HEADER TRANSFERASE 20-JUN-17 5O9U TITLE HSNMT1 IN COMPLEX WITH COA AND MYRISTOYLATED-GCSVSKKK OCTAPEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MYRISTOYL-COA:PROTEIN N-MYRISTOYLTRANSFERASE 1,TYPE I N- COMPND 5 MYRISTOYLTRANSFERASE,PEPTIDE N-MYRISTOYLTRANSFERASE 1; COMPND 6 EC: 2.3.1.97; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: CALCINEURIN B-LIKE PROTEIN 4; COMPND 10 CHAIN: C, D; COMPND 11 FRAGMENT: UNP RESIDUES 2-9; COMPND 12 SYNONYM: PROTEIN SALT OVERLY SENSITIVE 3; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: SYNTHETIC OCTAPEPTIDE GCSVSKKK MODIFIED BY NMT1 TO COMPND 15 (GLM)CSVSKKK. GLM: N-MYRISTOYL-GLYCINE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NMT1, NMT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2 PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28 DERIVATIVE; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 14 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 15 ORGANISM_TAXID: 3702 KEYWDS TRANSFERASE, GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE 1 N- KEYWDS 2 MYRISTOYLTRANSFERASE 1, N-MYRISTOYLTRANSFERASE TYPE1, NMT1, NMT, KEYWDS 3 ACYLTRANSFERASE, MYR-PEPTIDE, COA, MYR-COA, MYRISTOYL, GNAT EXPDTA X-RAY DIFFRACTION AUTHOR C.DIAN,T.MEINNEL,C.GIGLIONE REVDAT 3 17-JAN-24 5O9U 1 REMARK REVDAT 2 07-NOV-18 5O9U 1 JRNL REVDAT 1 27-JUN-18 5O9U 0 JRNL AUTH B.CASTREC,C.DIAN,S.CICCONE,C.L.EBERT,W.V.BIENVENUT, JRNL AUTH 2 J.P.LE CAER,J.M.STEYAERT,C.GIGLIONE,T.MEINNEL JRNL TITL STRUCTURAL AND GENOMIC DECODING OF HUMAN AND PLANT JRNL TITL 2 MYRISTOYLOMES REVEALS A DEFINITIVE RECOGNITION PATTERN. JRNL REF NAT. CHEM. BIOL. V. 14 671 2018 JRNL REFN ESSN 1552-4469 JRNL PMID 29892081 JRNL DOI 10.1038/S41589-018-0077-5 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 71432 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 3542 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.0524 - 5.4068 0.99 2987 127 0.1725 0.1705 REMARK 3 2 5.4068 - 4.2925 1.00 2839 130 0.1326 0.1659 REMARK 3 3 4.2925 - 3.7501 0.99 2778 141 0.1290 0.1451 REMARK 3 4 3.7501 - 3.4074 1.00 2764 134 0.1393 0.1501 REMARK 3 5 3.4074 - 3.1632 1.00 2759 154 0.1466 0.1826 REMARK 3 6 3.1632 - 2.9767 1.00 2751 139 0.1611 0.2020 REMARK 3 7 2.9767 - 2.8277 1.00 2725 149 0.1646 0.2075 REMARK 3 8 2.8277 - 2.7046 1.00 2764 131 0.1651 0.2055 REMARK 3 9 2.7046 - 2.6005 1.00 2707 143 0.1678 0.1964 REMARK 3 10 2.6005 - 2.5108 1.00 2732 148 0.1610 0.2074 REMARK 3 11 2.5108 - 2.4323 1.00 2706 140 0.1631 0.2183 REMARK 3 12 2.4323 - 2.3627 1.00 2745 156 0.1616 0.1940 REMARK 3 13 2.3627 - 2.3005 1.00 2685 151 0.1586 0.2130 REMARK 3 14 2.3005 - 2.2444 1.00 2685 139 0.1554 0.2075 