HEADER IMMUNE SYSTEM 18-JUL-08 3DVG TITLE CRYSTAL STRUCTURE OF K63-SPECIFIC FAB APU.3A8 BOUND TO K63-LINKED DI- TITLE 2 UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN IGG1 FAB FRAGMENT LIGHT CHAIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HUMAN IGG1 FAB FRAGMENT HEAVY CHAIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: UBIQUITIN D77; COMPND 11 CHAIN: X; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: UBIQUITIN; COMPND 16 CHAIN: Y; COMPND 17 ENGINEERED: YES; COMPND 18 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: FAB FRAGMENT LIGHT CHAIN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 10 OTHER_DETAILS: PROTEIN SELECTED BY PHAGE DISPLAY; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: FAB FRAGMENT LIGHT CHAIN; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 20 OTHER_DETAILS: PROTEIN SELECTED BY PHAGE DISPLAY; SOURCE 21 MOL_ID: 3; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_COMMON: HUMAN; SOURCE 24 ORGANISM_TAXID: 9606; SOURCE 25 GENE: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC; SOURCE 26 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 27 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 28 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 29 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 30 MOL_ID: 4; SOURCE 31 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 32 ORGANISM_COMMON: HUMAN; SOURCE 33 ORGANISM_TAXID: 9606; SOURCE 34 GENE: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC; SOURCE 35 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 36 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 37 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 38 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS DI-UBIQUITIN, FAB FRAGMENT, ANTIBODY, NUCLEUS, PHOSPHOPROTEIN, KEYWDS 2 RIBOSOMAL PROTEIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.G.HYMOWITZ REVDAT 4 20-OCT-21 3DVG 1 SEQADV LINK REVDAT 3 13-JUL-11 3DVG 1 VERSN REVDAT 2 24-FEB-09 3DVG 1 VERSN REVDAT 1 30-SEP-08 3DVG 0 JRNL AUTH K.NEWTON,M.L.MATSUMOTO,I.E.WERTZ,D.S.KIRKPATRICK,J.R.LILL, JRNL AUTH 2 J.TAN,D.DUGGER,N.GORDON,S.S.SIDHU,F.A.FELLOUSE,L.KOMUVES, JRNL AUTH 3 D.M.FRENCH,R.E.FERRANDO,C.LAM,D.COMPAAN,C.YU,I.BOSANAC, JRNL AUTH 4 S.G.HYMOWITZ,R.F.KELLEY,V.M.DIXIT JRNL TITL UBIQUITIN CHAIN EDITING REVEALED BY POLYUBIQUITIN JRNL TITL 2 LINKAGE-SPECIFIC ANTIBODIES. JRNL REF CELL(CAMBRIDGE,MASS.) V. 134 668 2008 JRNL REFN ISSN 0092-8674 JRNL PMID 18724939 JRNL DOI 10.1016/J.CELL.2008.07.039 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 21569 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) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2441 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 25 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1231 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.3170 REMARK 3 BIN FREE R VALUE SET COUNT : 139 REMARK 3 BIN FREE R VALUE : 0.4250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4466 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 25 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) : 64.09 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.666 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.323 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.287 