HEADER SIGNALING PROTEIN 02-JAN-14 2MJB TITLE SOLUTION NMR STRUCTURE OF UBIQUITIN REFINED AGAINST DIPOLAR COUPLINGS TITLE 2 IN 4 MEDIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-60S RIBOSOMAL PROTEIN L40; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UBIQUITIN-LIKE 3 DOMAIN; COMPND 5 SYNONYM: CEP52, UBIQUITIN A-52 RESIDUE RIBOSOMAL PROTEIN FUSION COMPND 6 PRODUCT 1, UBIQUITIN, 60S RIBOSOMAL PROTEIN L40, UBIQUITIN-40S COMPND 7 RIBOSOMAL PROTEIN S27A, UBIQUITIN CARBOXYL EXTENSION PROTEIN 80, COMPND 8 UBIQUITIN, 40S RIBOSOMAL PROTEIN S27A, POLYUBIQUITIN-B, UBIQUITIN, COMPND 9 POLYUBIQUITIN-C, UBIQUITIN; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UBA52, UBCEP2, RPS27A, UBA80, UBCEP1, UBB, UBC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET11A KEYWDS RESIDUAL DIPOLAR COUPLING, SQUALAMINE, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.MALTSEV,A.GRISHAEV,J.ROCHE,M.ZASLOFF,A.BAX REVDAT 2 14-JUN-23 2MJB 1 REMARK REVDAT 1 26-MAR-14 2MJB 0 JRNL AUTH A.S.MALTSEV,A.GRISHAEV,J.ROCHE,M.ZASLOFF,A.BAX JRNL TITL IMPROVED CROSS VALIDATION OF A STATIC UBIQUITIN STRUCTURE JRNL TITL 2 DERIVED FROM HIGH PRECISION RESIDUAL DIPOLAR COUPLINGS JRNL TITL 3 MEASURED IN A DRUG-BASED LIQUID CRYSTALLINE PHASE. JRNL REF J.AM.CHEM.SOC. V. 136 3752 2014 JRNL REFN ISSN 0002-7863 JRNL PMID 24568736 JRNL DOI 10.1021/JA4132642 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, X-PLOR NIH REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT AGAINST RESIDUAL DIPOLAR REMARK 3 COUPLINGS IN 4 ALIGNMENT MEDIA, DISTANCE, DIHEDRAL ANGLE, AND REMARK 3 THROUGH-H BOND (N/C) J-COUPLING RESTRAINTS WITH HYDROGEN-BONDING REMARK 3 DATABASE POTENTIAL STARTING FROM THE COORDINATES OF 1D3Z ENTRY. REMARK 4 REMARK 4 2MJB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000103681. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308; 298 REMARK 210 PH : 6.0; 6.0 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 13C; U-100% 15N; REMARK 210 U-100% 2H] UBIQUITIN, 20 MM [U- REMARK 210 100% 2H] D4-IMIDAZOLE, 4.8 MM REMARK 210 SQUALAMINE, 1.5 MM HEXANOL, 10 REMARK 210 MM SODIUM PHOSPHATE, 95% H2O/5% REMARK 210 D2O; 0.5 MM [U-100% 13C; U-100% REMARK 210 15N; U-100% 2H] UBIQUITIN, 20 MM REMARK 210 [U-100% 2H] D4-IMIDAZOLE, 1.5 MM REMARK 210 HEXANOL, 10 MM SODIUM PHOSPHATE, REMARK 210 95% H2O/5% D2O; 0.6 MM [U-100% REMARK 210 13C; U-100% 15N] UBIQUITIN, 13 REMARK 210 MG/ML PF1 PHAGE, 140 MM SODIUM REMARK 210 CHLORIDE, 95% H2O/5% D2O; 0.8 MM REMARK 210 [U-100% 13C; U-100% 15N; U-100% REMARK 210 2H] UBIQUITIN, 14 MG/ML PF1 REMARK 210 PHAGE, 150 MM SODIUM CHLORIDE, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N IPAP HSQC; 2D 1H-15N REMARK 210 TROSY HSQC; 3D TROSY HNCO; 3D REMARK 210 HN(CO)CA 1H-1H DECOUPLED; 1H-15N REMARK 210 ARTSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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: 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 4 ARG A 74 -54.44 -139.84 REMARK 500 12 ARG A 74 -56.89 -149.35 REMARK 500 18 LEU A 73 114.36 -160.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D3Z RELATED DB: PDB REMARK 900 SOLUTION NMR STRUCTURE OF UBIQUITIN REFINED AGAINST DIPOLAR REMARK 900 COUPLINGS IN 2 MEDIA REMARK 900 RELATED ID: 6457 RELATED DB: BMRB DBREF 2MJB A 1 76 UNP P62987 RL40_HUMAN 229 304 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 GLN 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 1 THR A 22 GLY A 35 1 14 HELIX 2 2 PRO A 37 ASP A 39 5 3 HELIX 3 3 LEU A 56 ASN A 60 5 5 SHEET 1 A 5 THR A 12 GLU A 16 0 SHEET 2 A 5 GLN A 2 LYS A 6 -1 N VAL A 5 O ILE A 13 SHEET 3 A 5 THR A 66 LEU A 71 1 O LEU A 67 N PHE A 4 SHEET 4 A 5 GLN A 41 PHE A 45 -1 N ILE A 44 O HIS A 68 SHEET 5 A 5 LYS A 48 GLN A 49 -1 O LYS A 48 N 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 MODEL 1