REMARK 3 15 2.2444 - 2.1934 1.00 2723 151 0.1505 0.1734 REMARK 3 16 2.1934 - 2.1467 1.00 2674 156 0.1556 0.1957 REMARK 3 17 2.1467 - 2.1038 1.00 2706 138 0.1583 0.2093 REMARK 3 18 2.1038 - 2.0641 0.99 2699 138 0.1581 0.2283 REMARK 3 19 2.0641 - 2.0272 0.98 2661 145 0.1639 0.2323 REMARK 3 20 2.0272 - 1.9928 0.98 2643 145 0.1654 0.2081 REMARK 3 21 1.9928 - 1.9607 0.98 2643 136 0.1731 0.2089 REMARK 3 22 1.9607 - 1.9305 0.97 2621 139 0.1749 0.2350 REMARK 3 23 1.9305 - 1.9021 0.98 2661 124 0.1801 0.2381 REMARK 3 24 1.9021 - 1.8753 0.96 2598 135 0.1832 0.2271 REMARK 3 25 1.8753 - 1.8500 0.97 2634 153 0.1811 0.2375 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 6837 REMARK 3 ANGLE : 0.886 9302 REMARK 3 CHIRALITY : 0.057 1008 REMARK 3 PLANARITY : 0.005 1170 REMARK 3 DIHEDRAL : 13.787 4061 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5O9U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1200005388. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9660 REMARK 200 MONOCHROMATOR : DIAMOND (C110) REMARK 200 OPTICS : COMPOUND REFRACTIVE LENS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71441 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 47.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07300 REMARK 200 FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26600 REMARK 200 FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4C2Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG 6000, 0.1M SODIUM CITRATE PH REMARK 280 5.6, 0.1M MAGNESIUM CHLORIDE, 0.1M SODIUM CHLORIDE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.88950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 89.37550 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.88950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 89.37550 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 95 REMARK 465 GLY A 96 REMARK 465 SER A 97 REMARK 465 GLU A 98 REMARK 465 PHE A 99 REMARK 465 SER A 100 REMARK 465 VAL A 101 REMARK 465 GLY A 102 REMARK 465 GLN A 103 REMARK 465 GLY B 95 REMARK 465 GLY B 96 REMARK 465 SER B 97 REMARK 465 GLU B 98 REMARK 465 PHE B 99 REMARK 465 SER B 100 REMARK 465 VAL B 101 REMARK 465 GLY B 102 REMARK 465 GLN B 103 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 GLU A 110 CG CD OE1 OE2 REMARK 470 LYS A 114 CG CD CE NZ REMARK 470 GLN A 118 CG CD OE1 NE2 REMARK 470 ASN A 133 CG OD1 ND2 REMARK 470 ARG A 166 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 308 CG CD OE1 OE2 REMARK 470 ARG A 316 CB CG CD NE CZ NH1 NH2 REMARK 470 GLN A 321 CG CD OE1 NE2 REMARK 470 LYS A 325 CG CD CE NZ REMARK 470 ARG A 328 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 110 CG CD OE1 OE2 