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 29.626 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4564 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6196 ; 1.131 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 578 ; 5.592 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 181 ;35.827 ;24.309 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 772 ;18.512 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;17.486 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 711 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3388 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1693 ; 0.193 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3017 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 152 ; 0.120 ; 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): 40 ; 0.173 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.097 ; 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): 2977 ; 2.141 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4686 ; 3.357 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1821 ; 2.159 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1510 ; 3.124 ; 5.000 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 5 A 109 REMARK 3 RESIDUE RANGE : B 1 B 112 REMARK 3 ORIGIN FOR THE GROUP (A): 7.1176 40.5591 19.1880 REMARK 3 T TENSOR REMARK 3 T11: -0.4661 T22: 0.0236 REMARK 3 T33: -0.2159 T12: -0.1367 REMARK 3 T13: -0.1498 T23: 0.0439 REMARK 3 L TENSOR REMARK 3 L11: 2.7630 L22: 5.0940 REMARK 3 L33: 1.4026 L12: -0.0205 REMARK 3 L13: 0.7631 L23: -0.1715 REMARK 3 S TENSOR REMARK 3 S11: 0.0515 S12: -0.1077 S13: 0.1945 REMARK 3 S21: 0.0562 S22: 0.0475 S23: 0.3214 REMARK 3 S31: -0.0832 S32: 0.1254 S33: -0.0990 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 110 A 214 REMARK 3 RESIDUE RANGE : B 113 B 221 REMARK 3 ORIGIN FOR THE GROUP (A): -19.5631 21.8648 7.4817 REMARK 3 T TENSOR REMARK 3 T11: -0.5061 T22: -0.0205 REMARK 3 T33: -0.0942 T12: -0.1088 REMARK 3 T13: -0.1956 T23: -0.0137 REMARK 3 L TENSOR REMARK 3 L11: 2.8373 L22: 3.4934 REMARK 3 L33: 2.4087 L12: 1.2816 REMARK 3 L13: -0.1652 L23: -0.1708 REMARK 3 S TENSOR REMARK 3 S11: 0.1232 S12: 0.0070 S13: 0.0329 REMARK 3 S21: 0.1583 S22: -0.3056 S23: 0.2486 REMARK 3 S31: 0.1058 S32: -0.2329 S33: 0.1823 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : X 1 X 73 REMARK 3 RESIDUE RANGE : Y 1 Y 76 REMARK 3 ORIGIN FOR THE GROUP (A): 29.6096 51.1761 35.3372 REMARK 3 T TENSOR REMARK 3 T11: -0.1063 T22: 0.4029 REMARK 3 T33: -0.1200 T12: -0.2677 REMARK 3 T13: -0.3387 T23: -0.0667 REMARK 3 L TENSOR REMARK 3 L11: 5.7950 L22: 7.9342 REMARK 3 L33: 5.4564 L12: -1.3352 REMARK 3 L13: -1.0324 L23: 1.8272 REMARK 3 S TENSOR REMARK 3 S11: 0.1045 S12: -0.8064 S13: 0.5003 REMARK 3 S21: 0.8926 S22: 0.3367 S23: -0.7035 REMARK 3 S31: -0.6018 S32: 0.5376 S33: -0.4412 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3DVG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048538. