PDB Short entry for 1ZW7 HEADER STRUCTURAL PROTEIN 03-JUN-05 1ZW7 TITLE ELIMINATION OF THE C-CAP IN UBIQUITIN STRUCTURE, DYNAMICS AND TITLE 2 THERMODYNAMIC CONSEQUENCES 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: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: UBI1, RPL40A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DYNAMICS, THERMODYNAMICS, STRUCTURAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 21 AUTHOR D.N.ERMOLENKO,B.DANGI,A.M.GRONENBORN,G.I.MAKHATADZE REVDAT 5 20-OCT-21 1ZW7 1 REMARK SEQADV REVDAT 4 24-FEB-09 1ZW7 1 VERSN REVDAT 3 06-MAR-07 1ZW7 1 JRNL REVDAT 2 16-JAN-07 1ZW7 1 JRNL REVDAT 1 16-MAY-06 1ZW7 0 JRNL AUTH D.N.ERMOLENKO,B.DANGI,A.GVRITISHVILI,A.M.GRONENBORN, JRNL AUTH 2 G.I.MAKHATADZE JRNL TITL ELIMINATION OF THE C-CAP IN UBIQUITIN-STRUCTURE, DYNAMICS JRNL TITL 2 AND THERMODYNAMIC CONSEQUENCES. JRNL REF BIOPHYS.CHEM. V. 126 25 2007 JRNL REFN ISSN 0301-4622 JRNL PMID 16713063 JRNL DOI 10.1016/J.BPC.2006.03.017 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0, CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE REMARK 3 -KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON, REMARK 3 WARREN (CNS), BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE, REMARK 3 JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZW7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000033194. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5 REMARK 210 IONIC STRENGTH : 30 MM ACTATE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1-2 MM OF APPROPRIATELY LABELED REMARK 210 MUTANT UBIQUITIN REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H-15N HSQC; 3D HNCACB; REMARK 210 CBCA(CO)NH; HNCO; HBHA(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : STRUCTURE CALCULATIONS WERE REMARK 210 PERFORMED USING CNS VERSION 1.0 REMARK 210 ON AN SGI PLATFORM. THE REMARK 210 REFINEMENT PROTOCOL FOR REMARK 210 ANNEALING INVOLVED TORSION ANGLE REMARK 210 HEATING (100 K, 1000 STEPS) REMARK 210 FOLLOWED BY COOLING IN TORSION REMARK 210 (100 K, 5000 STEPS) AND REMARK 210 CARTESIAN SPACE (1000 K, 10,000 REMARK 210 STEPS). REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM 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: 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 GLN A 31 32.92 -90.38 REMARK 500 1 ALA A 32 -70.22 -117.37 REMARK 500 1 PHE A 45 34.90 -89.30 REMARK 500 1 ALA A 46 -66.71 66.70 REMARK 500 1 LYS A 63 161.64 -33.66 REMARK 500 1 GLU A 64 77.91 66.69 REMARK 500 1 ARG A 74 15.28 -149.81 REMARK 500 2 LYS A 29 1.41 -65.04 REMARK 500 2 ALA A 46 -60.40 70.96 REMARK 500 2 ILE A 61 -159.99 -100.52 REMARK 500 2 LYS A 63 167.00 -39.83 REMARK 500 2 GLU A 64 82.28 77.27 REMARK 500 2 LEU A 71 68.71 -113.64 REMARK 500 2 ARG A 74 14.51 -146.01 REMARK 