HEADER TRANSFERASE 20-SEP-13 4C7I TITLE LEISMANIA MAJOR N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A TITLE 2 PEPTIDOMIMETIC (-OH) MOLECULE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 11-421; COMPND 5 EC: 2.3.1.97; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA MAJOR; SOURCE 3 ORGANISM_TAXID: 5664; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA2 PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET15-DERIVATIVE; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: MAC040-B01 KEYWDS TRANSFERASE, MYRISTOYLATION EXPDTA X-RAY DIFFRACTION AUTHOR T.O.OLALEYE,J.A.BRANNIGAN,V.GONCALVES,S.M.ROBERTS,R.J.LEATHERBARROW, AUTHOR 2 A.J.WILKINSON,E.W.TATE REVDAT 3 08-OCT-14 4C7I 1 JRNL REVDAT 2 01-OCT-14 4C7I 1 JRNL REVDAT 1 24-SEP-14 4C7I 0 JRNL AUTH T.O.OLALEYE,J.A.BRANNIGAN,S.M.ROBERTS,R.J.LEATHERBARROW, JRNL AUTH 2 A.J.WILKINSON,E.W.TATE JRNL TITL PEPTIDOMIMETIC INHIBITORS OF N-MYRISTOYLTRANSFERASE FROM JRNL TITL 2 HUMAN MALARIA AND LEISHMANIASIS PARASITES. JRNL REF ORG.BIOMOL.CHEM. V. 12 8132 2014 JRNL REFN ISSN 1477-0520 JRNL PMID 25230674 JRNL DOI 10.1039/C4OB01669F REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU, REMARK 3 STEINER,NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.14 REMARK 3 NUMBER OF REFLECTIONS : 95399 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 + TEST SET) : 0.16944 REMARK 3 R VALUE (WORKING SET) : 0.16793 REMARK 3 FREE R VALUE : 0.19861 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 5043 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.300 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.334 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5548 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.18 REMARK 3 BIN R VALUE (WORKING SET) : 0.264 REMARK 3 BIN FREE R VALUE SET COUNT : 321 REMARK 3 BIN FREE R VALUE : 0.325 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3650 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 116 REMARK 3 SOLVENT ATOMS : 579 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.309 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.56 REMARK 3 B22 (A**2) : 0.01 REMARK 3 B33 (A**2) : 0.37 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.10 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.053 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.057 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.855 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3912 ; 0.030 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5380 ; 2.745 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 507 ; 6.665 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 195 ;34.831 ;23.846 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 674 ;14.554 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;21.083 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 571 ; 0.203 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3054 ; 0.016 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4C7I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-SEP-13. REMARK 100 THE PDBE ID CODE IS EBI-58450. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9200 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL (PILATUS 6M) REMARK 200 DETECTOR MANUFACTURER : DECTRIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 100469 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.30 REMARK 200 RESOLUTION RANGE LOW (A) : 45.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 3.3 REMARK 200 R MERGE (I) : 0.04 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.50 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.3 REMARK 200 R MERGE FOR SHELL (I) : 0.37 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% PEG1500, 0.2M NACL, 0.1M REMARK 280 BIS-TRIS PH 5.