HEADER GENE REGULATION 14-AUG-09 2KN5 TITLE A CORRESPONDENCE BETWEEN SOLUTION-STATE DYNAMICS OF AN INDIVIDUAL TITLE 2 PROTEIN AND THE SEQUENCE AND CONFORMATIONAL DIVERSITY OF ITS FAMILY COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; 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: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BACKRUB, RESIDUAL DIPOLAR COUPLING, BACKBONE FLEXIBILITY, PROTEIN KEYWDS 2 DYNAMICS, CYTOPLASM, ISOPEPTIDE BOND, NUCLEUS, PHOSPHOPROTEIN, UBL KEYWDS 3 CONJUGATION, GENE REGULATION EXPDTA SOLUTION NMR NUMMDL 50 AUTHOR G.D.FRIEDLAND REVDAT 2 16-MAR-22 2KN5 1 REMARK REVDAT 1 17-NOV-09 2KN5 0 JRNL AUTH G.D.FRIEDLAND,N.A.LAKOMEK,C.GRIESINGER,J.MEILER,T.KORTEMME JRNL TITL A CORRESPONDENCE BETWEEN SOLUTION-STATE DYNAMICS OF AN JRNL TITL 2 INDIVIDUAL PROTEIN AND THE SEQUENCE AND CONFORMATIONAL JRNL TITL 3 DIVERSITY OF ITS FAMILY. JRNL REF PLOS COMPUT.BIOL. V. 5 00393 2009 JRNL REFN ISSN 1553-734X JRNL PMID 19478996 JRNL DOI 10.1371/JOURNAL.PCBI.1000393 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ROSETTA REMARK 3 AUTHORS : ROSETTA COMMONS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A 10,000-MEMBER SET OF STRUCTURES WAS REMARK 3 GENERATED USING ROSETTA AND BACKRUB CONFORMATIONAL SAMPLING. THE REMARK 3 50-MEMBER ENSEMBLE PRESENTED HERE WAS OPTIMIZED BY SELECTING REMARK 3 STRUCTURES FROM THIS SET THAT MAXIMIZE AGREEMENT WITH THE REMARK 3 RESIDUAL DIPOLAR COUPLINGS. SEVERAL OF THE STRUCTURES IN REMARK 3 ENSEMBLE ARE IDENTICAL AS CHOSEN BY THE OPTIMIZATION ALGORITHM. REMARK 4 REMARK 4 2KN5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000101327. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.9 MM [U-100% 13C; U-100% 15N] REMARK 210 HUMAN UBIQUITIN, 90% H2O/10% D2O; REMARK 210 0.6-0.9 MM [U-100% 13C; U-100% REMARK 210 15N] HUMAN UBIQUITIN, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ROSETTA REMARK 210 METHOD USED : MONTE CARLO OPTIMIZATION OF REMARK 210 ENSEMBLE MEMBERS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 50 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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 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: 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 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 4 LEU A 71 O - C - N ANGL. DEV. = -11.9 DEGREES REMARK 500 8 SER A 65 O - C - N ANGL. DEV. = -10.1 DEGREES REMARK 500 9 SER A 65 O - C - N ANGL. DEV. = -10.1 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 THR A 7 -162.49 -79.00 REMARK 500 1 ASP A 52 -5.02 -56.31 REMARK 500 1 ASN A 60 29.38 41.36 REMARK 500 1 ILE A 61 107.15 -51.44 REMARK 500 1 GLN A 62 -169.04 -107.00 REMARK 500 1 ARG A 72 79.85 -101.50 REMARK 500 1 ARG A 74 55.03 -95.34 REMARK 500 2 ALA A 46 76.54 58.07 REMARK 500 2 ASN A 60 16.08 53.97 REMARK 500 2 ILE A 61 90.46 -52.10 REMARK 500 2 ARG A 