HEADER ISOMERASE 27-JUL-05 2AGM TITLE SOLUTION STRUCTURE OF THE R-MODULE FROM ALGE4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLY(BETA-D-MANNURONATE) C5 EPIMERASE 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: R-MODULE; COMPND 5 SYNONYM: MANNURONAN EPIMERASE 4, R-MODULE; COMPND 6 EC: 5.1.3.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AZOTOBACTER VINELANDII; SOURCE 3 ORGANISM_TAXID: 354; SOURCE 4 GENE: R-MODULE SUBUNIT FROM ALGE4; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ER 2566; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PFA2 DERIVATIVE OF PTYB11 (NEB) KEYWDS PARALLEL BETA-ROLL, ISOMERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.L.AACHMANN,B.I.SVANEM,P.GUNTERT,S.B.PETERSEN,S.VALLA,R.WIMMER REVDAT 6 14-JUN-23 2AGM 1 REMARK REVDAT 5 26-FEB-20 2AGM 1 REMARK REVDAT 4 24-FEB-09 2AGM 1 VERSN REVDAT 3 04-APR-06 2AGM 1 JRNL REVDAT 2 24-JAN-06 2AGM 1 JRNL REVDAT 1 10-JAN-06 2AGM 0 JRNL AUTH F.L.AACHMANN,B.I.SVANEM,P.GUNTERT,S.B.PETERSEN,S.VALLA, JRNL AUTH 2 R.WIMMER JRNL TITL NMR STRUCTURE OF THE R-MODULE: A PARALLEL BETA-ROLL SUBUNIT JRNL TITL 2 FROM AN AZOTOBACTER VINELANDII MANNURONAN C-5 EPIMERASE. JRNL REF J.BIOL.CHEM. V. 281 7350 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16407237 JRNL DOI 10.1074/JBC.M510069200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1.5, OPALP 1.4 REMARK 3 AUTHORS : GUENTERT (CYANA), KORADI, R., BILLETER, M., REMARK 3 GUNTERT, P. (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 1714 UNIQUE RESTRAINTS, REMARK 3 1576 ARE NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 138 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 2AGM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1000033869. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : 0.17 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.6MM R-MODULE U-99% 13C; U-99% REMARK 210 15N, 50MM CACL2, 20MM NA- REMARK 210 HEPES(PH 6.9) REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, XEASY 1.1.13, TALOS REMARK 210 98.040.21.02, OPALP 1.4 REMARK 210 METHOD USED : DISTANCE GEOMETRY, TORSION ANGLE REMARK 210 DYNAMICS, ENERGY-MINIMISATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY AND TORSION ANGLES ESTIMATES FROM SECONDARY REMARK 210 CHEMICAL SHIFTS USING TALOS 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 REMARK 500 REMARK: NULL 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 3 ASP A 31 N - CA - CB ANGL. DEV. = -10.9 DEGREES REMARK 500 4 ASP A 11 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 11 ARG A 40 CB - CG - CD ANGL. DEV. = 15.7 DEGREES REMARK 500 11 ARG A 40 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 14 ARG A 62 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 15 ARG A 62 CD - NE - CZ ANGL. DEV. = 8.5 DEGREES REMARK 500 15 ARG A 62 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 19 SER A 60 C - N - CA ANGL. DEV. = 16.8 DEGREES REMARK 500 20 ARG A 62 NE - CZ - NH2 ANGL. DEV. = -3.0 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 14 -163.08 -175.72 REMARK 500 1 ALA A 49 68.77 -107.41 REMARK 500 1 ALA A 56 42.63 39.29 REMARK 500 1 SER A 60 -74.11 -146.34 REMARK 500 1 ASP A 74 46.38 31.94 REMARK 500 1 GLU A 79 -50.37 -127.61 REMARK 500 1 ASP A 94 10.53 -140.13 REMARK 500 1 TYR A 96 -129.65 -92.05 REMARK 500 1 PHE A 116 94.90 52.00 REMARK 500 1 ALA A 118 -147.47 -134.78 REMARK 500 1 ARG A 123 138.44 178.11 REMARK 500 1 ASP A 132 -52.79 -142.46 REMARK 500 1 HIS A 133 -112.04 -92.27 REMARK 500 1 THR A 150 48.77 -143.84 REMARK 500 1 THR A 151 34.48 -81.21 REMARK 500 1 ASP A 158 -167.92 -102.32 REMARK 500 1 THR A 161 22.43 -79.14 REMARK 500 2 SER A 2 -81.31 -152.96 REMARK 500 2 ASP A 11 -16.04 -147.64 REMARK 500 2 ALA A 29 84.63 -170.85 REMARK 500 2 SER A 55 -2.14 -150.42 REMARK 500 2 ALA A 66 112.89 -167.67 REMARK 500 2 GLU A 79 -52.61 -134.54 REMARK 500 2 TYR A 96 -155.72 -89.75 REMARK 500 2 ASN A 105 -179.72 -66.71 REMARK 500 2 PHE A 116 85.25 25.16 REMARK 500 2 ALA A 118 -142.36 -122.83 REMARK 500 2 ARG A 123 135.50 160.15 REMARK 500 2 HIS A 133 -9.89 64.30 REMARK 500 2 SER A 138 -70.83 -157.24 REMARK 500 2 ALA A 139 -33.26 -141.49 REMARK 500 2 GLU A 152 -157.00 -92.24 REMARK 500 2 LEU A 153 40.73 -73.25 REMARK 500 2 GLU A 154 72.71 25.83 REMARK 500 3 ASP A 13 123.08 -31.32 REMARK 500 3 ASP A 31 48.57 -79.80 REMARK 500 3 ALA A 38 107.86 -59.15 REMARK 500 3 ALA A 49 73.09 -150.25 REMARK 500 3 SER A 55 4.92 -160.75 REMARK 500 3 ASP A 59 90.95 -69.77 REMARK 500 3 SER A 60 -34.82 -171.22 REMARK 500 3 ASP A 64 -68.09 -28.88 REMARK 500 3 ASP A 74 63.85 39.16 REMARK 500 3 GLU A 79 -36.79 -130.41 REMARK 500 3 ASN A 105 -175.65 -69.44 REMARK 500 3 PHE A 116 67.57 36.95 REMARK 500 3 ALA A 118 -145.57 -126.51 REMARK 500 3 ARG A 123 128.65 -170.07 REMARK 500 3 ASP A 132 13.52 -140.51 REMARK 500 3 THR A 134 74.08 43.48 REMARK 500 REMARK 500 THIS ENTRY HAS 354 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 40 0.11 SIDE CHAIN REMARK 500 2 ARG A 42 0.09 SIDE CHAIN REMARK 500 2 ARG A 62 0.09 SIDE CHAIN REMARK 500 3 ARG A 62 0.17 SIDE CHAIN REMARK 500 4 ARG A 40 0.10 SIDE CHAIN REMARK 500 5 TYR A 61 0.07 SIDE CHAIN REMARK 500 5 ARG A 62 0.12 SIDE CHAIN REMARK 500 6 ARG A 24 0.12 SIDE CHAIN REMARK 500 6 ARG A 40 0.09 SIDE CHAIN REMARK 500 6 TYR A 112 0.11 SIDE CHAIN REMARK 500 7 ARG A 124 0.12 SIDE CHAIN REMARK 500 7 PHE A 125 0.08 SIDE CHAIN REMARK 500 8 ARG A 40 0.09 SIDE CHAIN REMARK 500 12 ARG A 81 0.08 SIDE CHAIN REMARK 500 12 ARG A 124 0.09 SIDE CHAIN REMARK 500 13 ARG A 62 0.16 SIDE CHAIN REMARK 500 14 ARG A 123 0.10 SIDE CHAIN REMARK 500 16 ARG A 24 0.11 SIDE CHAIN REMARK 500 17 ARG A 124 0.09 SIDE CHAIN REMARK 500 20 ARG A 57 0.15 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 8 GLY A 21 10.53 REMARK 500 15 GLY A 21 12.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6390 RELATED DB: BMRB DBREF 2AGM A 1 167 UNP Q44493 ALGE4_AZOVI 387 553 SEQRES 1 A 167 GLY SER ASP GLY GLU PRO LEU VAL GLY GLY ASP THR ASP SEQRES 2 A 167 ASP GLN LEU GLN GLY GLY SER GLY ALA ASP ARG LEU ASP SEQRES 3 A 167 GLY GLY ALA GLY ASP ASP ILE LEU ASP GLY GLY ALA GLY SEQRES 4 A 167 ARG ASP ARG LEU SER GLY GLY ALA GLY ALA ASP THR PHE SEQRES 5 A 167 VAL PHE SER ALA ARG GLU ASP SER TYR ARG THR ASP THR SEQRES 6 A 167 ALA VAL PHE ASN ASP LEU ILE LEU ASP PHE GLU ALA SER SEQRES 7 A 167 GLU ASP ARG ILE ASP LEU SER ALA LEU GLY PHE SER GLY SEQRES 8 A 167 LEU GLY ASP GLY TYR GLY GLY THR LEU LEU LEU LYS THR SEQRES 9 A 167 ASN ALA GLU GLY THR ARG THR TYR LEU LYS SER PHE GLU SEQRES 10 A 167 ALA ASP ALA GLU GLY ARG ARG PHE GLU VAL ALA LEU ASP SEQRES 11 A 167 GLY ASP HIS THR GLY ASP LEU SER ALA ALA ASN VAL VAL SEQRES 12 A 167 PHE ALA ALA THR GLY THR THR THR GLU LEU GLU VAL LEU SEQRES 13 A 167 GLY ASP SER GLY THR GLN ALA GLY ALA ILE VAL SHEET 1 A 7 LEU A 7 GLY A 10 0 SHEET 2 A 7 LEU A 25 GLY A 28 1 O ASP A 26 N LEU A 7 SHEET 3 A 7 ARG A 42 GLY A 46 1 O GLY A 45 N GLY A 28 SHEET 4 A 7 LEU A 71 PHE A 75 1 O LEU A 73 N LEU A 43 SHEET 5 A 7 ALA A 128 GLY A 131 1 O ASP A 130 N ILE A 72 SHEET 6 A 7 ARG A 110 SER A 115 -1 N THR A 111 O LEU A 129 SHEET 7 A 7 LEU A 100 THR A 104 -1 N LYS A 103 O TYR A 112 SHEET 1 B 4 GLN A 15 GLN A 17 0 SHEET 2 B 4 ILE A 33 ASP A 35 1 O ILE A 33 N LEU A 16 SHEET 3 B 4 THR A 51 VAL A 53 1 O VAL A 53 N LEU A 34 SHEET 4 B 4 ARG A 81 ASP A 83 1 O ARG A 81 N PHE A 52 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