HEADER HYDROLASE 02-SEP-06 2I8L TITLE SOLUTION STRUCTURE OF AN ENDOPEPTIDASE HYCI FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROGENASE 3 MATURATION PROTEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ENDOPEPTIDASE HYCI; COMPND 5 EC: 3.4.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET21A(+) KEYWDS ALPHA-BETA SANDWICH, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.YANG,W.HU,C.JIN REVDAT 4 01-MAY-24 2I8L 1 REMARK REVDAT 3 01-SEP-10 2I8L 1 JRNL REVDAT 2 24-FEB-09 2I8L 1 VERSN REVDAT 1 05-DEC-06 2I8L 0 JRNL AUTH F.YANG,W.HU,H.XU,C.LI,B.XIA,C.JIN JRNL TITL SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF AN ENDOPEPTIDASE JRNL TITL 2 HYCI FROM ESCHERICHIA COLI: IMPLICATIONS FOR MECHANISM OF JRNL TITL 3 THE [NIFE] HYDROGENASE MATURATION JRNL REF J.BIOL.CHEM. V. 282 3856 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17150961 JRNL DOI 10.1074/JBC.M609263200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, AMBER 7.0 REMARK 3 AUTHORS : BRUKER (XWINNMR), D. CASE (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2I8L COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-SEP-06. REMARK 100 THE DEPOSITION ID IS D_1000039273. 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 : 50MM NACL, 50MM SODIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM HYCI U-15N; 50MM PHOSPHATE REMARK 210 BUFFER; 50MM NACL; 1MM EDTA, 90% REMARK 210 H2O, 10% D2O; 1MM HYCI U-15N, REMARK 210 13C; 50MM PHOSPHATE BUFFER; 50MM REMARK 210 NACL; 1MM EDTA, 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, NMRVIEW 5, CYANA REMARK 210 2.0 REMARK 210 METHOD USED : MOLECULAR DYNAMICS SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 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 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: 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 2 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 13 ARG A 74 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 15 ARG A 57 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 ARG A 54 60.59 30.36 REMARK 500 1 HIS A 90 -26.61 -155.31 REMARK 500 1 LEU A 94 -9.56 -49.63 REMARK 500 1 LEU A 101 -35.19 -132.89 REMARK 500 1 ASP A 104 -32.72 -136.23 REMARK 500 1 ASP A 116 -31.16 -136.54 REMARK 500 1 GLU A 143 -48.67 67.78 REMARK 500 1 ALA A 152 38.96 -148.57 REMARK 500 1 VAL A 153 17.40 57.88 REMARK 500 2 ALA A 29 89.27 -151.30 REMARK 500 2 HIS A 90 -25.56 -155.70 REMARK 500 2 LEU A 94 -3.14 -53.11 REMARK 500 2 ASP A 116 -30.08 -131.03 REMARK 500 2 ASN A 145 -16.91 -146.20 REMARK 500 2 ALA A 152 -47.93 71.86 REMARK 500 3 MET A 13 40.12 -100.64 REMARK 500 3 PRO A 30 170.19 -53.04 REMARK 500 3 ASN A 33 22.29 -140.71 REMARK 500 3 ALA A 42 57.06 -141.48 REMARK 500 3 THR A 89 -52.38 118.72 REMARK 500 3 ASN A 91 -77.86 -140.45 REMARK 500 3 LEU A 94 -12.46 -47.69 REMARK 500 3 ASP A 116 -36.73 -137.82 REMARK 500 3 ALA A 152 56.18 -143.54 REMARK 500 4 ARG A 54 59.87 30.75 REMARK 500 4 HIS A 90 -60.05 -153.37 REMARK 500 4 LEU A 94 -8.47 -50.95 REMARK 500 4 ASP A 104 -32.39 -140.20 REMARK 500 4 GLU A 143 70.34 -151.30 REMARK 500 4 ALA A 152 -47.59 -139.82 REMARK 500 4 VAL A 153 -55.52 -164.09 REMARK 500 5 MET A 13 32.77 -97.84 REMARK 500 5 ALA A 29 88.53 -154.70 REMARK 500 5 ASN A 33 34.99 -140.91 REMARK 500 5 HIS A 90 -57.63 -152.64 REMARK 500 5 LEU A 94 -11.47 -48.94 REMARK 500 5 ASP A 104 -38.55 -134.35 REMARK 500 5 ASP A 116 -30.70 -137.29 REMARK 500 6 SER A 11 -5.33 -58.58 REMARK 500 6 ASN A 33 37.91 -141.44 REMARK 500 6 ARG A 54 61.85 28.68 REMARK 500 6 LEU A 68 -168.56 -107.84 REMARK 500 6 HIS A 90 -53.61 -142.15 REMARK 500 6 LEU A 94 -11.12 -47.20 REMARK 500 6 GLU A 143 15.70 -140.80 REMARK 500 6 ALA A 152 79.34 -150.66 REMARK 500 7 ARG A 54 61.79 33.15 REMARK 500 7 THR A 89 -46.51 -165.98 REMARK 500 7 HIS A 90 -44.39 -157.41 REMARK 500 7 ASN A 91 -138.87 47.80 REMARK 500 REMARK 500 THIS ENTRY HAS 151 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 11 PHE A 85 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2I8L A 1 156 UNP P0AEV9 HYCI_ECOLI 0 155 SEQRES 1 A 156 MET THR ASP VAL LEU LEU CYS VAL GLY ASN SER MET MET SEQRES 2 A 156 GLY ASP ASP GLY ALA GLY PRO LEU LEU ALA GLU LYS CYS SEQRES 3 A 156 ALA ALA ALA PRO LYS GLY ASN TRP VAL VAL ILE ASP GLY SEQRES 4 A 156 GLY SER ALA PRO GLU ASN ASP ILE VAL ALA ILE ARG GLU SEQRES 5 A 156 LEU ARG PRO THR ARG LEU LEU ILE VAL ASP ALA THR ASP SEQRES 6 A 156 MET GLY LEU ASN PRO GLY GLU ILE ARG ILE ILE ASP PRO SEQRES 7 A 156 ASP ASP ILE ALA GLU MET PHE MET MET THR THR HIS ASN SEQRES 8 A 156 MET PRO LEU ASN TYR LEU ILE ASP GLN LEU LYS GLU ASP SEQRES 9 A 156 ILE GLY GLU VAL ILE PHE LEU GLY ILE GLN PRO ASP ILE SEQRES 10 A 156 VAL GLY PHE TYR TYR PRO MET THR GLN PRO ILE LYS ASP SEQRES 11 A 156 ALA VAL GLU THR VAL TYR GLN ARG LEU GLU GLY TRP GLU SEQRES 12 A 156 GLY ASN GLY GLY PHE ALA GLN LEU ALA VAL GLU GLU GLU HELIX 1 1 MET A 13 ASP A 16 5 4 HELIX 2 2 GLY A 17 ALA A 29 1 13 HELIX 3 3 ALA A 42 ASN A 45 5 4 HELIX 4 4 ASP A 46 ARG A 54 1 9 HELIX 5 5 ASP A 77 PHE A 85 1 9 HELIX 6 6 MET A 86 THR A 89 5 4 HELIX 7 7 LEU A 94 GLN A 100 1 7 HELIX 8 8 THR A 125 LEU A 139 1 15 SHEET 1 A 5 VAL A 35 ASP A 38 0 SHEET 2 A 5 ASP A 3 CYS A 7 1 N CYS A 7 O ILE A 37 SHEET 3 A 5 ARG A 57 ALA A 63 1 O LEU A 59 N LEU A 6 SHEET 4 A 5 GLU A 107 ILE A 113 1 O LEU A 111 N ILE A 60 SHEET 5 A 5 ILE A 73 ILE A 76 -1 N ARG A 74 O GLY A 112 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