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 45.52800 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 OE2B GLU A 24 O HOH A 2033 1.75 REMARK 500 CE B MET A 63 CD1B ILE A 72 2.15 REMARK 500 OE1B GLN A 98 O HOH A 2216 2.19 REMARK 500 NZ B LYS A 318 O HOH A 2483 2.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TRP A 110 CG TRP A 110 CD1 0.113 REMARK 500 GLU A 147 CD GLU A 147 OE2 0.075 REMARK 500 ARG A 191 CZ ARG A 191 NH1 0.125 REMARK 500 ARG A 265 CZ ARG A 265 NH2 -0.082 REMARK 500 GLU A 388 CD A GLU A 388 OE2A 0.077 REMARK 500 GLU A 388 CG A GLU A 388 CD A 0.095 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 MET A 36 CA - CB - CG ANGL. DEV. = 12.2 DEGREES REMARK 500 ASP A 44 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 MET A 63 N - CA - CB ANGL. DEV. = -11.7 DEGREES REMARK 500 ASP A 68 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 TYR A 80 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP A 84 CB - CG - OD1 ANGL. DEV. = 7.4 DEGREES REMARK 500 ASP A 85 CB - CG - OD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 89 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 89 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 GLU A 95 CG - CD - OE1 ANGL. DEV. = 12.2 DEGREES REMARK 500 GLU A 95 OE1 - CD - OE2 ANGL. DEV. = -9.8 DEGREES REMARK 500 LEU A 122 CB - CG - CD1 ANGL. DEV. = 10.2 DEGREES REMARK 500 ARG A 134 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 MET A 141 CG - SD - CE ANGL. DEV. = -13.2 DEGREES REMARK 500 LEU A 184 CB - CG - CD2 ANGL. DEV. = 11.3 DEGREES REMARK 500 ARG A 191 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 191 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 ARG A 220 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ALA A 247 N - CA - CB ANGL. DEV. = 11.2 DEGREES REMARK 500 ALA A 247 C - N - CA ANGL. DEV. = -16.6 DEGREES REMARK 500 ALA A 247 O - C - N ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG A 265 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 265 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 265 NH1 - CZ - NH2 ANGL. DEV. = 6.6 DEGREES REMARK 500 PHE A 286 CB - CG - CD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 PHE A 286 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ASP A 294 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP A 294 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 TYR A 311 CB - CG - CD1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ASP A 321 CB - CG - OD1 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 370 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 384 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 TYR A 408 CB - CG - CD2 ANGL. DEV. = 4.8 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 MET A 135 27.16 -148.11 REMARK 500 VAL A 307 -64.84 -125.97 REMARK 500 HIS A 347 -155.85 -109.78 REMARK 500 GLU A 379 39.78 -78.20 REMARK 500 LEU A 381 -142.73 55.72 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 ALA A 247 1.5 L L EXPECTING SP3 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 A2203 DISTANCE = 5.19 ANGSTROMS 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 MG A1423 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MYA A1422 O2A REMARK 620 2 LEU A 175 O 154.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MYA A1422 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1423 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE JJ1 A1424 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A1425 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A1426 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4C68 RELATED DB: PDB REMARK 900 PLASMODIUM VIVAX N-MYRISTOYLTRANSFERASE IN COMPLEX WITH REMARK 900 A PEPTIDOMIMETIC INHIBITOR REMARK 900 RELATED ID: 4C7H RELATED DB: PDB REMARK 900 LEISMANIA MAJOR N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A