500 3 ILE A 30 31.75 -78.05 REMARK 500 3 ALA A 32 -73.95 -108.83 REMARK 500 3 PRO A 34 -158.67 -81.52 REMARK 500 3 ALA A 46 -61.35 69.12 REMARK 500 3 LYS A 63 164.64 -42.77 REMARK 500 3 GLU A 64 81.16 68.50 REMARK 500 3 ARG A 74 18.65 -149.53 REMARK 500 4 GLN A 2 116.65 -161.68 REMARK 500 4 ILE A 30 35.08 -79.00 REMARK 500 4 ALA A 33 131.13 66.55 REMARK 500 4 PRO A 34 -73.98 -82.42 REMARK 500 4 ALA A 46 -34.44 70.54 REMARK 500 4 GLN A 62 -157.10 -61.13 REMARK 500 4 GLU A 64 84.97 70.84 REMARK 500 4 ARG A 74 17.22 -149.46 REMARK 500 5 PRO A 34 -95.47 -69.98 REMARK 500 5 ALA A 46 -61.59 66.28 REMARK 500 5 TYR A 59 36.07 -141.54 REMARK 500 5 GLN A 62 -157.25 -69.07 REMARK 500 5 GLU A 64 85.44 73.10 REMARK 500 5 ARG A 74 14.88 -143.71 REMARK 500 6 GLN A 2 125.64 -171.85 REMARK 500 6 LEU A 8 34.32 -76.88 REMARK 500 6 ALA A 46 -61.64 69.29 REMARK 500 6 TYR A 59 36.44 -143.19 REMARK 500 6 LYS A 63 136.92 -39.12 REMARK 500 6 GLU A 64 84.67 75.83 REMARK 500 6 SER A 65 117.32 -160.95 REMARK 500 6 ARG A 74 16.09 -173.29 REMARK 500 7 GLN A 31 32.73 -89.71 REMARK 500 7 ALA A 32 -82.27 -105.47 REMARK 500 7 ALA A 46 -58.15 71.00 REMARK 500 7 TYR A 59 36.92 -146.39 REMARK 500 7 GLN A 62 -153.96 -85.36 REMARK 500 7 GLU A 64 76.62 66.06 REMARK 500 7 LEU A 71 66.45 -115.90 REMARK 500 REMARK 500 THIS ENTRY HAS 158 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1ZW7 A 1 76 UNP P61864 UBIQ_YEAST 1 76 SEQADV 1ZW7 ALA A 11 UNP P61864 LYS 11 ENGINEERED MUTATION SEQADV 1ZW7 ALA A 32 UNP P61864 ASP 32 ENGINEERED MUTATION SEQADV 1ZW7 ALA A 33 UNP P61864 LYS 33 ENGINEERED MUTATION SEQADV 1ZW7 PRO A 34 UNP P61864 GLU 34 ENGINEERED MUTATION SEQADV 1ZW7 GLU A 42 UNP P61864 ARG 42 ENGINEERED MUTATION SEQADV 1ZW7 HIS A 77 UNP P61864 EXPRESSION TAG SEQADV 1ZW7 HIS A 78 UNP P61864 EXPRESSION TAG SEQADV 1ZW7 HIS A 79 UNP P61864 EXPRESSION TAG SEQADV 1ZW7 HIS A 80 UNP P61864 EXPRESSION TAG SEQADV 1ZW7 HIS A 81 UNP P61864 EXPRESSION TAG SEQADV 1ZW7 HIS A 82 UNP P61864 EXPRESSION TAG SEQRES 1 A 82 MET GLN ILE PHE VAL LYS THR LEU THR GLY ALA THR ILE SEQRES 2 A 82 THR LEU GLU VAL GLU SER SER ASP THR ILE ASP ASN VAL SEQRES 3 A 82 LYS SER LYS ILE GLN ALA ALA PRO GLY ILE PRO PRO ASP SEQRES 4 A 82 GLN GLN GLU LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 82 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 82 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HIS HIS SEQRES 7 A 82 HIS HIS HIS HIS HELIX 1 1 THR A 22 LYS A 29 1 8 HELIX 2 2 PRO A 37 GLN A 41 5 5 HELIX 3 3 LEU A 56 ASN A 60 5 5 SHEET 1 A 4 ILE A 13 LEU A 15 0 SHEET 2 A 4 ILE A 3 LYS A 6 -1 N VAL A 5 O ILE A 13 SHEET 3 A 4 THR A 66 VAL A 70 1 O LEU A 67 N PHE A 4 SHEET 4 A 4 GLU A 42 LEU A 43 -1 N GLU A 42 O VAL A 70 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