PDB Short entry for 1C3T HEADER DE NOVO PROTEIN 28-JUL-99 1C3T TITLE ROTAMER STRAIN AS A DETERMINANT OF PROTEIN STRUCTURAL SPECIFICITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (1D8 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PAED4 KEYWDS PROTEIN DESIGN, HYDROPHOBIC CORE, PACKING, ROTAMERS, ROC, UBIQUITIN, KEYWDS 2 DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.A.LAZAR,E.C.JOHNSON,J.R.DESJARLAIS,T.M.HANDEL REVDAT 6 10-APR-24 1C3T 1 SEQADV REVDAT 5 14-MAR-18 1C3T 1 REMARK SEQADV REVDAT 4 24-FEB-09 1C3T 1 VERSN REVDAT 3 05-JUL-00 1C3T 1 SOURCE DBREF SEQADV HEADER REVDAT 2 10-JAN-00 1C3T 1 JRNL COMPND SOURCE REVDAT 1 20-AUG-99 1C3T 0 JRNL AUTH G.A.LAZAR,E.C.JOHNSON,J.R.DESJARLAIS,T.M.HANDEL JRNL TITL ROTAMER STRAIN AS A DETERMINANT OF PROTEIN STRUCTURAL JRNL TITL 2 SPECIFICITY. JRNL REF PROTEIN SCI. V. 8 2598 1999 JRNL REFN ISSN 0961-8368 JRNL PMID 10631975 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.A.LAZAR,J.R.DESJARLAIS,T.M.HANDEL REMARK 1 TITL DE NOVO DESIGN OF THE HYDROPHOBIC CORE OF UBIQUITIN REMARK 1 REF PROTEIN SCI. V. 6 1167 1997 REMARK 1 REFN ISSN 0961-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH E.C.JOHNSON,G.A.LAZAR,J.R.DESJARLAIS,T.M.HANDEL REMARK 1 TITL SOLUTION STRUCTURE AND DYNAMICS OF A DESIGNED HYDROPHOBIC REMARK 1 TITL 2 CORE VARIANT OF UBIQUITIN REMARK 1 REF STRUCTURE FOLD.DES. V. 7 967 1999 REMARK 1 REFN ISSN 0969-2126 REMARK 1 DOI 10.1016/S0969-2126(99)80123-3 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES WERE CALCULATED USING 3212 NONREDUNDANT NOE REMARK 3 RESTRAINTS, 84 REMARK 3 DIHEDRAL RESTRAINTS, AND 68 H-BOND RESTRAINTS. REMARK 4 REMARK 4 1C3T COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-AUG-99. REMARK 100 THE DEPOSITION ID IS D_1000009428. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303.00 REMARK 210 PH : 5.80 REMARK 210 IONIC STRENGTH : 50 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2 MM 13C/15N 1D8 UBIQUITIN, 25 REMARK 210 MM SODIUM PHOSPHATE, 25 MM REMARK 210 SODIUM ACETATE (D3), 0.02% REMARK 210 SODIUM AZIDE, PH 5.8 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 15N NOESY; 3D 13C NOESY; 4D REMARK 210 13C/13C NOESY; 2D JCCOC; 2D JCNC; REMARK 210 3D LRCC; 3D HACAHB AND HNHA; REMARK 210 HNHB; H/D EXCHANGE FOR H-BONDS REMARK 210 SPECTROMETER FIELD STRENGTH : 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 : RESTRAINED MOLECULAR REMARK 210 DYNAMICS/SIMULATED ANNEALING REMARK 210 USING THE ARIA PROCEDURE OF REMARK 210 NILGES (NILGES ET AL., J MOL REMARK 210 BIOL, 1997, 269: 408- 422) AND REMARK 210 EXPLICIT SWAPPING OF NON- REMARK 210 STEREOSPECIFICALLY ASSIGNED REMARK 210 METHYLS AND METHYLENES (FOLMER REMARK 210 ET AL. J BIOMOL NMR, 1997, 9: REMARK 210 245-258). REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 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: THIS STRUCTURE WAS DETERMINED USING TRIPLE- RESONANCE NMR REMARK 210 SPECTROSCOPY. 