REMARK 470 LYS B 114 CG CD CE NZ REMARK 470 GLN B 118 CG CD OE1 NE2 REMARK 470 ARG B 166 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 308 CG CD OE1 OE2 REMARK 470 ARG B 316 CB CG CD NE CZ NH1 NH2 REMARK 470 LYS B 325 CG CD CE NZ REMARK 470 ARG B 328 CZ NH1 NH2 REMARK 470 LYS D 8 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH A 809 O HOH A 865 2.01 REMARK 500 O HOH A 697 O HOH A 1026 2.07 REMARK 500 O HOH A 766 O HOH A 842 2.11 REMARK 500 O GLN A 321 O HOH A 601 2.13 REMARK 500 O HOH A 601 O HOH A 994 2.13 REMARK 500 O HOH A 653 O HOH B 934 2.13 REMARK 500 O3A COA A 501 O HOH A 602 2.13 REMARK 500 O HOH A 602 O HOH A 649 2.14 REMARK 500 O HOH B 944 O HOH B 1031 2.14 REMARK 500 OD1 ASN B 177 O HOH B 601 2.14 REMARK 500 O HOH A 870 O HOH C 203 2.15 REMARK 500 O HOH B 718 O HOH B 854 2.15 REMARK 500 O HOH B 784 O HOH B 851 2.15 REMARK 500 O HOH B 746 O HOH B 906 2.15 REMARK 500 O HOH A 711 O HOH A 739 2.16 REMARK 500 O HOH A 645 O HOH A 1016 2.19 REMARK 500 O HOH B 611 O HOH B 916 2.19 REMARK 500 NZ LYS B 240 O HOH B 602 2.19 REMARK 500 O HOH B 932 O HOH B 1031 2.19 REMARK 500 O HOH B 872 O HOH B 1013 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 922 O HOH A 1026 2555 2.11 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 TYR A 236 -114.71 49.06 REMARK 500 ARG A 316 -55.71 58.83 REMARK 500 ILE A 381 -62.50 -130.92 REMARK 500 THR A 412 -66.29 -104.35 REMARK 500 PHE A 422 -100.29 -110.28 REMARK 500 MET A 456 -132.12 41.86 REMARK 500 TYR B 236 -115.40 49.74 REMARK 500 SER B 256 19.13 51.66 REMARK 500 SER B 315 6.49 -66.39 REMARK 500 ARG B 316 -54.37 79.47 REMARK 500 ASN B 317 20.05 -77.45 REMARK 500 ILE B 381 -62.28 -131.48 REMARK 500 LYS B 414 -103.28 -49.96 REMARK 500 SER B 415 124.13 -25.74 REMARK 500 PHE B 422 -102.99 -112.09 REMARK 500 GLN B 428 -33.09 -131.40 REMARK 500 MET B 456 -130.02 41.99 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 HIS B 413 LYS B 414 -128.07 REMARK 500 LYS B 414 SER B 415 -125.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1054 DISTANCE = 6.94 ANGSTROMS REMARK 525 HOH B1046 DISTANCE = 5.82 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue COA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue COA B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide MYR E 101 and GLY E REMARK 800 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide MYR F 101 and GLY F REMARK 800 2 DBREF 5O9U A 99 496 UNP P30419 NMT1_HUMAN 19 416 DBREF 5O9U B 99 496 UNP P30419 NMT1_HUMAN 19 416 DBREF 5O9U C 2 9 UNP O81223 CNBL4_ARATH 2 9 DBREF 5O9U D 2 9 UNP O81223 CNBL4_ARATH 2 9 SEQADV 5O9U GLY A 95 UNP P30419 EXPRESSION TAG SEQADV 5O9U GLY A 96 UNP