HEADER HYDROLASE 31-JUL-09 2KML TITLE SOLUTION STRUCTURE OF AN ENDOPEPTIDASE FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: MATURATION ELEMENT FOR HYDROGENASE 2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 585034; SOURCE 4 STRAIN: IAI1; SOURCE 5 GENE: HYBD, ECIAI1_3142; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS ENDOPEPTIDASE, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 21 AUTHOR F.YANG,C.JIN REVDAT 1 04-AUG-10 2KML 0 JRNL AUTH F.YANG,C.JIN JRNL TITL 1H, 13C AND 15N RESONANCE ASSIGNMENTS OF AN HYDROGENASE JRNL TITL 2 MATURATING ENDOPEPTIDASE HYBD FROM ESCHERICHIA COLI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KML COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-AUG-09. REMARK 100 THE RCSB ID CODE IS RCSB101307. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 50MM SODIUM PHOSPHATE-1, 50MM REMARK 210 SODIUM CHLORIDE-2, 0.5MM [U-13C; REMARK 210 U-15N] PROTEIN-3, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW, XWINNMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 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 ILE A 11 24.76 -75.39 REMARK 500 1 THR A 14 -114.50 42.25 REMARK 500 1 THR A 43 -2.02 59.68 REMARK 500 1 ASN A 54 -5.67 62.15 REMARK 500 1 VAL A 65 -35.03 64.52 REMARK 500 1 ASP A 79 -66.43 -22.29 REMARK 500 1 ASN A 88 109.89 -58.72 REMARK 500 1 LYS A 113 84.29 -158.93 REMARK 500 1 PRO A 121 -161.53 -75.92 REMARK 500 1 GLU A 122 -62.03 -138.75 REMARK 500 1 ARG A 159 8.16 40.09 REMARK 500 2 ILE A 11 7.51 -56.52 REMARK 500 2 LEU A 13 63.02 -111.84 REMARK 500 2 THR A 14 -100.15 52.83 REMARK 500 2 VAL A 65 17.03 55.28 REMARK 500 2 LYS A 67 -172.06 59.72 REMARK 500 2 ASP A 79 -98.11 36.32 REMARK 500 2 PRO A 126 84.09 -67.47 REMARK 500 2 SER A 160 26.23 46.12 REMARK 500 3 LEU A 13 55.42 -101.78 REMARK 500 3 THR A 14 -102.11 49.60 REMARK 500 3 ASN A 54 13.81 53.08 REMARK 500 3 LYS A 67 173.93 63.55 REMARK 500 3 ASP A 79 -61.69 -28.97 REMARK 500 3 PRO A 92 -75.85 -70.92 REMARK 500 3 GLU A 109 31.04 -93.50 REMARK 500 3 PRO A 126 91.00 -65.85 REMARK 500 3 ARG A 159 -121.64 47.86 REMARK 500 4 ILE A 11 40.71 -67.84 REMARK 500 4 LEU A 13 62.77 -115.32 REMARK 500 4 THR A 14 -97.63 56.90 REMARK 500 4 ALA A 44 -131.32 50.07 REMARK 500 4 LYS A 67 -167.48 57.87 REMARK 500 4 ASP A 79 -102.11 38.05 REMARK 500 4 PRO A 126 87.58 -63.94 REMARK 500 4 HIS A 127 145.80 -176.76 REMARK 500 5 ILE A 11 40.29 -73.21 REMARK 500 5 THR A 14 -109.60 45.44 REMARK 500 5 VAL A 65 -48.21 70.54 REMARK 500 5 PRO A 158 98.07 -66.54 REMARK 500 5 ARG A 159 14.88 49.90 REMARK 500 6 ILE A 11 35.67 -62.64 REMARK 500 6 LEU A 13 60.19 -111.40 REMARK 500 6 THR A 14 -102.19 52.72 REMARK 500 6 ALA A 44 -84.78 -120.18 REMARK 500 6 ASN A 54 19.44 59.26 REMARK 500 6 LYS