HEADER MEMBRANE PROTEIN 14-JUN-16 5LAO TITLE S-NITROSYLATED 3D NMR STRUCTURE OF THE CYTOPLASMIC RHODANESE DOMAIN OF TITLE 2 THE INNER MEMBRANE PROTEIN YGAP FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: INNER MEMBRANE PROTEIN YGAP; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: YGAP, B2668, JW2643; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PLYSS KEYWDS S-NITROSYLATED RHODANESE DOMAIN OF YGAP, PROTEIN, MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.EICHMANN,C.TZITZILONIS,T.NAKAMURA,I.MASLENNIKOV,W.KWIATKOWSKI, AUTHOR 2 S.CHOE,S.A.LIPTON,P.GUNTERT,R.RIEK REVDAT 6 14-JUN-23 5LAO 1 REMARK REVDAT 5 30-OCT-19 5LAO 1 REMARK REVDAT 4 23-OCT-19 5LAO 1 REMARK ATOM REVDAT 3 31-JAN-18 5LAO 1 REMARK REVDAT 2 28-SEP-16 5LAO 1 JRNL REVDAT 1 17-AUG-16 5LAO 0 JRNL AUTH C.EICHMANN,C.TZITZILONIS,T.NAKAMURA,W.KWIATKOWSKI, JRNL AUTH 2 I.MASLENNIKOV,S.CHOE,S.A.LIPTON,R.RIEK JRNL TITL S-NITROSYLATION INDUCES STRUCTURAL AND DYNAMICAL CHANGES IN JRNL TITL 2 A RHODANESE FAMILY PROTEIN. JRNL REF J.MOL.BIOL. V. 428 3737 2016 JRNL REFN ESSN 1089-8638 JRNL PMID 27473602 JRNL DOI 10.1016/J.JMB.2016.07.010 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPAL 3.97 REMARK 3 AUTHORS : LUGINBUHL, GUNTERT, BILLETER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5LAO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1200000438. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303.15 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT PA REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 13C; U-99% 15N] S REMARK 210 -NITROSYLATED RHODANESE DOMAIN, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; 3D HCCH-TOCSY; 3D 1H-15N REMARK 210 TOCSY; 3D HNCACB; 3D HN(CO)CA; REMARK 210 2D TROSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.97, XEASY REMARK 210 METHOD USED : ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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: 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 20 ARG A 24 CD - NE - CZ ANGL. DEV. = 9.6 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 LEU A 2 105.15 -44.98 REMARK 500 1 ALA A 18 -169.38 -70.46 REMARK 500 1 ARG A 24 -77.63 -76.15 REMARK 500 1 ASP A 38 -100.01 -115.32 REMARK 500 1 LEU A 39 136.13 172.84 REMARK 500 1 ALA A 40 76.56 -171.46 REMARK 500 1 GLN A 47 -88.96 -89.06 REMARK 500 1 ALA A 52 0.05 -63.88 REMARK 500 1 THR A 69 -80.34 -73.20 REMARK 500 1 ALA A 83 168.11 156.46 REMARK 500 1 GLU A 89 -72.63 -61.62 REMARK 500 1 ALA A 103 39.12 -81.84 REMARK 500 2 LEU A 2 109.08 -58.84 REMARK 500 2 ALA A 18 -174.92 -66.97 REMARK 500 2 ARG A 24 -93.62 -57.70 REMARK 500 2 ARG A 31 -76.14 -57.51 REMARK 500 2 ASP A 38 -97.01 -106.30 REMARK 500 2 LEU A 39 125.19 162.18 REMARK 500 2 ALA A 40 77.96 -154.72 REMARK 500 2 ARG A 55 29.51 -71.61 REMARK 500 2 ALA A 65 -122.74 -145.06 REMARK 500 2 LYS A 67 -7.68 -53.40 REMARK 500 2 THR A 69 -71.49 -71.22 REMARK 500 2 ALA A 83 170.31 159.13 REMARK 500 2 VAL A 104 -168.74 -116.10 REMARK 500 2 ASN A 105 -56.66 -129.71 REMARK 500 3 ALA A 18 -175.98 -69.79 REMARK 500 3 ARG A 31 -73.98 -65.11 REMARK 500 3 LEU A 39 143.22 121.40 REMARK 500 3 ALA A 40 81.56 -165.47 REMARK 500 3 ALA A 65 25.76 -153.68 