P30419 EXPRESSION TAG SEQADV 5O9U SER A 97 UNP P30419 EXPRESSION TAG SEQADV 5O9U GLU A 98 UNP P30419 EXPRESSION TAG SEQADV 5O9U GLY B 95 UNP P30419 EXPRESSION TAG SEQADV 5O9U GLY B 96 UNP P30419 EXPRESSION TAG SEQADV 5O9U SER B 97 UNP P30419 EXPRESSION TAG SEQADV 5O9U GLU B 98 UNP P30419 EXPRESSION TAG SEQRES 1 A 402 GLY GLY SER GLU PHE SER VAL GLY GLN GLY PRO ALA LYS SEQRES 2 A 402 THR MET GLU GLU ALA SER LYS ARG SER TYR GLN PHE TRP SEQRES 3 A 402 ASP THR GLN PRO VAL PRO LYS LEU GLY GLU VAL VAL ASN SEQRES 4 A 402 THR HIS GLY PRO VAL GLU PRO ASP LYS ASP ASN ILE ARG SEQRES 5 A 402 GLN GLU PRO TYR THR LEU PRO GLN GLY PHE THR TRP ASP SEQRES 6 A 402 ALA LEU ASP LEU GLY ASP ARG GLY VAL LEU LYS GLU LEU SEQRES 7 A 402 TYR THR LEU LEU ASN GLU ASN TYR VAL GLU ASP ASP ASP SEQRES 8 A 402 ASN MET PHE ARG PHE ASP TYR SER PRO GLU PHE LEU LEU SEQRES 9 A 402 TRP ALA LEU ARG PRO PRO GLY TRP LEU PRO GLN TRP HIS SEQRES 10 A 402 CYS GLY VAL ARG VAL VAL SER SER ARG LYS LEU VAL GLY SEQRES 11 A 402 PHE ILE SER ALA ILE PRO ALA ASN ILE HIS ILE TYR ASP SEQRES 12 A 402 THR GLU LYS LYS MET VAL GLU ILE ASN PHE LEU CYS VAL SEQRES 13 A 402 HIS LYS LYS LEU ARG SER LYS ARG VAL ALA PRO VAL LEU SEQRES 14 A 402 ILE ARG GLU ILE THR ARG ARG VAL HIS LEU GLU GLY ILE SEQRES 15 A 402 PHE GLN ALA VAL TYR THR ALA GLY VAL VAL LEU PRO LYS SEQRES 16 A 402 PRO VAL GLY THR CYS ARG TYR TRP HIS ARG SER LEU ASN SEQRES 17 A 402 PRO ARG LYS LEU ILE GLU VAL LYS PHE SER HIS LEU SER SEQRES 18 A 402 ARG ASN MET THR MET GLN ARG THR MET LYS LEU TYR ARG SEQRES 19 A 402 LEU PRO GLU THR PRO LYS THR ALA GLY LEU ARG PRO MET SEQRES 20 A 402 GLU THR LYS ASP ILE PRO VAL VAL HIS GLN LEU LEU THR SEQRES 21 A 402 ARG TYR LEU LYS GLN PHE HIS LEU THR PRO VAL MET SER SEQRES 22 A 402 GLN GLU GLU VAL GLU HIS TRP PHE TYR PRO GLN GLU ASN SEQRES 23 A 402 ILE ILE ASP THR PHE VAL VAL GLU ASN ALA ASN GLY GLU SEQRES 24 A 402 VAL THR ASP PHE LEU SER PHE TYR THR LEU PRO SER THR SEQRES 25 A 402 ILE MET ASN HIS PRO THR HIS LYS SER LEU LYS ALA ALA SEQRES 26 A 402 TYR SER PHE TYR ASN VAL HIS THR GLN THR PRO LEU LEU SEQRES 27 A 402 ASP LEU MET SER ASP ALA LEU VAL LEU ALA LYS MET LYS SEQRES 28 A 402 GLY PHE ASP VAL PHE ASN ALA LEU ASP LEU MET GLU ASN SEQRES 29 A 402 LYS THR PHE LEU GLU LYS LEU LYS PHE GLY ILE GLY ASP SEQRES 30 A 402 GLY ASN LEU GLN TYR TYR LEU TYR ASN TRP LYS CYS PRO SEQRES 31 A 402 SER MET GLY ALA GLU LYS VAL GLY LEU VAL LEU GLN SEQRES 1 B 402 GLY GLY SER GLU PHE SER VAL GLY GLN GLY PRO ALA LYS SEQRES 2 B 402 THR MET GLU GLU ALA SER LYS ARG SER TYR GLN PHE TRP SEQRES 3 B 402 ASP THR GLN PRO VAL PRO LYS LEU GLY GLU VAL VAL ASN SEQRES 4 B 402 THR HIS GLY PRO VAL GLU PRO ASP LYS