PDB Short entry for 1IID HEADER TRANSFERASE 22-APR-01 1IID TITLE CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE N-MYRISTOYLTRANSFERASE TITLE 2 WITH BOUND S-(2-OXO)PENTADECYLCOA AND THE OCTAPEPTIDE GLYASKLA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE N-MYRISTOYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-MYRISTOYLTRANSFERASE (N-TERMINAL 33 RESIDUES DELETED); COMPND 5 SYNONYM: GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE; COMPND 6 EC: 2.3.1.97; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: OCTAPEPTIDE GLYASKLA; COMPND 10 CHAIN: O; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: NMT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM101; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PBB502; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.A.FARAZI,J.I.GORDON,G.WAKSMAN REVDAT 5 16-AUG-23 1IID 1 REMARK LINK REVDAT 4 24-FEB-09 1IID 1 VERSN REVDAT 3 01-APR-03 1IID 1 JRNL REVDAT 2 06-JUN-01 1IID 1 JRNL REVDAT 1 02-MAY-01 1IID 0 JRNL AUTH T.A.FARAZI,G.WAKSMAN,J.I.GORDON JRNL TITL STRUCTURES OF SACCHAROMYCES CEREVISIAE JRNL TITL 2 N-MYRISTOYLTRANSFERASE WITH BOUND MYRISTOYLCOA AND PEPTIDE JRNL TITL 3 PROVIDE INSIGHTS ABOUT SUBSTRATE RECOGNITION AND CATALYSIS. JRNL REF BIOCHEMISTRY V. 40 6335 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11371195 JRNL DOI 10.1021/BI0101401 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 454763.730 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 17550 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 849 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2612 REMARK 3 BIN R VALUE (WORKING SET) : 0.3530 REMARK 3 BIN FREE R VALUE : 0.3960 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 123 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.036 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3448 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 124 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.98000 REMARK 3 B22 (A**2) : -7.68000 REMARK 3 B33 (A**2) : -4.29000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.48 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.46 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.65 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.930 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.250 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.140 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.510 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.660 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 58.04 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NHM_CORR1.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NHM.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IID COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013296. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-00 REMARK 200 TEMPERATURE (KELVIN) : 103 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : YALE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17552 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 5.40000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2NMT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 2000 MME, NICKEL CHLORIDE, SODIUM REMARK 280 CACODYLATE, PH 6.