HEADER PLANT PROTEIN 24-MAR-24 8YSY TITLE UBIQUITIN(NATIVE) FROM ORYZA SATIVA SUBSP. JAPONICA (RICE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA JAPONICA GROUP; SOURCE 3 ORGANISM_COMMON: JAPANESE RICE; SOURCE 4 ORGANISM_TAXID: 39947; SOURCE 5 GENE: UB-CEP52-1, UBQ1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS UBIQUITIN, MONOMER, PLANT PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.T.ADHADA,S.P.SARMA REVDAT 3 30-OCT-24 8YSY 1 JRNL REVDAT 2 16-OCT-24 8YSY 1 JRNL REVDAT 1 09-OCT-24 8YSY 0 JRNL AUTH S.T.ADHADA,S.P.SARMA JRNL TITL SLOW CONFORMATIONAL EXCHANGE BETWEEN PARTIALLY FOLDED AND JRNL TITL 2 NEAR-NATIVE STATES OF UBIQUITIN: EVIDENCE FOR A MULTISTATE JRNL TITL 3 FOLDING MODEL. JRNL REF BIOCHEMISTRY V. 63 2565 2024 JRNL REFN ISSN 0006-2960 JRNL PMID 39351677 JRNL DOI 10.1021/ACS.BIOCHEM.4C00321 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.98.15, X-PLOR NIH 3.4 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES WERE CALCULATED USING REMARK 3 AUTOMATED NOE ASSIGNMENT PROTOCOL WITH 15N NOES ASSIGNED AND 13C REMARK 3 NOES UNASSIGNED REMARK 4 REMARK 4 8YSY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1300046287. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 25 REMARK 210 PRESSURE : 1 BAR REMARK 210 SAMPLE CONTENTS : 1 MM [U-15N] UBIQUITIN FROM RICE REMARK 210 (ORYZA SATIVA), 90% H2O/10% D2O; REMARK 210 1 MM [U-13C; U-15N] UBIQUITIN REMARK 210 FROM RICE (ORYZA SATIVA), 90% REMARK 210 H2O/10% D2O; 1 MM UBIQUITIN FROM REMARK 210 RICE (ORYZA SATIVA), 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCACB; 3D C(CO)NH; 3D 1H-15N REMARK 210 TOCSY; 3D 1H-13C NOESY; 3D 1H- REMARK 210 15N NOESY; 3D H(CCO)NH; 1D DOSY; REMARK 210 3D HNCO REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : DIRECT DRIVE; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : AGILENT; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS 2.5.2, VNMRJ REMARK 210 4.2, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 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 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 HZ3 LYS A 28 OD1 ASP A 53 1.57 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 2 GLU A 65 14.35 83.48 REMARK 500 3 THR A 8 -179.12 -67.10 REMARK 500 3 ASN A 61 61.87 60.69 REMARK 500 3 GLU A 65 9.86 90.28 REMARK 500 4 GLU A 65 16.59 86.21 REMARK 500 4 ARG A 75 -72.40 68.61 REMARK 500 5 GLU A 65 16.64 82.00 REMARK 500 5 ARG A 75 111.95 -164.42 REMARK 500 6 GLU A 65 16.24 82.96 REMARK 500 6 ARG A 75 -47.52 179.86 REMARK 500 7 THR A 8 -179.37 -63.15 REMARK 500 7 PRO A 39 5.60 -66.90 REMARK 500 7 ALA A 47 18.80 55.15 REMARK 500 7 ARG A 75 -66.05 72.42 REMARK 500 8 ALA A 47 18.48 54.76 REMARK 500 8 ASN A 61 62.97 60.06 REMARK 500 8 LEU A 74 -164.61 63.25 REMARK 500 9 ASN A 61 60.70 60.68 REMARK 500 9 GLU A 65 29.57 80.52 REMARK 500 9 ARG A 75 -52.60 -151.20 REMARK 500 10 LEU A 74 -82.35 65.93 REMARK 500 11 PRO A 39 7.93 -69.70 REMARK 500 12 ASN A 61 61.76 67.22 REMARK 500 12 ARG A 75 -60.25 -102.63 REMARK 500 13 ASN A 61 62.12 63.42 REMARK 500 13 GLU A 65 31.34 80.89 REMARK 500 16 GLU A 65 30.13 83.12 REMARK 500 16 ARG A 75 89.28 -169.70 REMARK 500 18 ASN A 61 62.73 60.70 REMARK 500 18 LEU A 74 -98.53 61.81 REMARK 500 19 THR A 8 -176.26 -63.36 REMARK 500 19 GLU A 65 18.01 82.73 REMARK 500 19 LEU A 74 103.86 -59.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36652 RELATED DB: BMRB REMARK 900 UBIQUITIN(NATIVE) FROM ORYZA SATIVA SUBSP. JAPONICA (RICE) DBREF 8YSY A 2 77 UNP P0CH34 RL40A_ORYSJ 1 76 SEQADV 8YSY MET A 1 UNP P0CH34 INITIATING METHIONINE SEQRES 1 A 77 MET MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR SEQRES 2 A 77 ILE THR LEU GLU VAL GLU SER SER ASP THR ILE ASP ASN SEQRES 3 A 77 VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO SEQRES 4 A 77 ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU SEQRES 5 A 77 ASP GLY ARG THR LEU ALA ASP TYR ASN ILE GLN LYS GLU SEQRES 6 A 77 SER THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HELIX 1 AA1 THR A 23 GLY A 36 1 14 SHEET 1 AA1 5 THR A 13 VAL A 18 0 SHEET 2 AA1 5 MET A 2 LYS A 7 -1 N ILE A 4 O LEU A 16 SHEET 3 AA1 5 SER A 66 LEU A 72 1 O LEU A 68 N LYS A 7 SHEET 4 AA1 5 GLN A 42 PHE A 46 -1 N ILE A 45 O HIS A 69 SHEET 5 AA1 5 LYS A 49 GLN A 50 -1 O LYS A 49 N PHE A 46 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 143 0 0 1 5 0 0 6 607 1 0 6 END