ASP ASN ILE ARG SEQRES 5 B 402 GLN GLU PRO TYR THR LEU PRO GLN GLY PHE THR TRP ASP SEQRES 6 B 402 ALA LEU ASP LEU GLY ASP ARG GLY VAL LEU LYS GLU LEU SEQRES 7 B 402 TYR THR LEU LEU ASN GLU ASN TYR VAL GLU ASP ASP ASP SEQRES 8 B 402 ASN MET PHE ARG PHE ASP TYR SER PRO GLU PHE LEU LEU SEQRES 9 B 402 TRP ALA LEU ARG PRO PRO GLY TRP LEU PRO GLN TRP HIS SEQRES 10 B 402 CYS GLY VAL ARG VAL VAL SER SER ARG LYS LEU VAL GLY SEQRES 11 B 402 PHE ILE SER ALA ILE PRO ALA ASN ILE HIS ILE TYR ASP SEQRES 12 B 402 THR GLU LYS LYS MET VAL GLU ILE ASN PHE LEU CYS VAL SEQRES 13 B 402 HIS LYS LYS LEU ARG SER LYS ARG VAL ALA PRO VAL LEU SEQRES 14 B 402 ILE ARG GLU ILE THR ARG ARG VAL HIS LEU GLU GLY ILE SEQRES 15 B 402 PHE GLN ALA VAL TYR THR ALA GLY VAL VAL LEU PRO LYS SEQRES 16 B 402 PRO VAL GLY THR CYS ARG TYR TRP HIS ARG SER LEU ASN SEQRES 17 B 402 PRO ARG LYS LEU ILE GLU VAL LYS PHE SER HIS LEU SER SEQRES 18 B 402 ARG ASN MET THR MET GLN ARG THR MET LYS LEU TYR ARG SEQRES 19 B 402 LEU PRO GLU THR PRO LYS THR ALA GLY LEU ARG PRO MET SEQRES 20 B 402 GLU THR LYS ASP ILE PRO VAL VAL HIS GLN LEU LEU THR SEQRES 21 B 402 ARG TYR LEU LYS GLN PHE HIS LEU THR PRO VAL MET SER SEQRES 22 B 402 GLN GLU GLU VAL GLU HIS TRP PHE TYR PRO GLN GLU ASN SEQRES 23 B 402 ILE ILE ASP THR PHE VAL VAL GLU ASN ALA ASN GLY GLU SEQRES 24 B 402 VAL THR ASP PHE LEU SER PHE TYR THR LEU PRO SER THR SEQRES 25 B 402 ILE MET ASN HIS PRO THR HIS LYS SER LEU LYS ALA ALA SEQRES 26 B 402 TYR SER PHE TYR ASN VAL HIS THR GLN THR PRO LEU LEU SEQRES 27 B 402 ASP LEU MET SER ASP ALA LEU VAL LEU ALA LYS MET LYS SEQRES 28 B 402 GLY PHE ASP VAL PHE ASN ALA LEU ASP LEU MET GLU ASN SEQRES 29 B 402 LYS THR PHE LEU GLU LYS LEU LYS PHE GLY ILE GLY ASP SEQRES 30 B 402 GLY ASN LEU GLN TYR TYR LEU TYR ASN TRP LYS CYS PRO SEQRES 31 B 402 SER MET GLY ALA GLU LYS VAL GLY LEU VAL LEU GLN SEQRES 1 C 8 GLY CYS SER VAL SER LYS LYS LYS SEQRES 1 D 8 GLY CYS SER VAL SER LYS LYS LYS HET COA A 501 48 HET GOL A 502 6 HET COA B 501 48 HET GOL B 502 6 HET GOL B 503 6 HET MYR C 101 15 HET MYR D 101 15 HETNAM COA COENZYME A HETNAM GOL GLYCEROL HETNAM MYR MYRISTIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 COA 2(C21 H36 N7 O16 P3 S) FORMUL 6 GOL 3(C3 H8 O3) FORMUL 10 MYR 2(C14 H28 O2) FORMUL 12 HOH *912(H2 O) HELIX 1 AA1 THR A 108 LYS A 114 1 7 HELIX 2 AA2 PHE A 119 GLN A 123 5 5 HELIX 3 AA3 ASP A 165 TYR A 180 1 16 HELIX 4 AA4 SER A 193 ARG A 202 1 10 HELIX 5 AA5 LEU A 207 GLN A 209 5 3 HELIX 6 AA6 LYS A 252 ARG A 255 5 4 HELIX 7 AA7 ARG A 258 LEU A 273 1 16 HELIX 8 AA8 ASN A 302 VAL A 309 1 8 HELIX 9 AA9 THR A 319 TYR A 327 1 9 HELIX 10 AB1 GLU A 342 LYS A 344 5 3 HELIX 11 AB2 ASP