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.90450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.90450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 37.56450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.53000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.56450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.53000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 70.90450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.56450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.53000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 70.90450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.56450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.53000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, O 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 36 CG CD CE NZ REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 GLU A 141 CG CD OE1 OE2 REMARK 470 LYS A 161 CG CD CE NZ REMARK 470 GLN A 176 CG CD OE1 NE2 REMARK 470 LYS A 180 CG CD CE NZ REMARK 470 TYR A 230 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 249 CG CD OE1 OE2 REMARK 470 LYS A 266 CG CD CE NZ REMARK 470 GLU A 302 CG CD OE1 OE2 REMARK 470 LEU A 337 CG CD1 CD2 REMARK 470 LYS A 341 CG CD CE NZ REMARK 470 LYS A 362 CG CD CE NZ REMARK 470 ASP A 363 CG OD1 OD2 REMARK 470 LYS A 371 CG CD CE NZ REMARK 470 LYS A 412 CG CD CE NZ REMARK 470 LYS A 445 CG CD CE NZ REMARK 470 LEU O 703 CG CD1 CD2 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 TYR O 699 N - CA - C ANGL. DEV. = 22.1 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 ASP A 37 40.85 -78.26 REMARK 500 PRO A 45 63.87 -69.42 REMARK 500 ILE A 59 -64.45 -92.08 REMARK 500 ASP A 67 45.71 -91.33 REMARK 500 CYS A 82 148.19 178.81 REMARK 500 GLU A 105 71.22 -106.87 REMARK 500 ASP A 106 33.39 39.77 REMARK 500 ARG A 107 54.12 -114.39 REMARK 500 ALA A 109 16.84 -148.87 REMARK 500 HIS A 134 78.12 -109.85 REMARK 500 GLN A 143 15.15 54.57 REMARK 500 GLN A 176 56.22 -105.26 REMARK 500 LEU A 177 9.45 -170.12 REMARK 500 SER A 179 12.19 52.38 REMARK 500 ILE A 208 151.66 -45.79 REMARK 500 PRO A 211 109.19 -52.78 REMARK 500 ALA A 212 56.58 92.72 REMARK 500 LEU A 224 -61.97 -123.35 REMARK 500 TRP A 226 -73.86 -49.58 REMARK 500 ASP A 233 9.71 83.12 REMARK 500 THR A 242 135.40 6.60 REMARK 500 GLU A 243 -45.42 -19.21 REMARK 500 MET A 246 -75.81 -57.03 REMARK 500 ALA A 251 154.53 -33.66 REMARK 500 PRO A 253 161.36 -44.92 REMARK 500 LEU A 261 91.97 -60.87 REMARK 500 ARG A 262 -138.27 -100.05 REMARK 500 ILE A 269 -72.03 -39.62 REMARK 500 PHE A 326 141.89 -172.17 REMARK 500 LEU A 337 -21.02 -152.70 REMARK 500 LYS A 343 3.66 -159.99 REMARK 500 TYR A 351 -122.60 -94.00 REMARK 500 ALA A 372 -78.99 -45.04 REMARK 500 GLU A 379 -70.00 -64.01 REMARK 500 ASN A 392 16.58 92.83 REMARK 500 THR A 400 -1.58 57.47 REMARK 500 GLN A 402 -123.62 61.72 REMARK 500 ASP A 410 -66.44 151.20 REMARK 500 ASP A 443 74.19 -117.94 REMARK 500 ILE A 444 -18.63 -48.32 REMARK 500 LYS A 445 -80.04 -68.54 REMARK 500 ARG A 447 -130.40 58.40 REMARK 500 LEU O 698 -75.24 -95.45 REMARK 500 TYR O 699 -110.48 132.21 REMARK 500 ALA O 700 -35.95 -23.20 REMARK 500 SER O 701 176.53 54.28 REMARK 500 LEU O 703 141.71 -175.72 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 TYR O 699 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NHM A 500 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 1 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 34 O REMARK 620 2 ASP A 37 OD2 143.8 REMARK 620 3 ASP A 37 OD1 90.3 54.0 REMARK 620 4 HIS A 38 NE2 73.4 104.3 100.