A 68 42.13 -86.20 REMARK 500 6 PRO A 126 90.89 -66.09 REMARK 500 6 HIS A 127 145.24 -176.98 REMARK 500 7 ILE A 11 40.97 -76.76 REMARK 500 REMARK 500 THIS ENTRY HAS 191 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 66 LYS A 67 1 147.24 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 29 0.08 SIDE CHAIN REMARK 500 4 HIS A 57 0.12 SIDE CHAIN REMARK 500 5 TYR A 30 0.09 SIDE CHAIN REMARK 500 6 TYR A 30 0.07 SIDE CHAIN REMARK 500 7 TYR A 30 0.10 SIDE CHAIN REMARK 500 8 HIS A 57 0.09 SIDE CHAIN REMARK 500 9 PHE A 86 0.08 SIDE CHAIN REMARK 500 10 TYR A 30 0.10 SIDE CHAIN REMARK 500 10 HIS A 127 0.28 SIDE CHAIN REMARK 500 13 TYR A 30 0.09 SIDE CHAIN REMARK 500 14 TYR A 30 0.09 SIDE CHAIN REMARK 500 15 TYR A 30 0.12 SIDE CHAIN REMARK 500 17 TYR A 30 0.10 SIDE CHAIN REMARK 500 19 TYR A 30 0.11 SIDE CHAIN REMARK 500 21 TYR A 30 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 15 VAL A 65 22.6 L L OUTSIDE RANGE REMARK 500 15 ILE A 128 23.4 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16433 RELATED DB: BMRB DBREF 2KML A 1 159 UNP B7LZE7 B7LZE7_ECO8A 1 159 SEQADV 2KML SER A 160 UNP B7LZE7 EXPRESSION TAG SEQADV 2KML ASP A 161 UNP B7LZE7 EXPRESSION TAG SEQADV 2KML SER A 162 UNP B7LZE7 EXPRESSION TAG SEQRES 1 A 162 MET ARG ILE LEU VAL LEU GLY VAL GLY ASN ILE LEU LEU SEQRES 2 A 162 THR ASP GLU ALA ILE GLY VAL ARG ILE VAL GLU ALA LEU SEQRES 3 A 162 GLU GLN ARG TYR ILE LEU PRO ASP TYR VAL GLU ILE LEU SEQRES 4 A 162 ASP GLY GLY THR ALA GLY MET GLU LEU LEU GLY ASP MET SEQRES 5 A 162 ALA ASN ARG ASP HIS LEU ILE ILE ALA ASP ALA ILE VAL SEQRES 6 A 162 SER LYS LYS ASN THR PRO GLY THR MET MET ILE LEU ARG SEQRES 7 A 162 ASP GLU GLU VAL PRO ALA LEU PHE THR ASN LYS ILE SER SEQRES 8 A 162 PRO HIS GLN LEU GLY LEU ALA ASP VAL LEU SER ALA LEU SEQRES 9 A 162 ARG PHE THR GLY GLU PHE PRO LYS LYS LEU THR LEU VAL SEQRES 10 A 162 GLY VAL ILE PRO GLU SER LEU GLU PRO HIS ILE GLY LEU SEQRES 11 A 162 THR PRO THR VAL GLU ALA MET ILE GLU PRO ALA LEU GLU SEQRES 12 A 162 GLN VAL LEU ALA ALA LEU ARG GLU SER GLY VAL GLU ALA SEQRES 13 A 162 ILE PRO ARG SER ASP SER HELIX 1 1 LEU A 13 GLU A 16 5 4 HELIX 2 2 ALA A 17 GLN A 28 1 12 HELIX 3 3 ALA A 44 GLY A 50 5 7 HELIX 4 4 GLU A 80 PHE A 86 1 7 HELIX 5 5 SER A 91 GLY A 108 1 18 HELIX 6 6 THR A 131 ALA A 136 1 6 HELIX 7 7 MET A 137 SER A 152 1 16 SHEET 1 A 5 VAL A 36 ASP A 40 0 SHEET 2 A 5 ILE A 3 GLY A 7 1 N VAL A 5 O LEU A 39 SHEET 3 A 5 HIS A 57 ALA A 63 1 O ILE A 59 N LEU A 6 SHEET 4 A 5 LYS A 113 VAL A 119 1 O THR A 115 N ILE A 60 SHEET 5 A 5 MET A 74 ARG A 78 -1 N MET A 75 O GLY A 118 SHEET 1 B 2 TYR A 30 ILE A 31 0 SHEET 2 B 2 ILE A 157 PRO A 158 -1 O ILE A 157 N ILE A 31 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 ENDMDL MASTER 181 0 0 7 7 0 0 6 0 0 0 13 END