A 345 LYS A 358 1 14 HELIX 12 AB3 SER A 367 TYR A 376 1 10 HELIX 13 AB4 PRO A 430 LYS A 445 1 16 HELIX 14 AB5 ASN A 458 GLU A 463 1 6 HELIX 15 AB6 GLY A 487 VAL A 491 5 5 HELIX 16 AB7 THR B 108 LYS B 114 1 7 HELIX 17 AB8 PHE B 119 GLN B 123 5 5 HELIX 18 AB9 ASP B 165 TYR B 180 1 16 HELIX 19 AC1 SER B 193 ARG B 202 1 10 HELIX 20 AC2 LEU B 207 GLN B 209 5 3 HELIX 21 AC3 LYS B 252 ARG B 255 5 4 HELIX 22 AC4 ARG B 258 LEU B 273 1 16 HELIX 23 AC5 ASN B 302 VAL B 309 1 8 HELIX 24 AC6 THR B 319 ARG B 328 1 10 HELIX 25 AC7 GLU B 342 LYS B 344 5 3 HELIX 26 AC8 ASP B 345 LYS B 358 1 14 HELIX 27 AC9 SER B 367 TYR B 376 1 10 HELIX 28 AD1 PRO B 430 GLY B 446 1 17 HELIX 29 AD2 GLU B 457 PHE B 461 5 5 HELIX 30 AD3 GLY B 487 VAL B 491 5 5 SHEET 1 AA111 PHE A 156 ALA A 160 0 SHEET 2 AA111 HIS A 211 VAL A 216 -1 O ARG A 215 N THR A 157 SHEET 3 AA111 LEU A 222 ILE A 235 -1 O VAL A 223 N VAL A 214 SHEET 4 AA111 THR A 238 VAL A 250 -1 O MET A 242 N ALA A 231 SHEET 5 AA111 ALA A 279 ALA A 283 1 O VAL A 280 N VAL A 243 SHEET 6 AA111 GLY A 468 TYR A 479 -1 O GLN A 475 N ALA A 283 SHEET 7 AA111 GLY A 292 SER A 300 -1 N HIS A 298 O GLY A 468 SHEET 8 AA111 VAL A 449 LEU A 453 -1 O PHE A 450 N ARG A 299 SHEET 9 AA111 ALA A 418 SER A 421 1 N ALA A 419 O ASN A 451 SHEET 10 AA111 VAL A 394 THR A 402 -1 N TYR A 401 O TYR A 420 SHEET 11 AA111 LEU A 362 PRO A 364 0 SHEET 1 AA211 LEU A 338 PRO A 340 0 SHEET 2 AA211 ILE A 382 GLU A 388 -1 O VAL A 386 N ARG A 339 SHEET 3 AA211 VAL A 394 THR A 402 -1 O LEU A 398 N PHE A 385 SHEET 4 AA211 ALA A 418 SER A 421 -1 O TYR A 420 N TYR A 401 SHEET 5 AA211 VAL A 449 LEU A 453 1 O ASN A 451 N ALA A 419 SHEET 6 AA211 GLY A 292 SER A 300 -1 N ARG A 299 O PHE A 450 SHEET 7 AA211 GLY A 468 TYR A 479 -1 O GLY A 468 N HIS A 298 SHEET 8 AA211 ALA A 279 ALA A 283 -1 N ALA A 283 O GLN A 475 SHEET 9 AA211 THR A 238 VAL A 250 1 N VAL A 243 O VAL A 280 SHEET 10 AA211 LEU A 222 ILE A 235 -1 N ALA A 231 O MET A 242 SHEET 11 AA211 VAL A 425 HIS A 426 0 SHEET 1 AA3 3 PHE A 188 PHE A 190 0 SHEET 2 AA3 3 SER A 405 ILE A 407 -1 O THR A 406 N ARG A 189 SHEET 3 AA3 3 SER A 415 LEU A 416 -1 O LEU A 416 N SER A 405 SHEET 1 AA411 PHE B 156 ALA B 160 0 SHEET 2 AA411 HIS B 211 VAL B 216 -1 O ARG B 215 N THR B 157 SHEET 3 AA411 LEU B 222 ILE B 235 -1 O VAL B 223 N VAL B 214 SHEET 4 AA411 THR B 238 VAL B 250 -1 O MET B 242 N ALA B 231 SHEET 5 AA411 ALA B 279 ALA B 283 1 O VAL B 280 N VAL B 243 SHEET 6 AA411 GLY B 468 TYR B 479 -1 O TYR B 479 N ALA B 279 SHEET 7 AA411 GLY B 292 SER B 300 -1 N HIS B 298 O GLY B 468 SHEET 8 AA411 VAL B 449 LEU B 453 -1 O ALA B 452 N TRP B 297 SHEET 9 AA411 ALA B 418 SER B 421 1 N ALA B 419 O