HEADER UNKNOWN FUNCTION 20-FEB-08 2K14 TITLE SOLUTION STRUCTURE OF THE SOLUBLE DOMAIN OF THE NFED TITLE 2 PROTEIN YUAF FROM BACILLUS SUBTILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: YUAF PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN (UNP RESIDUES 97-174); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 STRAIN: MARBURG 168; SOURCE 4 GENE: YUAF; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PHIHO1421; SOURCE 8 OTHER_DETAILS: THE PLASMID PHIHO1421 WAS CONSTRUCTED BY SOURCE 9 FUSING THE CODING SEQUENCE OF RESIDUES 97-174 OF YUAF TO SOURCE 10 THE 3'-END OF THE MALE GENE CONTAINING AN ADDITIONAL SOURCE 11 THROMBIN CLEAVAGE SITE. THE SOLUBLE C-TERMINAL DOMAIN OF SOURCE 12 YUAF WAS GENERATED BY CLEAVING OFF THE MALE PART BY SOURCE 13 DIGESTION WITH THROMBIN. KEYWDS YUAF, BACILLUS SUBTILIS, NFED-LIKE PROTEIN, CELLULAR STRESS, KEYWDS 2 UNKNOWN FUNCTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.A.WALKER,M.HINDERHOFER,D.J.WITTE,W.BOOS,H.M.MOLLER REVDAT 3 24-FEB-09 2K14 1 VERSN REVDAT 2 30-SEP-08 2K14 1 JRNL REVDAT 1 26-AUG-08 2K14 0 JRNL AUTH C.A.WALKER,M.HINDERHOFER,D.J.WITTE,W.BOOS, JRNL AUTH 2 H.M.MOLLER JRNL TITL SOLUTION STRUCTURE OF THE SOLUBLE DOMAIN OF THE JRNL TITL 2 NFED PROTEIN YUAF FROM BACILLUS SUBTILIS. JRNL REF J.BIOMOL.NMR V. 42 69 2008 JRNL REFN ISSN 0925-2738 JRNL PMID 18696230 JRNL DOI 10.1007/S10858-008-9261-3 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 8 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 400 STARTING STRUCTURES FOR REMARK 3 REFINEMENT WERE GENERATED WITH THE FINAL SET OF CONSTRAINTS BY REMARK 3 TORSION ANGLE DYNAMICS IN CYANA 2.0., REFINEMENT OF THE FINAL REMARK 3 STRUCTURAL ENSEMBLE WAS CARRIED OUT BY MOLECULAR DYNAMICS REMARK 3 SIMULATED ANNEALING IN AMBER 8. THE 100 STRUCTURES WITH LOWEST REMARK 3 TARGET FUNCTION IN CYANA 2.0 WERE IMPORTED INTO AMBER 8, REMARK 3 MINIMIZED AND SUBJECTED TO SIMULATED ANNEALING IN VACUUM WITH REMARK 3 CHARGES REDUCED TO 20% OF THEIR ORIGINAL VALUE. THE FINAL REMARK 3 ROUND OF SIMULATED ANNEALING WAS CARRIED OUT WITHIN A REMARK 3 GENERALIZED-BORN SOLVATION MODEL WITH FULL CHARGES FOLLOWED BY REMARK 3 ENERGY MINIMIZATION. CONSTRAINTS FROM CYANA WERE TRANSLATED REMARK 3 INTO AMBER 8 FORMAT TAKING STEREOSPECIFIC ASSIGNMENTS, REMARK 3 PSEUDOATOM CORRECTIONS AND NOE-AVERAGING INTO ACCOUNT. REMARK 4 REMARK 4 2K14 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-08. REMARK 100 THE RCSB ID CODE IS RCSB100543. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 280 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 300 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 0.9 MM [U-13C; U-15N] YUAF, REMARK 210 50 MM TRIS, 300 MM SODIUM REMARK 210 CHLORIDE, 4 MM SODIUM AZIDE, REMARK 210 95% H2O/5% D2O; 0.9 MM [U-13C; REMARK 210 U-15N] YUAF, 50 MM TRIS, 300 REMARK 210 MM SODIUM CHLORIDE, 4 MM REMARK 210 SODIUM AZIDE, 100% D2O; 1 MM REMARK 210 [U-15N] YUAF, 50 MM TRIS, 300 REMARK 210 MM SODIUM CHLORIDE, 4 MM REMARK 210 SODIUM AZIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC, 2D 1H-13C REMARK 210 HSQC, 3D CBCA(CO)NH, 3D HNCO, REMARK 210 3D HN(CA)CO, 3D HNCACB, 3D 1H- REMARK 210 15N TOCSY, 3D 1H-15N NOESY, 3D REMARK 210 HCCH-COSY, 3D (H)CCH-TOCSY, 3D REMARK 210 1H-13C NOESY, (HB)CB(CGCD)HD, REMARK 210 (HB)CB(CGCDCE)HE, 2D 1H-13C REMARK 210 HSQC AROMATIC, 3D 1H-13C NOESY REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE DRX, AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.0, XWINNMR 3.6, CARA REMARK 210 1.8.4, TOPSPIN 1.3.B.20 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 9 ARG A 16 