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 180 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97607 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24012 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05100 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.58000 REMARK 200 FOR SHELL : 1.800 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 17.0 MG/ML IN 20 MM TRIS-HCL REMARK 280 PH 7.3, 150 MM NACL WELL SOLUTION: 0.1M TRIS-HCL PH 8.0, 1.6M REMARK 280 LIS04 , VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 53.40300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.05850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.40300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 44.05850 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, X, Y 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 SER A 0 REMARK 465 ASP A 1 REMARK 465 ILE A 2 REMARK 465 GLN A 3 REMARK 465 MET A 4 REMARK 465 GLU A 215 REMARK 465 CYS A 216 REMARK 465 GLU B -2 REMARK 465 ILE B -1 REMARK 465 SER B 0 REMARK 465 SER B 222 REMARK 465 CYS B 223 REMARK 465 ASP B 224 REMARK 465 LYS B 225 REMARK 465 THR B 226 REMARK 465 HIS B 227 REMARK 465 GLY X -2 REMARK 465 ARG X 74 REMARK 465 GLY X 75 REMARK 465 GLY X 76 REMARK 465 ASP X 77 REMARK 465 GLY Y -2 REMARK 465 SER Y -1 REMARK 465 HIS Y 0 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 LYS B 221 CG CD CE NZ REMARK 470 SER X -1 OG REMARK 470 HIS X 0 CG ND1 CD2 CE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLY X 10 C GLY X 10 O 0.173 REMARK 500 GLY X 10 C LYS X 11 N 0.157 REMARK 500 LEU X 73 C LEU X 73 O 0.125 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 ALA A 51 -45.08 70.14 REMARK 500 ARG A 52 21.61 -141.64 REMARK 500 ALA A 84 -162.26 -165.51 REMARK 500 ARG A 213 111.75 -32.99 REMARK 500 SER B 63 2.26 -67.04 REMARK 500 VAL B 64 -22.56 -141.04 REMARK 500 THR B 105 -22.72 100.14 REMARK 500 SER B 134 -179.74 -171.80 REMARK 500 LYS B 136 6.31 -62.68 REMARK 500 SER B 137 20.30 -145.34 REMARK 500 ASP B 151 61.43 63.44 REMARK 500 SER B 163 17.51 56.26 REMARK 500 THR B 198 -46.09 -134.43 REMARK 500 THR Y 7 -138.87 -91.18 REMARK 500 ALA Y 46 -2.28 60.41 REMARK 500 ASP Y 52 34.17 -73.95 REMARK 500 ASN Y 60 73.41 49.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DVN RELATED DB: PDB DBREF 3DVG A 0 216 PDB 3DVG 3DVG 0 216 DBREF 3DVG B -2 227 PDB 3DVG 3DVG -2 227 DBREF 3DVG X 1 76 UNP P62988 UBIQ_HUMAN 1 76 DBREF 3DVG Y 1 76 UNP P62988 UBIQ_HUMAN 1 76 SEQADV 3DVG GLY X -2 UNP P62988 EXPRESSION TAG SEQADV 3DVG SER X -1 UNP P62988 EXPRESSION TAG SEQADV 3DVG HIS X 0 UNP P62988 EXPRESSION TAG SEQADV 3DVG ASP X 77 UNP P62988 ENGINEERED MUTATION SEQADV 3DVG GLY Y -2 UNP P62988 EXPRESSION TAG SEQADV 3DVG SER Y -1 UNP P62988 EXPRESSION TAG SEQADV 3DVG HIS Y 0 UNP P62988 EXPRESSION TAG SEQADV 3DVG ARG Y 63 UNP P62988 LYS 63 ENGINEERED MUTATION SEQRES 1 A 217 SER ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER SEQRES 2 A 217 ALA SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SEQRES 3 A 217 SER GLN SER VAL SER SER ALA VAL ALA TRP TYR GLN GLN SEQRES 4 A 217 LYS PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR SER ALA SEQRES 5 A 217 ARG SER LEU TYR SER GLY VAL PRO SER ARG PHE SER GLY SEQRES 6 A 217 SER ARG SER GLY THR ASP PHE THR LEU THR ILE SER SER SEQRES 7 A 217 LEU GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN SEQRES 8 A 217 TYR SER SER TYR SER SER LEU PHE THR PHE GLY GLN GLY SEQRES 9 A 217 THR LYS VAL GLU ILE LYS ARG THR VAL ALA ALA PRO SER SEQRES 10 A 217 VAL PHE ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SER