HEADER STRUCTURAL PROTEIN 06-MAR-19 6JLT OBSLTE 30-OCT-19 6JLT 6K4I TITLE THE PARTIALLY DISORDERED CONFORMATION OF UBIQUITIN (Q41N VARIANT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 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: UBB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN, PRESSURE, PARTIALLY DISORDERED CONFORMATION, STRUCTURAL KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.WAKAMOTO,T.IKEYA,S.KITAZAWA,N.J.BAXTER,M.P.WILLIAMSON,R.KITAHARA REVDAT 2 30-OCT-19 6JLT 1 OBSLTE REVDAT 1 20-MAR-19 6JLT 0 JRNL AUTH T.WAKAMOTO,T.IKEYA,S.KITAZAWA,N.J.BAXTER,M.P.WILLIAMSON, JRNL AUTH 2 R.KITAHARA JRNL TITL PARAMAGNETIC RELAXATION ENHANCEMENT-ASSISTED STRUCTURAL JRNL TITL 2 DETERMINATION OF A PARTIALLY DISORDERED CONFORMATION OF JRNL TITL 3 UBIQUITIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.98.OMP REMARK 3 AUTHORS : IKEYA, T., IKEDA, S., KIGAWA, T., ITO, Y. & REMARK 3 GUNTERT, P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6JLT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1300011229. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 4.0 REMARK 210 IONIC STRENGTH : 30 REMARK 210 PRESSURE : 2500 BAR REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 13C; U-99% 15N] REMARK 210 PROTEIN, 30 MM DEUTERIUM SODIUM REMARK 210 ACETATE, 0.2 MM DSS, 90% H2O/10% REMARK 210 D2O; 0.3 MM [U-99% 15N] PROTEIN, REMARK 210 30 MM DEUTERIUM SODIUM ACETATE, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : SIMULTANEOUS ACQUISITION 13C/15N REMARK 210 -E; 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800.34 MHZ; 600.23 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE3; AVNACE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.98, NMRVIEW REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1900 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 6 VAL A 17 CA - CB - CG1 ANGL. DEV. = 13.2 DEGREES REMARK 500 8 ARG A 42 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 9 ARG A 42 N - CA - CB ANGL. DEV. = -11.4 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 PRO A 38 3.68 -63.43 REMARK 500 1 ASN A 60 70.33 53.26 REMARK 500 1 ARG A 74 -167.53 -72.90 REMARK 500 2 ASP A 32 -8.11 -59.74 REMARK 500 2 SER A 65 -176.00 -69.08 REMARK 500 3 ASP A 32 0.26 -64.43 REMARK 500 3 GLN A 40 16.52 59.72 REMARK 500 3 ASN A 60 73.65 49.10 REMARK 500 3 ARG A 74 -167.71 -74.40 REMARK 500 4 ASN A 60 71.38 43.05 REMARK 500 4 GLU A 64 18.85 52.69 REMARK 500 4 ARG A 72 101.54 -167.36 REMARK 500 4 ARG A 74 -177.47 -68.67 REMARK 500 5 ALA A 46 55.52 -172.83 REMARK 500 6 ASN A 60 73.55 50.95 REMARK 500 6 ARG A 74 -164.06 -70.76 REMARK 500 7 LYS A 33 -31.14 -132.61 REMARK 500 8 ASN A 60 75.34 46.23 REMARK 500 9 GLN A 40 -74.84 70.81 REMARK 500 10 ALA A 46 49.06 -159.54 REMARK 500 10 ARG A 54 -167.96 -127.37 REMARK 500 11 ASN A 60 74.11 46.82 REMARK 500 12 LYS A 33 -38.93 -133.25 REMARK 500 14 ASP A 32 -9.72 -57.86 REMARK 500 14 ASN A 41 132.83 -173.89 REMARK 500 14 ARG A 72 109.53 -169.11 REMARK 500 14 ARG A 74 -176.34 -66.40 REMARK 500 15 GLU A 34 -34.08 -130.66 REMARK 500 15 ASN A 60 74.74 49.92 REMARK 500 16 GLN A 40 15.82 58.82 REMARK 500 16 ASN A 60 75.61 45.60 REMARK 500 19 GLU A 34 -33.63 -133.55 REMARK 500 19 GLN A 40 33.89 70.89 REMARK 500 20 GLN A 40 6.59 59.08 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 9 ARG A 42 0.10 SIDE CHAIN REMARK 500 14 ARG A 74 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36241 RELATED DB: BMRB REMARK 900 THE PARTIALLY DISORDERED CONFORMATION OF UBIQUITIN (Q41N VARIANT) DBREF 6JLT A 1 76 UNP J3QS39 J3QS39_HUMAN 1 76 SEQADV 6JLT ASN A 41 UNP J3QS39 GLN 41 ENGINEERED MUTATION 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 ASN 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 AA1 THR A 22 GLY A 35 1 14 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 VAL A 70 1 O LEU A 67 N PHE A 4 SHEET 4 AA1 5 ARG A 42 PHE A 45 -1 N ARG A 42 O VAL A 70 SHEET 5 AA1 5 LYS A 48 LEU A 50 -1 O LEU A 50 N LEU A 43 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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