HEADER SIGNALING PROTEIN 22-JAN-08 2JZZ TITLE SOLID-STATE NMR STRUCTURE OF MICROCRYSTALLINE UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS PROTEIN MICROCRYSTAL, CYTOPLASM, UBL CONJUGATION, SIGNALING PROTEIN EXPDTA SOLID-STATE NMR NUMMDL 20 AUTHOR T.MANOLIKAS,T.HERRMANN,B.H.MEIER REVDAT 6 08-MAY-24 2JZZ 1 REMARK REVDAT 5 14-JUN-23 2JZZ 1 REMARK REVDAT 4 19-FEB-20 2JZZ 1 REMARK REVDAT 3 24-FEB-09 2JZZ 1 VERSN REVDAT 2 29-APR-08 2JZZ 1 JRNL REVDAT 1 25-MAR-08 2JZZ 0 JRNL AUTH T.MANOLIKAS,T.HERRMANN,B.H.MEIER JRNL TITL PROTEIN STRUCTURE DETERMINATION FROM 13C SPIN-DIFFUSION JRNL TITL 2 SOLID-STATE NMR SPECTROSCOPY. JRNL REF J.AM.CHEM.SOC. V. 130 3959 2008 JRNL REFN ISSN 0002-7863 JRNL PMID 18321098 JRNL DOI 10.1021/JA078039S REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ATNOS/CANDID, OPALP REMARK 3 AUTHORS : HERRMANN, GUNTERT AND WUTHRICH (ATNOS/CANDID), REMARK 3 LUGINBUHL, GUNTERT, BILLETER AND WUTHRICH (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: OPALP, LUGINBUHL, P. ET AL., J. BIOMOL. REMARK 3 NMR 1996,8,(2),136-146; KONRADI, R. ET AL., COMPUT. PHYS. REMARK 3 COMMUN. 2000, 124, 139-147. REMARK 4 REMARK 4 2JZZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000100502. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 270 REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 5.5 MG/ML [U-99% 13C; U-98% 15N] REMARK 210 UBIQUITIN, 20 MM AMMONIUM REMARK 210 ACETATE, 20 MM CITRIC ACID, 60 V/ REMARK 210 V 2-METHYL-2,4-PENTANDIOL, 0.05 % REMARK 210 SODIUM AZIDE, 100 % H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 13C-13C PROTON DRIVEN SPIN REMARK 210 -DIFFUSION REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: PROTON DRIVEN SPIN-DIFFUSION EXPERIMENTS WERE CARRIED OUT REMARK 210 USING A TRIPLE 2.5-MM CHEMAGNETICS/VARIAN T3 PROBE AT A STATIC REMARK 210 MAGNETIC FIELD OF 14.09 T. THREE 2D 13C-13C CORRELATION SPECTRA REMARK 210 HAVE BEEN RECORDED WITH 100, 250 AND 400 MS MIXING TIME AT 12 REMARK 210 KHZ MAGIC ANGLE SPINNING (MAS) AND A SAMPLE TEMPERATURE OF 269 K. REMARK 217 REMARK 217 SOLID STATE NMR STUDY REMARK 217 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLID REMARK 217 STATE NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 217 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 217 THESE RECORDS ARE MEANINGLESS. 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 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 2 PHE A 45 CB - CG - CD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 2 PHE A 45 CB - CG - CD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 3 PHE A 45 CB - CG - CD2 ANGL. DEV. = -4.9 DEGREES REMARK 500 3 PHE A 45 CB - CG - CD1 ANGL. DEV. = 4.5 DEGREES REMARK 500 8 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 9 LEU A 50 CB - CG - CD2 ANGL. DEV. = -10.3 DEGREES REMARK 500 10 PHE A 45 CB - CG - CD1 ANGL. DEV. = -4.8 DEGREES REMARK 500 10 TYR A 59 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 12 PHE A 45 CB - CG - CD2 ANGL. DEV. = 5.3 DEGREES REMARK 500 12 PHE A 45 CB - CG - CD1 ANGL. DEV. = -5.2 DEGREES REMARK 500 14 TYR A 59 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES REMARK 500 17 PHE A 45 CB - CG - CD2 ANGL. DEV. = 4.4 DEGREES REMARK 500 17 PHE A 45 CB - CG - CD1 ANGL. DEV. = -4.7 DEGREES REMARK 500 18 THR A 7 OG1 - CB - CG2 ANGL. DEV. = -14.2 DEGREES REMARK 500 18 THR A 7 CA - CB - CG2 ANGL. DEV. = 11.1 DEGREES REMARK 