SEQRES 11 A 217 GLY THR ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR SEQRES 12 A 217 PRO ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA SEQRES 13 A 217 LEU GLN SER GLY ASN SER GLN GLU SER VAL THR GLU GLN SEQRES 14 A 217 ASP SER LYS ASP SER THR TYR SER LEU SER SER THR LEU SEQRES 15 A 217 THR LEU SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR SEQRES 16 A 217 ALA CYS GLU VAL THR HIS GLN GLY LEU SER SER PRO VAL SEQRES 17 A 217 THR LYS SER PHE ASN ARG GLY GLU CYS SEQRES 1 B 230 GLU ILE SER GLU VAL GLN LEU VAL GLU SER GLY GLY GLY SEQRES 2 B 230 LEU VAL GLN PRO GLY GLY SER LEU ARG LEU SER CYS ALA SEQRES 3 B 230 ALA SER GLY PHE ASN VAL LYS THR GLY LEU ILE HIS TRP SEQRES 4 B 230 VAL ARG GLN ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA SEQRES 5 B 230 TYR ILE THR PRO TYR TYR GLY SER THR SER TYR ALA ASP SEQRES 6 B 230 SER VAL LYS GLY ARG PHE THR ILE SER ALA ASP THR SER SEQRES 7 B 230 LYS ASN THR ALA TYR LEU GLN MET ASN SER LEU ARG ALA SEQRES 8 B 230 GLU ASP THR ALA VAL TYR TYR CYS ALA ARG GLU TYR TYR SEQRES 9 B 230 ARG TRP TYR THR ALA ILE ASP TYR TRP GLY GLN GLY THR SEQRES 10 B 230 LEU VAL THR VAL SER SER ALA SER THR LYS GLY PRO SER SEQRES 11 B 230 VAL PHE PRO LEU ALA PRO SER SER LYS SER THR SER GLY SEQRES 12 B 230 GLY THR ALA ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE SEQRES 13 B 230 PRO GLU PRO VAL THR VAL SER TRP ASN SER GLY ALA LEU SEQRES 14 B 230 THR SER GLY VAL HIS THR PHE PRO ALA VAL LEU GLN SER SEQRES 15 B 230 SER GLY LEU TYR SER LEU SER SER VAL VAL THR VAL PRO SEQRES 16 B 230 SER SER SER LEU GLY THR GLN THR TYR ILE CYS ASN VAL SEQRES 17 B 230 ASN HIS LYS PRO SER ASN THR LYS VAL ASP LYS LYS VAL SEQRES 18 B 230 GLU PRO LYS SER CYS ASP LYS THR HIS SEQRES 1 X 80 GLY SER HIS MET GLN ILE PHE VAL LYS THR LEU THR GLY SEQRES 2 X 80 LYS THR ILE THR LEU GLU VAL GLU PRO SER ASP THR ILE SEQRES 3 X 80 GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE SEQRES 4 X 80 PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN SEQRES 5 X 80 LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN ILE GLN SEQRES 6 X 80 LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU ARG GLY SEQRES 7 X 80 GLY ASP SEQRES 1 Y 79 GLY SER HIS MET GLN ILE PHE VAL LYS THR LEU THR GLY SEQRES 2 Y 79 LYS THR ILE THR LEU GLU VAL GLU PRO SER ASP THR ILE SEQRES 3 Y 79 GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE SEQRES 4 Y 79 PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN SEQRES 5 Y 79 LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN ILE GLN SEQRES 6 Y 79 ARG GLU SER THR LEU HIS LEU VAL LEU ARG LEU ARG GLY SEQRES 7 Y 79 GLY FORMUL 5 HOH *25(H2 O) HELIX 1 1 GLN A 79 PHE A 83 5 5 HELIX 2 2 SER A 123 LYS A 128 1 6 HELIX 3 3 LYS A 185 LYS A 190 1 6 HELIX 4 4 ASN B 28 GLY B 32 5 5 HELIX 5 5 ARG B 87 THR B 91 5 5 HELIX 6 6 TYR B 101 TYR B 104 5 4 HELIX 7 7 SER B 134 LYS B 136 5 3 HELIX 8 8 SER B 163 ALA B 165 5 3 HELIX 9 9 SER B 194 LEU B 196 5 3 HELIX 10 10 LYS B 208 ASN B 211 5 4 HELIX 11 11 THR X 22 GLY X 35 1 14 HELIX 12 12 PRO X 37 ASP X 39 5 3 HELIX 13 13 LEU X 56 ASN X 60 5 5 HELIX 14 14 THR Y 22 GLY Y 35 1 14 HELIX 15 15 PRO Y 37 ASP Y 39 5 3 SHEET 1 A 6 SER A 9 ALA A 13 0 SHEET 2 A 6 THR A 104 ILE A 108 1 O LYS A 105 N LEU A 11 SHEET 3 A 6 THR A 85 TYR A 91 -1 N TYR