ASN B 451 SHEET 10 AA411 VAL B 394 THR B 402 -1 N TYR B 401 O TYR B 420 SHEET 11 AA411 LEU B 362 PRO B 364 0 SHEET 1 AA511 LEU B 338 PRO B 340 0 SHEET 2 AA511 ILE B 382 GLU B 388 -1 O VAL B 386 N ARG B 339 SHEET 3 AA511 VAL B 394 THR B 402 -1 O LEU B 398 N PHE B 385 SHEET 4 AA511 ALA B 418 SER B 421 -1 O TYR B 420 N TYR B 401 SHEET 5 AA511 VAL B 449 LEU B 453 1 O ASN B 451 N ALA B 419 SHEET 6 AA511 GLY B 292 SER B 300 -1 N TRP B 297 O ALA B 452 SHEET 7 AA511 GLY B 468 TYR B 479 -1 O GLY B 468 N HIS B 298 SHEET 8 AA511 ALA B 279 ALA B 283 -1 N ALA B 279 O TYR B 479 SHEET 9 AA511 THR B 238 VAL B 250 1 N VAL B 243 O VAL B 280 SHEET 10 AA511 LEU B 222 ILE B 235 -1 N ALA B 231 O MET B 242 SHEET 11 AA511 VAL B 425 HIS B 426 0 SHEET 1 AA6 2 PHE B 188 PHE B 190 0 SHEET 2 AA6 2 SER B 405 ILE B 407 -1 O THR B 406 N ARG B 189 LINK N GLY C 2 C1 MYR C 101 1555 1555 1.32 LINK N GLY D 2 C1 MYR D 101 1555 1555 1.34 CISPEP 1 PRO A 288 LYS A 289 0 -9.95 CISPEP 2 PRO B 288 LYS B 289 0 -11.14 SITE 1 AC1 23 TYR A 117 GLN A 118 PHE A 119 TRP A 120 SITE 2 AC1 23 ASN A 179 TYR A 180 VAL A 181 LEU A 248 SITE 3 AC1 23 CYS A 249 VAL A 250 ARG A 255 SER A 256 SITE 4 AC1 23 ARG A 258 ALA A 260 PRO A 261 ALA A 283 SITE 5 AC1 23 LEU A 287 HOH A 602 HOH A 677 HOH A 812 SITE 6 AC1 23 HOH A 823 GLY C 2 MYR C 101 SITE 1 AC2 8 LYS A 289 PRO A 290 VAL A 291 LEU A 478 SITE 2 AC2 8 TRP A 481 LYS A 482 CYS A 483 HOH A 640 SITE 1 AC3 23 TYR B 117 GLN B 118 PHE B 119 TRP B 120 SITE 2 AC3 23 ASN B 179 TYR B 180 VAL B 181 LEU B 248 SITE 3 AC3 23 CYS B 249 VAL B 250 ARG B 255 SER B 256 SITE 4 AC3 23 ARG B 258 VAL B 259 ALA B 260 PRO B 261 SITE 5 AC3 23 THR B 282 ALA B 283 LEU B 287 HOH B 756 SITE 6 AC3 23 HOH B 794 GLY D 2 MYR D 101 SITE 1 AC4 9 PRO B 126 LYS B 289 VAL B 291 TYR B 477 SITE 2 AC4 9 LEU B 478 TRP B 481 LYS B 482 CYS B 483 SITE 3 AC4 9 HOH B 605 SITE 1 AC5 8 GLU B 244 PRO B 364 MET B 366 TRP B 374 SITE 2 AC5 8 TYR B 423 VAL B 494 GLN B 496 HOH B 775 SITE 1 AC6 15 TRP A 120 TYR A 180 ASN A 246 PHE A 247 SITE 2 AC6 15 LEU A 248 THR A 268 VAL A 271 PHE A 277 SITE 3 AC6 15 TYR A 281 THR A 282 ALA A 283 TYR A 479 SITE 4 AC6 15 COA A 501 HOH A 734 CYS C 3 SITE 1 AC7 18 TRP B 120 TYR B 180 ASN B 246 PHE B 247 SITE 2 AC7 18 LEU B 248 THR B 268 VAL B 271 PHE B 277 SITE 3 AC7 18 GLN B 278 ALA B 279 TYR B 281 THR B 282 SITE 4 AC7 18 ALA B 283 TYR B 479 COA B 501 HOH B 666 SITE 5 AC7 18 HOH B 759 CYS D 3 CRYST1 58.236 79.779 178.751 90.00 90.00 90.00 P 2 21 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 0.017172 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012535 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005594 0.00000