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 18 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES 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 ASP A 34 23.45 -145.80 REMARK 500 1 ASN A 73 99.18 -50.21 REMARK 500 1 GLU A 82 58.60 35.17 REMARK 500 2 ASP A 34 24.41 -141.29 REMARK 500 2 GLU A 82 56.88 35.71 REMARK 500 3 ASP A 34 24.44 -141.03 REMARK 500 3 ASN A 73 98.76 -50.33 REMARK 500 3 GLU A 82 56.53 37.16 REMARK 500 4 ASP A 34 31.57 -143.26 REMARK 500 4 GLU A 82 55.98 38.79 REMARK 500 5 ASP A 34 24.07 -143.05 REMARK 500 5 GLU A 82 55.53 35.80 REMARK 500 6 ASP A 34 24.35 -140.83 REMARK 500 6 ASN A 73 55.96 34.60 REMARK 500 6 GLU A 82 52.03 35.21 REMARK 500 7 ASP A 34 30.99 -145.03 REMARK 500 7 GLU A 42 -19.30 -49.76 REMARK 500 7 GLU A 82 53.93 39.00 REMARK 500 8 ASP A 34 31.46 -142.85 REMARK 500 8 ASN A 73 95.78 -47.52 REMARK 500 8 GLU A 82 54.27 38.95 REMARK 500 9 ASP A 34 31.67 -142.42 REMARK 500 9 GLU A 82 56.05 38.12 REMARK 500 10 ASP A 34 30.86 -145.46 REMARK 500 10 GLU A 42 -9.93 -58.30 REMARK 500 10 GLU A 82 53.63 38.99 REMARK 500 11 ASP A 34 24.06 -143.13 REMARK 500 11 GLU A 82 56.50 35.36 REMARK 500 12 ASP A 34 24.02 -143.23 REMARK 500 12 ASN A 73 99.39 -50.30 REMARK 500 12 GLU A 82 61.68 28.89 REMARK 500 13 ASP A 34 31.38 -142.59 REMARK 500 13 GLU A 82 56.20 38.29 REMARK 500 14 ASP A 34 31.58 -142.62 REMARK 500 14 GLU A 82 61.14 35.18 REMARK 500 15 ASP A 34 30.83 -143.62 REMARK 500 15 ASN A 73 99.11 -50.42 REMARK 500 15 GLU A 82 56.30 36.28 REMARK 500 16 ASP A 34 31.26 -142.18 REMARK 500 16 GLU A 82 54.27 37.15 REMARK 500 17 ASP A 34 31.19 -145.54 REMARK 500 17 ASN A 73 99.28 -50.25 REMARK 500 17 GLU A 82 56.42 36.05 REMARK 500 18 ASP A 34 31.08 -145.47 REMARK 500 18 GLU A 82 51.36 36.71 REMARK 500 19 ASP A 34 30.84 -145.89 REMARK 500 19 ASN A 73 99.17 -49.83 REMARK 500 19 GLU A 82 54.24 37.21 REMARK 500 20 ASP A 34 32.19 -142.55 REMARK 500 20 GLU A 82 53.72 39.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15475 RELATED DB: BMRB REMARK 900 ENTRY CONTAINING THE CHEMICAL SHIFT ASSIGNMENT OF THE C- REMARK 900 TERMINAL DOMAIN OF YUAF REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS PBD ENTRY CONTAINS THE STRUCTURE OF RESIDUES 97 TO 174 OF REMARK 999 YUAF (RESIDUES 7 TO 84 OF THIS ENTRY). IN ADDITION, THE REMARK 999 STRUCTURE INCLUDES SIX FURTHER RESIDUES (1-6) THAT ORIGINATE REMARK 999 FROM THE MBP FUSION CONSTRUCT. DBREF 2K14 A 7 84 UNP O32077 O32077_BACSU 97 174 SEQADV 2K14 GLY A 1 UNP O32077 SEE REMARK 999 SEQADV 2K14 SER A 2 UNP O32077 SEE REMARK 999 SEQADV 2K14 HIS A 3 UNP O32077 SEE REMARK 999 SEQADV 2K14 MET A 4 UNP O32077 SEE REMARK 999 SEQADV 2K14 LEU A 5 UNP O32077 SEE REMARK 999 SEQADV 2K14 GLU A 6 UNP O32077 SEE REMARK 999 SEQRES 1 A 84 GLY SER HIS MET LEU GLU SER SER ALA GLU GLU SER LEU SEQRES 2 A 84 ALA TYR ARG GLU ASP ASP LEU ARG GLY ARG LEU GLY LYS SEQRES 3 A 84 VAL ILE THR ALA VAL PRO VAL ASP GLY PHE GLY GLU VAL SEQRES 4 A 84 VAL ILE GLU GLY ILE GLY GLY THR ILE SER LYS SER ALA SEQRES 5 A 84 VAL SER PHE ASP ASN GLN GLN ILE SER TYR GLY THR THR SEQRES 6 A 84 VAL LEU VAL VAL ASP ILE ASN ASN GLY VAL LEU SER VAL SEQRES 7 A 84 THR PRO HIS GLU PRO ILE HELIX 1 1 GLY A 1 LEU A 20 1 20 SHEET 1 A 6 LEU A 24 THR A 29 0 SHEET 2 A 6 PHE A 36 ILE A 41 -1 O VAL A 40 N LYS A 26 SHEET 3 A 6 LYS A 50 SER A 54 -1 O LYS A 50 N VAL A 39 SHEET 4 A 6 VAL A 75 THR A 79 1 O VAL A 78 N VAL A 53 SHEET 5 A 6 THR A 65 ASN A 72 -1 N ASP A 70 O SER A 77 SHEET 6 A 6 LEU A 24 THR A 29 -1 N GLY A 25 O VAL A 66 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 177 0 0 1 6 0 0 6 0 0 0 7 END