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 2 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 296 ND1 REMARK 620 2 HOH A 534 O 95.5 REMARK 620 3 HOH A 552 O 91.5 95.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NHM A 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2NMT RELATED DB: PDB REMARK 900 2NMT CONTAINS THE SAME PROTEIN COMPLEXED WITH S-(2-OXO) REMARK 900 PENTADECYLCOA AND THE PEPTIDOMIMETIC SC-58272 DBREF 1IID A 34 455 UNP P14743 NMT_YEAST 34 455 DBREF 1IID O 697 704 PDB 1IID 1IID 697 704 SEQRES 1 A 422 ALA MET LYS ASP HIS LYS PHE TRP ARG THR GLN PRO VAL SEQRES 2 A 422 LYS ASP PHE ASP GLU LYS VAL VAL GLU GLU GLY PRO ILE SEQRES 3 A 422 ASP LYS PRO LYS THR PRO GLU ASP ILE SER ASP LYS PRO SEQRES 4 A 422 LEU PRO LEU LEU SER SER PHE GLU TRP CYS SER ILE ASP SEQRES 5 A 422 VAL ASP ASN LYS LYS GLN LEU GLU ASP VAL PHE VAL LEU SEQRES 6 A 422 LEU ASN GLU ASN TYR VAL GLU ASP ARG ASP ALA GLY PHE SEQRES 7 A 422 ARG PHE ASN TYR THR LYS GLU PHE PHE ASN TRP ALA LEU SEQRES 8 A 422 LYS SER PRO GLY TRP LYS LYS ASP TRP HIS ILE GLY VAL SEQRES 9 A 422 ARG VAL LYS GLU THR GLN LYS LEU VAL ALA PHE ILE SER SEQRES 10 A 422 ALA ILE PRO VAL THR LEU GLY VAL ARG GLY LYS GLN VAL SEQRES 11 A 422 PRO SER VAL GLU ILE ASN PHE LEU CYS VAL HIS LYS GLN SEQRES 12 A 422 LEU ARG SER LYS ARG LEU THR PRO VAL LEU ILE LYS GLU SEQRES 13 A 422 ILE THR ARG ARG VAL ASN LYS CYS ASP ILE TRP HIS ALA SEQRES 14 A 422 LEU TYR THR ALA GLY ILE VAL LEU PRO ALA PRO VAL SER SEQRES 15 A 422 THR CYS ARG TYR THR HIS ARG PRO LEU ASN TRP LYS LYS SEQRES 16 A 422 LEU TYR GLU VAL ASP PHE THR GLY LEU PRO ASP GLY HIS SEQRES 17 A 422 THR GLU GLU ASP MET ILE ALA GLU ASN ALA LEU PRO ALA SEQRES 18 A 422 LYS THR LYS THR ALA GLY LEU ARG LYS LEU LYS LYS GLU SEQRES 19 A 422 ASP ILE ASP GLN VAL PHE GLU LEU PHE LYS ARG TYR GLN SEQRES 20 A 422 SER ARG PHE GLU LEU ILE GLN ILE PHE THR LYS GLU GLU SEQRES 21 A 422 PHE GLU HIS ASN PHE ILE GLY GLU GLU SER LEU PRO LEU SEQRES 22 A 422 ASP LYS GLN VAL ILE PHE SER TYR VAL VAL GLU GLN PRO SEQRES 23 A 422 ASP GLY LYS ILE THR ASP PHE PHE SER PHE TYR SER LEU SEQRES 24 A 422 PRO PHE THR ILE LEU ASN ASN THR LYS TYR LYS ASP LEU SEQRES 25 A 422 GLY ILE GLY TYR LEU TYR TYR TYR ALA THR ASP ALA ASP SEQRES 26 A 422 PHE GLN PHE LYS ASP ARG PHE ASP PRO LYS ALA THR LYS SEQRES 27 A 422 ALA LEU LYS THR ARG LEU CYS GLU LEU ILE TYR ASP ALA SEQRES 28 A 422 CYS ILE LEU ALA LYS ASN ALA ASN MET ASP VAL PHE ASN SEQRES 29 A 422 ALA LEU THR SER GLN ASP ASN THR LEU PHE LEU ASP ASP SEQRES 30 A 422 LEU LYS PHE GLY PRO GLY ASP GLY PHE LEU ASN PHE TYR SEQRES 31 A 422 LEU PHE ASN TYR ARG ALA LYS PRO ILE THR GLY GLY LEU SEQRES 32 A 422 ASN PRO ASP ASN SER ASN ASP ILE LYS ARG ARG SER ASN SEQRES 33 A 422 VAL GLY VAL VAL MET LEU SEQRES 1 O 8 GLY LEU TYR ALA