500 19 ARG A 72 NE - CZ - NH2 ANGL. DEV. = -3.2 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 1 LEU A 8 -119.20 34.21 REMARK 500 1 THR A 12 130.34 68.27 REMARK 500 1 PRO A 19 44.33 -78.67 REMARK 500 1 SER A 20 -5.09 -148.71 REMARK 500 1 ASP A 52 -64.70 68.66 REMARK 500 1 ASN A 60 95.53 46.00 REMARK 500 1 LYS A 63 -71.62 64.22 REMARK 500 1 GLU A 64 -19.66 -41.16 REMARK 500 1 SER A 65 -73.11 -38.23 REMARK 500 1 THR A 66 62.58 24.28 REMARK 500 1 HIS A 68 156.75 50.51 REMARK 500 1 ARG A 72 149.77 146.49 REMARK 500 1 LEU A 73 -49.55 61.16 REMARK 500 2 GLN A 2 82.12 24.71 REMARK 500 2 THR A 7 36.05 -145.94 REMARK 500 2 LEU A 8 62.79 -165.10 REMARK 500 2 THR A 9 -114.37 52.79 REMARK 500 2 ILE A 13 -46.99 69.82 REMARK 500 2 THR A 14 126.70 69.70 REMARK 500 2 LEU A 15 106.68 -160.44 REMARK 500 2 PRO A 19 44.82 -79.82 REMARK 500 2 SER A 20 -21.36 -143.36 REMARK 500 2 PHE A 45 -91.73 -68.49 REMARK 500 2 ALA A 46 -81.71 -88.00 REMARK 500 2 LEU A 50 66.05 83.20 REMARK 500 2 ASN A 60 103.29 65.01 REMARK 500 2 LYS A 63 -63.11 66.70 REMARK 500 2 GLU A 64 -35.25 -25.13 REMARK 500 2 THR A 66 52.63 24.30 REMARK 500 2 LEU A 73 93.81 47.87 REMARK 500 3 LYS A 11 3.61 -158.65 REMARK 500 3 ILE A 13 -30.74 -160.09 REMARK 500 3 THR A 14 121.21 78.02 REMARK 500 3 PRO A 19 -177.49 -64.03 REMARK 500 3 SER A 20 -19.52 62.53 REMARK 500 3 PHE A 45 10.33 -162.06 REMARK 500 3 ALA A 46 25.03 -142.96 REMARK 500 3 ASN A 60 143.24 67.37 REMARK 500 3 GLN A 62 100.78 -175.44 REMARK 500 3 LYS A 63 -47.66 65.27 REMARK 500 3 THR A 66 84.68 24.78 REMARK 500 3 VAL A 70 78.25 -107.45 REMARK 500 3 ARG A 72 -45.47 -131.05 REMARK 500 3 LEU A 73 112.87 -165.57 REMARK 500 4 THR A 7 49.12 -90.03 REMARK 500 4 THR A 9 162.79 62.56 REMARK 500 4 SER A 20 -2.01 69.46 REMARK 500 4 ASP A 21 -176.67 -57.38 REMARK 500 4 ALA A 46 -76.35 51.48 REMARK 500 4 LEU A 50 -21.17 69.76 REMARK 500 REMARK 500 THIS ENTRY HAS 316 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 60 ILE A 61 3 -148.61 REMARK 500 GLY A 75 GLY A 76 3 143.46 REMARK 500 LYS A 63 GLU A 64 5 145.31 REMARK 500 TYR A 59 ASN A 60 7 -144.81 REMARK 500 LEU A 50 GLU A 51 15 142.96 REMARK 500 TYR A 59 ASN A 60 15 -147.62 REMARK 500 ASN A 60 ILE A 61 15 -149.86 REMARK 500 GLU A 34 GLY A 35 18 -149.48 REMARK 500 GLY A 10 LYS A 11 20 -138.25 REMARK 500 ASN A 60 ILE A 61 20 142.62 REMARK 500 ARG A 74 GLY A 75 20 -147.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 3 PHE A 45 0.10 SIDE CHAIN REMARK 500 5 ARG A 54 0.08 SIDE CHAIN REMARK 500 6 ARG A 54 0.11 SIDE CHAIN REMARK 500 8 ARG A 42 0.08 SIDE CHAIN REMARK 500 9 PHE A 45 0.07 SIDE CHAIN REMARK 500 11 ARG A 74 0.11 SIDE CHAIN REMARK 500 12 TYR A 59 0.08 SIDE CHAIN REMARK 500 14 TYR A 59 0.08 SIDE CHAIN REMARK 500 17 ARG A 42 0.10 SIDE CHAIN REMARK 500 17 PHE A 45 0.09 SIDE CHAIN REMARK 500 18 TYR A 59 0.10 SIDE CHAIN REMARK 500 18 ARG A 74 0.16 SIDE CHAIN REMARK 500 19 ARG A 54 0.10 SIDE CHAIN REMARK 500 20 PHE A 45 0.13 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7111 RELATED DB: BMRB REMARK 900 13C/15N CHEMICAL SHIFT ASSIGNMENTS DBREF 2JZZ A 1 76 UNP P62988 UBIQ_HUMAN 1 76 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 HELIX 1 1 THR A 22 GLU A 34 1 13 HELIX 2 2 THR A 55 ASN A 60 1 6 SHEET 1 A 2 ILE A 3 VAL A 5 0 SHEET 2 A 2 ILE A 13 LEU A 15 -1 O LEU A 15 N ILE A 3 SHEET 1 B 2 ILE A 44 PHE A 45 0 SHEET 2 B 2 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1