REMARK 500 3 LYS A 67 -7.63 -59.15 REMARK 500 3 ALA A 83 179.02 178.01 REMARK 500 3 ALA A 103 40.63 -84.66 REMARK 500 4 LEU A 2 108.52 -38.77 REMARK 500 4 ARG A 24 -80.86 -60.38 REMARK 500 4 GLU A 36 5.37 -69.30 REMARK 500 4 ASP A 38 -74.71 -99.04 REMARK 500 4 LEU A 39 124.24 141.67 REMARK 500 4 ALA A 40 81.42 -161.50 REMARK 500 4 GLN A 47 -78.84 -78.29 REMARK 500 4 ARG A 55 31.81 -75.19 REMARK 500 4 GLN A 64 -82.77 -68.08 REMARK 500 4 ALA A 65 -4.83 -142.94 REMARK 500 4 LYS A 67 -85.41 -67.59 REMARK 500 4 ARG A 68 -36.41 73.45 REMARK 500 4 THR A 69 -81.14 -54.89 REMARK 500 4 GLU A 89 -148.47 -103.44 REMARK 500 4 ASP A 90 -2.32 50.43 REMARK 500 4 ALA A 103 68.00 -103.25 REMARK 500 REMARK 500 THIS ENTRY HAS 261 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 55 0.10 SIDE CHAIN REMARK 500 2 ARG A 31 0.09 SIDE CHAIN REMARK 500 5 ARG A 24 0.09 SIDE CHAIN REMARK 500 6 TYR A 29 0.10 SIDE CHAIN REMARK 500 7 ARG A 31 0.08 SIDE CHAIN REMARK 500 8 ARG A 16 0.08 SIDE CHAIN REMARK 500 9 ARG A 24 0.11 SIDE CHAIN REMARK 500 10 ARG A 31 0.09 SIDE CHAIN REMARK 500 12 ARG A 24 0.08 SIDE CHAIN REMARK 500 17 ARG A 16 0.08 SIDE CHAIN REMARK 500 17 ARG A 24 0.08 SIDE CHAIN REMARK 500 18 ARG A 24 0.14 SIDE CHAIN REMARK 500 19 ARG A 31 0.08 SIDE CHAIN REMARK 500 19 ARG A 55 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34010 RELATED DB: BMRB DBREF 5LAO A 1 108 UNP P55734 YGAP_ECOLI 2 109 SEQRES 1 A 108 ALA LEU THR THR ILE SER PRO HIS ASP ALA GLN GLU LEU SEQRES 2 A 108 ILE ALA ARG GLY ALA LYS LEU ILE ASP ILE ARG ASP ALA SEQRES 3 A 108 ASP GLU TYR LEU ARG GLU HIS ILE PRO GLU ALA ASP LEU SEQRES 4 A 108 ALA PRO LEU SER VAL LEU GLU GLN SER GLY LEU PRO ALA SEQRES 5 A 108 LYS LEU ARG HIS GLU GLN ILE ILE PHE HIS CYS GLN ALA SEQRES 6 A 108 GLY LYS ARG THR SER ASN ASN ALA ASP LYS LEU ALA ALA SEQRES 7 A 108 ILE ALA ALA PRO ALA GLU ILE PHE LEU LEU GLU ASP GLY SEQRES 8 A 108 ILE ASP GLY TRP LYS LYS ALA GLY LEU PRO VAL ALA VAL SEQRES 9 A 108 ASN LYS SER GLN HELIX 1 AA1 HIS A 8 GLY A 17 1 10 HELIX 2 AA2 ASP A 25 GLU A 32 1 8 HELIX 3 AA3 PRO A 41 SER A 48 1 8 HELIX 4 AA4 THR A 69 ASN A 71 5 3 HELIX 5 AA5 ASN A 72 ALA A 81 1 10 HELIX 6 AA6 ASP A 90 ALA A 98 1 9 SHEET 1 AA1 4 THR A 3 ILE A 5 0 SHEET 2 AA1 4 GLU A 84 LEU A 88 1 O LEU A 87 N THR A 3 SHEET 3 AA1 4 GLN A 58 HIS A 62 1 N ILE A 59 O GLU A 84 SHEET 4 AA1 4 LEU A 20 ASP A 22 1 N ILE A 21 O ILE A 60 CISPEP 1 ALA A 81 PRO A 82 1 -0.51 CISPEP 2 ALA A 81 PRO A 82 2 -0.69 CISPEP 3 ALA A 81 PRO A 82 3 -1.13 CISPEP 4 ALA A 81 PRO A 82 4 -0.44 CISPEP 5 ALA A 81 PRO A 82 5 1.32 CISPEP 6 ALA A 81 PRO A 82 6 -0.97 CISPEP 7 ALA A 81 PRO A 82 7 -0.72 CISPEP 8 ALA A 81 PRO A 82 8 0.04 CISPEP 9 ALA A 81 PRO A 82 9 0.83 CISPEP 10 ALA A 81 PRO A 82 10 0.19 CISPEP 11 ALA A 81 PRO A 82 11 -0.99 CISPEP 12 ALA A 81 PRO A 82 12 -0.31 CISPEP 13 ALA A 81 PRO A 82 13 0.52 CISPEP 14 ALA A 81 PRO A 82 14 0.39 CISPEP 15 ALA A 81 PRO A 82 15 1.56 CISPEP 16 ALA A 81 PRO A 82 16 -1.12 CISPEP 17 ALA A 81 PRO A 82 17 -0.70 CISPEP 18 ALA A 81 PRO A 82 18 -0.16 CISPEP 19 ALA A 81 PRO A 82 19 0.27 CISPEP 20 ALA A 81 PRO A 82 20 -0.23 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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