HEADER DE NOVO PROTEIN 13-MAR-25 9M8W TITLE NMR STRUCTURE OF PROTEINMPNN-DESIGHED UBIQUITIN VARIANT R4 AT PH 3 TITLE 2 WITH 8 M UREA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEINMPNN-DESIGNED UBIQUITIN VARIANT R4; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI BL21(DE3); SOURCE 3 ORGANISM_TAXID: 469008; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS UBIQUITIN VARIANT, R4, UREA, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.-P.WU,L.-Y.CHEN,W.-C.CHUANG REVDAT 1 11-FEB-26 9M8W 0 JRNL AUTH K.-P.WU,L.-Y.CHEN JRNL TITL NMR STRUCTURE OF R4 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NOE REMARK 4 REMARK 4 9M8W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1300057447. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 3 REMARK 210 IONIC STRENGTH : 80 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-15N] PROTEINMPNN REMARK 210 -DESIGNED UBIQUITIN VARIANT R4, REMARK 210 93% H2O/7% D2O; 1 MM [U-13C; U- REMARK 210 15N] PROTEINMPNN-DESIGNED REMARK 210 UBIQUITIN VARIANT R4, 93% H2O/7% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 3D HN(CO)CA; 3D HNCACB; REMARK 210 3D CBCA(CO)NH; 3D HNCO; 3D HN(CA) REMARK 210 CO; 3D HCCH-TOCSY; 3D CCH-TOCSY; REMARK 210 3D H(CCO)NH; 3D C(CCO)NH; 3D 1H- REMARK 210 15N NOESY; 3D 1H-15N TOCSY; 2D REMARK 210 1H-13C HSQC; 2D 1H-15N HSQC; 3D REMARK 210 1H-13C NOESY; 3D HBHA(CO)NH; 3D REMARK 210 HNCANNH REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, ARTINA, I-PINE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 150 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: 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 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: 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 12 -176.08 -56.99 REMARK 500 1 ASP A 24 -82.27 27.41 REMARK 500 1 ASP A 26 -87.67 -61.85 REMARK 500 1 THR A 27 147.62 161.70 REMARK 500 1 ASP A 58 35.93 -88.12 REMARK 500 1 ASN A 65 57.37 71.04 REMARK 500 2 THR A 12 174.56 -55.26 REMARK 500 2 THR A 27 151.88 89.57 REMARK 500 2 ASP A 58 36.18 -85.88 REMARK 500 2 ARG A 77 32.72 -88.38 REMARK 500 2 GLU A 82 -177.73 53.79 REMARK 500 3 THR A 12 -179.85 -54.45 REMARK 500 3 ASP A 24 -26.68 -38.50 REMARK 500 3 THR A 27 153.16 88.09 REMARK 500 3 ASP A 58 35.60 -87.32 REMARK 500 3 ASN A 69 -2.11 78.44 REMARK 500 4 THR A 12 174.02 -51.12 REMARK 500 4 THR A 27 143.78 73.94 REMARK 500 4 ASP A 58 34.21 -91.50 REMARK 500 4 ASN A 65 50.48 71.85 REMARK 500 5 THR A 12 176.50 -58.71 REMARK 500 5 ASP A 24 -27.22 -37.55 REMARK 500 5 THR A 27 148.84 70.62 REMARK 500 5 LYS A 59 142.79 -170.57 REMARK 500 5 THR A 60 153.89 -42.55 REMARK 500 5 ASN A 69 31.79 71.67 REMARK 500 6 THR A 12 176.12 -56.37 REMARK 500 6 VAL A 22 -160.72 -127.78 REMARK 500 6 ASP A 26 -90.00 -87.87 REMARK 500 6 THR A 27 157.11 165.92 REMARK 500 6 ASN A 65 35.90 72.60 REMARK 500 6 ASN A 69 -8.47 81.52 REMARK 500 6 ARG A 77 32.13 -92.74 REMARK 500 7 THR A 12 174.58 -53.28 REMARK 500 7 ASP A 24 -27.69 -38.95 REMARK 500 7 THR A 27 153.37 81.89 REMARK 500 7 ASP A 58 32.09 -88.61 REMARK 500 7 THR A 60 151.16 -44.48 REMARK 500 7 ASN A 65 48.26 79.43 REMARK 500 7 ARG A 77 56.53 -92.52 REMARK 500 8 THR A 12 -177.98 -53.90 REMARK 500 8 ASP A 24 -31.34 -37.08 REMARK 500 8 ASP A 26 -92.97 -103.73 REMARK 500 8 THR A 27 156.01 165.95 REMARK 500 8 ASP A 58 36.59 -90.48 REMARK 500 8 ASN A 69 33.87 70.67 REMARK 500 9 THR A 12 174.52 -56.82 REMARK 500 9 THR A 27 142.88 112.11 REMARK 500 9 LYS A 67 -169.77 -120.71 REMARK 500 9 ASN A 69 -2.04 81.77 REMARK 500 REMARK 500 THIS ENTRY HAS 107 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36736 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF PROTEINMPNN-DESIGHED UBIQUITIN VARIANT R4 AT PH 3 REMARK 900 WITH 8 M UREA DBREF 9M8W A 1 83 PDB 9M8W 9M8W 1 83 SEQRES 1 A 83 GLY SER GLY GLY SER MET THR ILE TYR VAL LYS THR GLN SEQRES 2 A 83 ASP GLY LYS ILE ILE LYS LEU GLU VAL ASN ASP ASP ASP SEQRES 3 A 83 THR ILE LEU ASN VAL LYS LYS LYS ILE GLU GLU LYS THR SEQRES 4 A 83 GLY ILE PRO PRO GLU ASP GLN ILE LEU ILE TYR LYS GLY SEQRES 5 A 83 LYS VAL LEU GLU ASP ASP LYS THR LEU ALA ASP TYR ASN SEQRES 6 A 83 ILE LYS GLU ASN ASP THR LEU TYR LEU VAL LYS ARG LEU SEQRES 7 A 83 LYS SER PRO GLU ARG HELIX 1 AA1 THR A 27 GLY A 40 1 14 HELIX 2 AA2 LEU A 61 ASN A 65 5 5 SHEET 1 AA1 5 ILE A 17 ASN A 23 0 SHEET 2 AA1 5 SER A 5 LYS A 11 -1 N ILE A 8 O LEU A 20 SHEET 3 AA1 5 ASP A 70 LYS A 76 1 O LEU A 72 N TYR A 9 SHEET 4 AA1 5 GLN A 46 TYR A 50 -1 N ILE A 49 O TYR A 73 SHEET 5 AA1 5 LYS A 53 VAL A 54 -1 O LYS A 53 N TYR A 50 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL MASTER 152 0 0 2 5 0 0 6 662 1 0 7 END