SER LYS LEU ALA HET NI A 1 1 HET NI A 2 1 HET NHM A 500 64 HETNAM NI NICKEL (II) ION HETNAM NHM S-(2-OXO)PENTADECYLCOA FORMUL 3 NI 2(NI 2+) FORMUL 5 NHM C36 H64 N7 O17 P3 S FORMUL 6 HOH *124(H2 O) HELIX 1 1 PHE A 40 GLN A 44 5 5 HELIX 2 2 THR A 64 ILE A 68 5 5 HELIX 3 3 ASN A 88 TYR A 103 1 16 HELIX 4 4 THR A 116 LEU A 124 1 9 HELIX 5 5 LYS A 175 ARG A 178 5 4 HELIX 6 6 LEU A 182 LYS A 196 1 15 HELIX 7 7 ASN A 225 ASP A 233 1 9 HELIX 8 8 PRO A 238 HIS A 241 5 4 HELIX 9 9 THR A 242 ALA A 251 1 10 HELIX 10 10 LYS A 265 GLU A 267 5 3 HELIX 11 11 ASP A 268 SER A 281 1 14 HELIX 12 12 THR A 290 ILE A 299 1 10 HELIX 13 13 ALA A 357 PHE A 361 5 5 HELIX 14 14 LYS A 368 ALA A 391 1 24 HELIX 15 15 ASP A 403 ASP A 409 1 7 SHEET 1 A 2 GLY A 57 PRO A 58 0 SHEET 2 A 2 TYR A 427 ARG A 428 -1 N ARG A 428 O GLY A 57 SHEET 1 B11 ILE A 311 GLU A 317 0 SHEET 2 B11 ILE A 323 SER A 331 -1 N THR A 324 O VAL A 316 SHEET 3 B11 ILE A 347 THR A 355 -1 N TYR A 349 O TYR A 330 SHEET 4 B11 VAL A 395 ALA A 398 1 O VAL A 395 N GLY A 348 SHEET 5 B11 SER A 215 PRO A 223 -1 O THR A 220 N ALA A 398 SHEET 6 B11 GLY A 414 PHE A 425 -1 N GLY A 414 O HIS A 221 SHEET 7 B11 ALA A 202 ALA A 206 -1 O ALA A 202 N PHE A 425 SHEET 8 B11 LYS A 161 VAL A 173 1 O VAL A 166 N LEU A 203 SHEET 9 B11 LEU A 145 VAL A 158 -1 O PHE A 148 N CYS A 172 SHEET 10 B11 HIS A 134 VAL A 139 -1 O ILE A 135 N ILE A 149 SHEET 11 B11 PHE A 79 CYS A 82 -1 O GLU A 80 N ARG A 138 SHEET 1 C10 ILE A 311 GLU A 317 0 SHEET 2 C10 ILE A 323 SER A 331 -1 N THR A 324 O VAL A 316 SHEET 3 C10 ILE A 347 THR A 355 -1 N TYR A 349 O TYR A 330 SHEET 4 C10 VAL A 395 ALA A 398 1 O VAL A 395 N GLY A 348 SHEET 5 C10 SER A 215 PRO A 223 -1 O THR A 220 N ALA A 398 SHEET 6 C10 GLY A 414 PHE A 425 -1 N GLY A 414 O HIS A 221 SHEET 7 C10 ALA A 202 ALA A 206 -1 O ALA A 202 N PHE A 425 SHEET 8 C10 LYS A 161 VAL A 173 1 O VAL A 166 N LEU A 203 SHEET 9 C10 LEU A 145 VAL A 158 -1 O PHE A 148 N CYS A 172 SHEET 10 C10 LEU A 285 GLN A 287 -1 O ILE A 286 N GLY A 157 SHEET 1 D 3 ARG A 112 PHE A 113 0 SHEET 2 D 3 PHE A 334 THR A 335 -1 N THR A 335 O ARG A 112 SHEET 3 D 3 ASP A 344 LEU A 345 -1 O LEU A 345 N PHE A 334 LINK NI NI A 1 O ALA A 34 1555 1555 2.32 LINK NI NI A 1 OD2 ASP A 37 1555 1555 2.61 LINK NI NI A 1 OD1 ASP A 37 1555 1555 2.15 LINK NI NI A 1 NE2 HIS A 38 1555 1555 2.47 LINK NI NI A 2 ND1 HIS A 296 1555 1555 2.43 LINK NI NI A 2 O HOH A 534 1555 1555 2.43 LINK NI NI A 2 O HOH A 552 1555 1555 2.68 SITE 1 AC1 3 ALA A 34 ASP A 37 HIS A 38 SITE 1 AC2 3 HIS A 296 HOH A 534 HOH A 552 SITE 1 AC3 30 HIS A 38 LYS A 39 PHE A 40 TRP A 41 SITE 2 AC3 30 ASN A 102 TYR A 103 GLU A 105 ILE A 168 SITE 3 AC3 30 ASN A 169 PHE A 170 LEU A 171 CYS A 172 SITE 4 AC3 30 VAL A 173 ARG A 178 SER A 179 LYS A 180 SITE 5 AC3 30 ARG A 181 LEU A 182 THR A 183 PRO A 184 SITE 6 AC3 30 ILE A 187 THR A 191 VAL A 194 TYR A 204 SITE 7 AC3 30 THR A 205 ILE A 208 LEU A 210 PHE A 425 SITE 8 AC3 30 HOH A 510 HOH A 549 CRYST1 75.129 97.060 141.809 90.00 90.00 90.00 C 2 2 21 8 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 0.013310 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010303 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007052 0.00000