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 <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) : 2.60
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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
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