HEADER SIGNALING PROTEIN 09-JAN-19 6QF8 TITLE SOLUTION NMR ENSEMBLE FOR HUMAN UBIQUITIN AT 298K COMPILED USING THE TITLE 2 COMAND METHOD COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYUBIQUITIN-B; COMPND 3 CHAIN: A; COMPND 4 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: UBB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMAND METHOD, R-FACTOR REFINEMENT, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.ELGAMACY,V.TRUFFAULT,H.ZHU,M.COLES REVDAT 2 15-MAY-19 6QF8 1 JRNL REMARK REVDAT 1 10-APR-19 6QF8 0 JRNL AUTH M.ELGAMACY,M.RISS,H.ZHU,V.TRUFFAULT,M.COLES JRNL TITL MAPPING LOCAL CONFORMATIONAL LANDSCAPES OF PROTEINS IN JRNL TITL 2 SOLUTION. JRNL REF STRUCTURE V. 27 853 2019 JRNL REFN ISSN 0969-2126 JRNL PMID 30930065 JRNL DOI 10.1016/J.STR.2019.03.005 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NAMD 2.12, SHINE, COMAND REMARK 3 AUTHORS : UNIVERSITY OF ILLINOIS (NAMD 2.12), RISS & COLES REMARK 3 (SHINE), IN HOUSE (COMAND) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FRAMES SELECTED FROM UNRESTRAINED MD REMARK 3 SIMULATIONS TO MINIMISE THE OVERALL NOESY-BASED R-FACTOR REMARK 4 REMARK 4 6QF8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1292100069. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.8 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-99% 13C; U-99% 15N] REMARK 210 HUMAN UBIQUITIN, 40 MM SODIUM REMARK 210 PHOSPHATE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D CNH-NOESY; 3D C(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCEIII REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, ROSETTA 3.6 REMARK 210 METHOD USED : R-FACTOR BASED FRAME PICKING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : NOESY-BASED R-FACTOR SELECTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 ALA A -2 REMARK 465 MET A -1 REMARK 465 GLY A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 REMARK 500 REMARK: NULL 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 5 GLU A 64 CB GLU A 64 CG 0.120 REMARK 500 9 ARG A 54 CZ ARG A 54 NH2 -0.085 REMARK 500 10 HIS A 68 CG HIS A 68 CD2 0.054 REMARK 500 20 ARG A 72 CZ ARG A 72 NH2 -0.090 REMARK 500 REMARK 500 REMARK: NULL 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 1 ASP A 39 CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 ASP A 39 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 ARG A 42 NH1 - CZ - NH2 ANGL. DEV. = -7.0 DEGREES REMARK 500 1 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 9.3 DEGREES REMARK 500 1 ASP A 52 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 TYR A 59 CB - CG - CD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 1 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 7.9 DEGREES REMARK 500 1 ARG A 72 NE - CZ - NH2 ANGL. DEV. = -6.7 DEGREES REMARK 500 1 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 ARG A 74 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 ARG A 74 NH1 - CZ - NH2 ANGL. DEV. = -9.1 DEGREES REMARK 500 2 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 ARG A 74 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 3 TYR A 59 CB - CG - CD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 3 LEU A 67 CB - CG - CD1 ANGL. DEV. = 11.3 DEGREES REMARK 500 3 LEU A 69 CB - CG - CD1 ANGL. DEV. = 10.6 DEGREES REMARK 500 3 ARG A 72 NH1 - CZ - NH2 ANGL. DEV. = -7.7 DEGREES REMARK 500 3 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 4 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 PHE A 45 CB - CG - CD2 ANGL. DEV. = -4.9 DEGREES REMARK 500 4 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 6.1 DEGREES REMARK 500 4 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -7.9 DEGREES REMARK 500 4 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 ARG A 74 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 5 ARG A 42 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 5 TYR A 59 CB - CG - CD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 5 TYR A 59 CB - CG - CD1 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 6 VAL A 26 CA - CB - CG2 ANGL. DEV. = -9.3 DEGREES REMARK 500 6 ARG A 42 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 