A 86 O THR A 104 SHEET 4 A 6 ALA A 34 GLN A 38 -1 N GLN A 38 O THR A 85 SHEET 5 A 6 LYS A 45 TYR A 49 -1 O LEU A 47 N TRP A 35 SHEET 6 A 6 SER A 53 LEU A 54 -1 O SER A 53 N TYR A 49 SHEET 1 B 4 SER A 9 ALA A 13 0 SHEET 2 B 4 THR A 104 ILE A 108 1 O LYS A 105 N LEU A 11 SHEET 3 B 4 THR A 85 TYR A 91 -1 N TYR A 86 O THR A 104 SHEET 4 B 4 PHE A 98 PHE A 100 -1 O THR A 99 N GLN A 90 SHEET 1 C 3 VAL A 19 CYS A 23 0 SHEET 2 C 3 ASP A 70 ILE A 75 -1 O PHE A 71 N CYS A 23 SHEET 3 C 3 PHE A 62 SER A 67 -1 N SER A 65 O THR A 72 SHEET 1 D 4 SER A 116 PHE A 120 0 SHEET 2 D 4 THR A 131 PHE A 141 -1 O LEU A 137 N PHE A 118 SHEET 3 D 4 TYR A 175 SER A 184 -1 O LEU A 177 N LEU A 138 SHEET 4 D 4 SER A 161 VAL A 165 -1 N GLN A 162 O THR A 180 SHEET 1 E 4 ALA A 155 LEU A 156 0 SHEET 2 E 4 LYS A 147 VAL A 152 -1 N VAL A 152 O ALA A 155 SHEET 3 E 4 VAL A 193 THR A 199 -1 O GLU A 197 N GLN A 149 SHEET 4 E 4 VAL A 207 ASN A 212 -1 O LYS A 209 N CYS A 196 SHEET 1 F 4 GLN B 3 SER B 7 0 SHEET 2 F 4 LEU B 18 SER B 25 -1 O SER B 21 N SER B 7 SHEET 3 F 4 THR B 78 MET B 83 -1 O MET B 83 N LEU B 18 SHEET 4 F 4 PHE B 68 ASP B 73 -1 N SER B 71 O TYR B 80 SHEET 1 G 6 GLY B 10 VAL B 12 0 SHEET 2 G 6 THR B 114 VAL B 118 1 O THR B 117 N GLY B 10 SHEET 3 G 6 ALA B 92 GLU B 99 -1 N ALA B 92 O VAL B 116 SHEET 4 G 6 LEU B 33 GLN B 39 -1 N VAL B 37 O TYR B 95 SHEET 5 G 6 LEU B 45 ILE B 51 -1 O GLU B 46 N ARG B 38 SHEET 6 G 6 THR B 58 TYR B 60 -1 O SER B 59 N TYR B 50 SHEET 1 H 4 GLY B 10 VAL B 12 0 SHEET 2 H 4 THR B 114 VAL B 118 1 O THR B 117 N GLY B 10 SHEET 3 H 4 ALA B 92 GLU B 99 -1 N ALA B 92 O VAL B 116 SHEET 4 H 4 ILE B 107 TRP B 110 -1 O ASP B 108 N ARG B 98 SHEET 1 I 4 SER B 127 LEU B 131 0 SHEET 2 I 4 THR B 142 TYR B 152 -1 O LEU B 148 N PHE B 129 SHEET 3 I 4 TYR B 183 PRO B 192 -1 O VAL B 191 N ALA B 143 SHEET 4 I 4 VAL B 170 THR B 172 -1 N HIS B 171 O VAL B 188 SHEET 1 J 4 THR B 138 SER B 139 0 SHEET 2 J 4 THR B 142 TYR B 152 -1 O THR B 142 N SER B 139 SHEET 3 J 4 TYR B 183 PRO B 192 -1 O VAL B 191 N ALA B 143 SHEET 4 J 4 VAL B 176 LEU B 177 -1 N VAL B 176 O SER B 184 SHEET 1 K 3 THR B 158 TRP B 161 0 SHEET 2 K 3 ILE B 202 HIS B 207 -1 O ASN B 204 N SER B 160 SHEET 3 K 3 THR B 212 LYS B 217 -1 O VAL B 214 N VAL B 205 SHEET 1 L 5 THR X 12 VAL X 17 0 SHEET 2 L 5 MET X 1 THR X 7 -1 N MET X 1 O VAL X 17 SHEET 3 L 5 THR X 66 LEU X 71 1 O LEU X 67 N LYS X 6 SHEET 4 L 5 GLN X 41 PHE X 45 -1 N ILE X 44 O HIS X 68 SHEET 5 L 5 LYS X 48 GLN X 49 -1 O LYS X 48 N PHE X 45 SHEET 1 M 5 ILE Y 13 GLU Y 16 0 SHEET 2 M 5 GLN Y 2 LYS Y 6 -1 N VAL Y 5 O ILE Y 13 SHEET 3 M 5 THR Y 66 LEU Y 71 1 O LEU Y 67 N LYS Y 6 SHEET 4 M 5 GLN Y 41 PHE Y 45 -1 N ARG Y 42 O VAL Y 70 SHEET 5 M 5 LYS Y 48 GLN Y 49 -1 O LYS Y 48 N PHE Y 45 SSBOND 1 CYS A 23 CYS A 88 1555 1555 2.06 SSBOND 2 CYS A 136 CYS A 196 1555 1555 2.03 SSBOND 3 CYS B 22 CYS B 96 1555 1555 2.04 SSBOND 4 CYS B 147 CYS B 203 1555 1555 2.05 LINK NZ LYS X 63 C GLY Y 76 1555 1555 1.49 CISPEP 1 TYR A 142 PRO A 143 0 -1.06 CISPEP 2 PHE B 153 PRO B 154 0 -9.98 CISPEP 3 GLU B 155 PRO B 156 0 -3.29 CRYST1 106.806 88.117 90.226 90.00 108.28 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 0.009363 0.000000 0.003092 0.00000 SCALE2 0.000000 0.011349 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011672 0.00000