1 192.200 44.420 69.170 90.00 108.98 90.00 C 1 2 1 12 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 0.005203 0.000000 0.001789 0.00000 SCALE2 0.000000 0.022512 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015288 0.00000