6 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 PHE A 4 CB - CG - CD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 7 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 LEU A 67 CB - CG - CD1 ANGL. DEV. = 10.2 DEGREES REMARK 500 7 ARG A 74 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 8 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 8 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 8 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 8 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 8 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 8 ARG A 74 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 9 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 9 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 9 ARG A 72 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 9 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 10 ARG A 42 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 10 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 106 ANGLE DEVIATIONS. 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 2 LYS A 63 150.24 -42.97 REMARK 500 3 ALA A 46 68.03 33.73 REMARK 500 6 ASP A 52 -65.47 -15.05 REMARK 500 7 PRO A 37 117.59 -35.01 REMARK 500 7 GLU A 64 14.75 81.77 REMARK 500 9 ALA A 46 13.86 55.88 REMARK 500 9 LYS A 63 125.35 -25.63 REMARK 500 10 LYS A 63 139.20 -33.34 REMARK 500 11 ALA A 46 96.33 7.53 REMARK 500 11 ASN A 60 38.11 78.30 REMARK 500 11 GLU A 64 23.05 83.50 REMARK 500 12 ARG A 72 132.14 -32.90 REMARK 500 13 THR A 9 -8.26 -59.97 REMARK 500 13 ARG A 72 154.39 -44.69 REMARK 500 16 GLU A 34 -8.06 -140.13 REMARK 500 17 ALA A 46 42.97 38.82 REMARK 500 19 LYS A 63 151.95 -41.57 REMARK 500 19 GLU A 64 -9.88 72.99 REMARK 500 20 LYS A 33 -77.49 -80.93 REMARK 500 20 ASN A 60 64.95 63.43 REMARK 500 20 GLU A 64 29.56 82.80 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 1 GLN A 62 0.09 SIDE CHAIN REMARK 500 2 ARG A 42 0.12 SIDE CHAIN REMARK 500 3 ARG A 54 0.10 SIDE CHAIN REMARK 500 3 ARG A 74 0.10 SIDE CHAIN REMARK 500 4 ARG A 42 0.07 SIDE CHAIN REMARK 500 4 ARG A 54 0.10 SIDE CHAIN REMARK 500 5 ARG A 42 0.09 SIDE CHAIN REMARK 500 5 ARG A 54 0.09 SIDE CHAIN REMARK 500 5 ARG A 72 0.09 SIDE CHAIN REMARK 500 6 ARG A 42 0.12 SIDE CHAIN REMARK 500 6 TYR A 59 0.12 SIDE CHAIN REMARK 500 7 ARG A 74 0.10 SIDE CHAIN REMARK 500 8 ARG A 74 0.10 SIDE CHAIN REMARK 500 9 TYR A 59 0.08 SIDE CHAIN REMARK 500 10 ARG A 42 0.09 SIDE CHAIN REMARK 500 11 PHE A 4 0.09 SIDE CHAIN REMARK 500 11 ARG A 74 0.11 SIDE CHAIN REMARK 500 12 PHE A 4 0.12 SIDE CHAIN REMARK 500 12 ARG A 74 0.14 SIDE CHAIN REMARK 500 13 TYR A 59 0.07 SIDE CHAIN REMARK 500 14 ARG A 42 0.12 SIDE CHAIN REMARK 500 15 ARG A 54 0.14 SIDE CHAIN REMARK 500 18 ARG A 42 0.10 SIDE CHAIN REMARK 500 18 ARG A 54 0.19 SIDE CHAIN REMARK 500 19 ARG A 54 0.15 SIDE CHAIN REMARK 500 20 ARG A 42 0.09 SIDE CHAIN REMARK 500 20 ARG A 54 0.17 SIDE CHAIN REMARK 500 20 ARG A 72 0.10 SIDE CHAIN REMARK 500 20 ARG A 74 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34351 RELATED DB: BMRB REMARK 900 SOLUTION NMR ENSEMBLE FOR HUMAN UBIQUITIN AT 298K COMPILED USING REMARK 900 THE COMAND METHOD DBREF 6QF8 A 1 76 UNP J3QS39 J3QS39_HUMAN 1 76 SEQADV 6QF8 ALA A -2 UNP J3QS39 EXPRESSION TAG SEQADV 6QF8 MET A -1 UNP J3QS39 EXPRESSION TAG SEQADV 6QF8 GLY A 0 UNP J3QS39 EXPRESSION TAG SEQRES 1 A 79 ALA MET GLY MET GLN ILE PHE VAL LYS THR LEU THR GLY SEQRES 2 A 79 LYS THR ILE THR LEU GLU VAL GLU PRO SER ASP THR ILE SEQRES 3 A 79 GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE SEQRES 4 A 79 PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN SEQRES 5 A 79 LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN ILE GLN SEQRES 6 A 79 LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU ARG GLY SEQRES 7 A 79 GLY HELIX 1 AA1 THR A 22 GLY A 35 1 14 HELIX 2 AA2 PRO A 37 ASP A 39 5 3 SHEET 1 AA1 5 THR A 12 GLU A 16 0 SHEET 2 AA1 5 GLN A 2 LYS A 6 -1 N VAL A 5 O ILE A 13 SHEET 3 AA1 5 THR A 66 LEU A 71 1 O LEU A 67 N PHE A 4 SHEET 4 AA1 5 GLN A 41 PHE A 45 -1 N ILE A 44 O HIS A 68 SHEET 5 AA1 5 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