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 THR A 7 -156.23 -117.16 REMARK 500 1 TYR A 59 -78.88 -113.61 REMARK 500 1 ASN A 60 41.43 163.41 REMARK 500 1 GLU A 64 76.83 62.00 REMARK 500 1 ARG A 74 150.52 -37.71 REMARK 500 2 LYS A 11 132.87 -36.65 REMARK 500 2 ASN A 60 70.53 41.96 REMARK 500 2 GLU A 64 71.09 62.99 REMARK 500 2 ARG A 74 132.25 -171.91 REMARK 500 3 ARG A 72 150.36 -35.53 REMARK 500 3 LEU A 73 146.40 -34.66 REMARK 500 4 ASP A 21 155.04 -45.68 REMARK 500 4 LYS A 33 -61.31 -103.48 REMARK 500 4 TYR A 59 33.18 -98.66 REMARK 500 4 GLU A 64 40.87 74.89 REMARK 500 4 ARG A 72 96.95 40.74 REMARK 500 5 ASP A 21 157.72 -41.74 REMARK 500 5 ASP A 52 103.59 -53.88 REMARK 500 5 ASN A 60 33.93 38.81 REMARK 500 5 GLU A 64 84.58 46.95 REMARK 500 5 LEU A 73 94.95 -38.63 REMARK 500 6 ASP A 21 151.88 -41.51 REMARK 500 6 ASP A 52 103.49 -53.08 REMARK 500 6 GLU A 64 77.62 84.24 REMARK 500 6 ARG A 72 102.22 -40.64 REMARK 500 6 ARG A 74 -89.06 157.75 REMARK 500 7 THR A 7 -167.98 -115.50 REMARK 500 7 ASN A 60 33.38 37.00 REMARK 500 8 LYS A 33 -67.87 -120.57 REMARK 500 8 TYR A 59 34.21 -92.91 REMARK 500 8 ASN A 60 45.55 36.50 REMARK 500 8 LYS A 63 124.32 -38.33 REMARK 500 8 GLU A 64 72.98 84.14 REMARK 500 8 LEU A 73 42.83 36.16 REMARK 500 8 ARG A 74 92.78 45.80 REMARK 500 9 LYS A 11 130.89 -38.98 REMARK 500 9 ILE A 44 71.52 -101.88 REMARK 500 9 ASP A 52 106.54 -51.17 REMARK 500 9 ASN A 60 57.55 39.33 REMARK 500 9 ARG A 72 104.62 -43.43 REMARK 500 10 ILE A 44 78.99 -117.64 REMARK 500 10 ARG A 72 64.10 33.58 REMARK 500 11 GLU A 64 89.93 58.73 REMARK 500 11 ARG A 72 65.64 -64.63 REMARK 500 11 LEU A 73 91.09 68.13 REMARK 500 11 ARG A 74 131.68 -38.24 REMARK 500 12 LYS A 11 104.17 -41.79 REMARK 500 12 ASP A 52 93.00 -63.59 REMARK 500 12 GLU A 64 81.46 70.45 REMARK 500 12 ARG A 72 65.14 -118.00 REMARK 500 REMARK 500 THIS ENTRY HAS 104 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1C3T A 1 76 UNP P62988 UBIQ_HUMAN 87 162 SEQADV 1C3T LEU A 3 UNP P62988 ILE 89 ENGINEERED MUTATION SEQADV 1C3T LEU A 13 UNP P62988 ILE 99 ENGINEERED MUTATION SEQADV 1C3T VAL A 15 UNP P62988 LEU 101 ENGINEERED MUTATION SEQADV 1C3T LEU A 17 UNP P62988 VAL 103 ENGINEERED MUTATION SEQADV 1C3T VAL A 23 UNP P62988 ILE 109 ENGINEERED MUTATION SEQADV 1C3T LEU A 26 UNP P62988 VAL 112 ENGINEERED MUTATION SEQADV 1C3T LEU A 61 UNP P62988 ILE 147 ENGINEERED MUTATION SEQADV 1C3T ILE A 67 UNP P62988 LEU 153 ENGINEERED MUTATION SEQRES 1 A 76 MET GLN LEU PHE VAL LYS THR LEU THR GLY LYS THR LEU SEQRES 2 A 76 THR VAL GLU LEU GLU PRO SER ASP THR VAL GLU ASN LEU 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 LEU GLN LYS GLU SER SEQRES 6 A 76 THR ILE HIS LEU VAL LEU ARG LEU ARG GLY GLY HELIX 1 1 THR A 22 LYS A 33 1 12 HELIX 2 2 PRO A 37 GLN A 41 5 5 HELIX 3 3 LEU A 56 TYR A 59 5 4 SHEET 1 A 5 THR A 12 GLU A 16 0 SHEET 2 A 5 GLN A 2 LYS A 6 -1 N LEU A 3 O VAL A 15 SHEET 3 A 5 THR A 66 VAL A 70 1 O ILE A 67 N LYS A 6 SHEET 4 A 5 ARG A 42 PHE A 45 -1 O ARG A 42 N VAL A 70 SHEET 5 A 5 LYS A 48 GLN A 49 -1 N LYS A 48 O 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