74 77.61 -106.16 REMARK 500 3 GLN A 49 128.13 -36.93 REMARK 500 3 ASN A 60 36.74 76.54 REMARK 500 5 GLU A 64 26.19 46.40 REMARK 500 7 ASP A 21 136.88 -38.82 REMARK 500 7 ILE A 23 -19.19 -47.52 REMARK 500 7 PHE A 45 113.15 -160.17 REMARK 500 8 THR A 7 -168.95 -101.55 REMARK 500 8 ALA A 28 -3.28 -57.80 REMARK 500 8 ASP A 32 -60.90 -25.98 REMARK 500 9 THR A 7 -168.95 -101.55 REMARK 500 9 ALA A 28 -3.28 -57.80 REMARK 500 9 ASP A 32 -60.90 -25.98 REMARK 500 10 ASP A 58 5.59 -68.67 REMARK 500 10 GLU A 64 32.86 80.02 REMARK 500 10 LEU A 73 170.29 -57.39 REMARK 500 11 ASP A 58 5.59 -68.67 REMARK 500 11 GLU A 64 32.86 80.02 REMARK 500 11 LEU A 73 170.29 -57.39 REMARK 500 12 LEU A 8 -6.85 -57.44 REMARK 500 12 LYS A 33 -30.10 -139.26 REMARK 500 12 ASN A 60 40.67 71.52 REMARK 500 12 GLU A 64 44.18 80.31 REMARK 500 13 ILE A 23 -35.64 -37.69 REMARK 500 13 GLN A 31 -38.62 -39.92 REMARK 500 13 GLU A 64 39.58 34.42 REMARK 500 14 THR A 7 -172.27 -67.44 REMARK 500 14 GLU A 64 37.93 73.09 REMARK 500 14 ARG A 74 61.45 -115.35 REMARK 500 15 ASP A 32 -35.79 -34.57 REMARK 500 15 GLU A 64 46.87 71.69 REMARK 500 16 LYS A 33 -75.93 -80.28 REMARK 500 16 GLU A 34 -70.02 -55.18 REMARK 500 17 ASP A 58 -16.33 -46.92 REMARK 500 17 LYS A 63 146.20 -36.54 REMARK 500 18 GLN A 62 -166.64 -110.33 REMARK 500 18 ARG A 74 59.95 -105.51 REMARK 500 19 GLU A 34 -77.26 -117.22 REMARK 500 20 THR A 7 -169.80 -72.04 REMARK 500 20 ILE A 23 -30.52 -37.56 REMARK 500 REMARK 500 THIS ENTRY HAS 96 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 4 LEU A 71 -20.73 REMARK 500 6 GLN A 2 13.57 REMARK 500 6 GLY A 75 -13.02 REMARK 500 7 GLY A 53 10.09 REMARK 500 8 LEU A 8 -19.15 REMARK 500 8 SER A 65 19.84 REMARK 500 9 LEU A 8 -19.15 REMARK 500 9 SER A 65 19.84 REMARK 500 21 GLY A 75 -10.68 REMARK 500 22 GLY A 75 -10.68 REMARK 500 23 VAL A 17 -11.21 REMARK 500 24 ASP A 21 -14.20 REMARK 500 25 GLY A 10 -10.25 REMARK 500 31 GLY A 75 -17.85 REMARK 500 40 SER A 65 12.14 REMARK 500 48 THR A 7 -11.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D3Z RELATED DB: PDB REMARK 900 RELATED ID: 1XQQ RELATED DB: PDB REMARK 900 RELATED ID: 2NR2 RELATED DB: PDB REMARK 900 RELATED ID: 2K39 RELATED DB: PDB DBREF 2KN5 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 PRO A 37 ASP A 39 5 3 HELIX 3 3 THR A 55 ASN A 60 5 6 SHEET 1 A 5 THR A 12 GLU A 16 0 SHEET 2 A 5 GLN A 2 LYS A 6 -1 N ILE A 3 O LEU A 15 SHEET 3 A 5 THR A 66 LEU A 71 1 O LEU A 67 N LYS A 6 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 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 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20 MODEL 21 MODEL 22 MODEL 23 MODEL 24 MODEL 25 MODEL 26 MODEL 27 MODEL 28 MODEL 29 MODEL 30 MODEL 31 MODEL 32 MODEL 33 MODEL 34 MODEL 35 MODEL 36 MODEL 37 MODEL 38 MODEL 39 MODEL 40 MODEL 41 MODEL 42 MODEL 43 MODEL 44 MODEL 45 MODEL 46 MODEL 47 MODEL 48 MODEL 49 MODEL 50