REMARK 900 PEPTIDOMIMETIC (-NH2) MOLECULE DBREF 4C7I A 11 421 UNP Q4Q5S8 Q4Q5S8_LEIMA 11 421 SEQRES 1 A 411 ALA HIS ALA PHE TRP SER THR GLN PRO VAL PRO GLN THR SEQRES 2 A 411 GLU ASP GLU THR GLU LYS ILE VAL PHE ALA GLY PRO MET SEQRES 3 A 411 ASP GLU PRO LYS THR VAL ALA ASP ILE PRO GLU GLU PRO SEQRES 4 A 411 TYR PRO ILE ALA SER THR PHE GLU TRP TRP THR PRO ASN SEQRES 5 A 411 MET GLU ALA ALA ASP ASP ILE HIS ALA ILE TYR GLU LEU SEQRES 6 A 411 LEU ARG ASP ASN TYR VAL GLU ASP ASP ASP SER MET PHE SEQRES 7 A 411 ARG PHE ASN TYR SER GLU GLU PHE LEU GLN TRP ALA LEU SEQRES 8 A 411 CYS PRO PRO ASN TYR ILE PRO ASP TRP HIS VAL ALA VAL SEQRES 9 A 411 ARG ARG LYS ALA ASP LYS LYS LEU LEU ALA PHE ILE ALA SEQRES 10 A 411 GLY VAL PRO VAL THR LEU ARG MET GLY THR PRO LYS TYR SEQRES 11 A 411 MET LYS VAL LYS ALA GLN GLU LYS GLY GLU GLY GLU GLU SEQRES 12 A 411 ALA ALA LYS TYR ASP GLU PRO ARG HIS ILE CYS GLU ILE SEQRES 13 A 411 ASN PHE LEU CYS VAL HIS LYS GLN LEU ARG GLU LYS ARG SEQRES 14 A 411 LEU ALA PRO ILE LEU ILE LYS GLU ALA THR ARG ARG VAL SEQRES 15 A 411 ASN ARG THR ASN VAL TRP GLN ALA VAL TYR THR ALA GLY SEQRES 16 A 411 VAL LEU LEU PRO THR PRO TYR ALA SER GLY GLN TYR PHE SEQRES 17 A 411 HIS ARG SER LEU ASN PRO GLU LYS LEU VAL GLU ILE ARG SEQRES 18 A 411 PHE SER GLY ILE PRO ALA GLN TYR GLN LYS PHE GLN ASN SEQRES 19 A 411 PRO MET ALA MET LEU LYS ARG ASN TYR GLN LEU PRO SER SEQRES 20 A 411 ALA PRO LYS ASN SER GLY LEU ARG GLU MET LYS PRO SER SEQRES 21 A 411 ASP VAL PRO GLN VAL ARG ARG ILE LEU MET ASN TYR LEU SEQRES 22 A 411 ASP SER PHE ASP VAL GLY PRO VAL PHE SER ASP ALA GLU SEQRES 23 A 411 ILE SER HIS TYR LEU LEU PRO ARG ASP GLY VAL VAL PHE SEQRES 24 A 411 THR TYR VAL VAL GLU ASN ASP LYS LYS VAL THR ASP PHE SEQRES 25 A 411 PHE SER PHE TYR ARG ILE PRO SER THR VAL ILE GLY ASN SEQRES 26 A 411 SER ASN TYR ASN LEU LEU ASN ALA ALA TYR VAL HIS TYR SEQRES 27 A 411 TYR ALA ALA THR SER ILE PRO LEU HIS GLN LEU ILE LEU SEQRES 28 A 411 ASP LEU LEU ILE VAL ALA HIS SER ARG GLY PHE ASP VAL SEQRES 29 A 411 CYS ASN MET VAL GLU ILE LEU ASP ASN ARG SER PHE VAL SEQRES 30 A 411 GLU GLN LEU LYS PHE GLY ALA GLY ASP GLY HIS LEU ARG SEQRES 31 A 411 TYR TYR PHE TYR ASN TRP ALA TYR PRO LYS ILE LYS PRO SEQRES 32 A 411 SER GLN VAL ALA LEU VAL MET LEU HET MYA A1422 63 HET MG A1423 1 HET JJ1 A1424 36 HET DMS A1425 8 HET DMS A1426 8 HETNAM MYA TETRADECANOYL-COA HETNAM JJ1 N-[(1S)-1-{[(1S)-5-AMINO-1-[(2- HETNAM 2 JJ1 CYCLOHEXYLETHYL)CARBAMOYL]PENTYL]CARBAMOYL}-2-HYDROXYETHYL] HETNAM 3 JJ1 -10-HYDROXYDECANAMIDE HETNAM DMS DIMETHYL SULFOXIDE HETNAM MG MAGNESIUM ION HETSYN MYA MYRISTOYL-COA HETSYN JJ1 2-DEOXY-L-GLYCERO-D-MANNO-HEPTOSE FORMUL 2 MYA C35 H62 N7 O17 P3 S FORMUL 3 JJ1 C27 H52 N4 O5 FORMUL 4 DMS 2(C2 H6 O S) FORMUL 5 MG MG 2+ FORMUL 6 HOH *579(H2 O) HELIX 1 1 PHE A 14 GLN A 18 5 5 HELIX 2 2 THR A 23 ILE A 30 1 8 HELIX 3 3 THR A 41 ILE A 45 5 5 HELIX 4 4 ALA A 65 TYR A 80 1 16 HELIX 5 5 SER A 93 CYS A 102 1 10 HELIX 6 6 ILE A 107 ASP A 109 5 3 HELIX 7 7 PRO A 138 LYS A 148 1 11 HELIX 8 8 GLU A 150 LYS A 156 1 7 HELIX 9 9 LYS A 173 ARG A 176 5 4 HELIX 10 10 ARG A 179 ARG A 194 1 16 HELIX 11 11 ASN A 223 ILE A 230 1 8 HELIX 12 12 PRO A 236 PHE A 242 5 7 HELIX 13 13 ASN A 244 GLN A 254 1 11 HELIX 14 14 LYS A 268 SER A 270 5 3 HELIX 15 15 ASP A 271 ASP A 284 1 14 HELIX 16 16 SER A 293 LEU A 302 1 10 HELIX 17 17 PRO A 355 ARG A 370 1 16 HELIX 18 18 ASP A 382 VAL A 387 5 6 HELIX 19 19 LYS A 412 GLN A 415 5 4 SHEET 1 AA 4 PHE A 56 TRP A 59 0 SHEET 2 AA 4 HIS A 111 ARG A 116 -1 O ALA A 113 N TRP A 59 SHEET 3 AA 4 LEU A 122 ARG A 134 -1 N LEU A 123 O VAL A 114 SHEET 4 AA 4 GLY A 289 PRO A 290 -1 O GLY A 289 N ARG A 134 SHEET 1 AB12 PHE A 56 TRP A 59 0 SHEET 2 AB12 HIS A 111 ARG A 116 -1 O ALA A 113 N TRP A 59 SHEET 3 AB12 LEU A 122 ARG A 134 -1 N LEU A 123 O VAL A 114 SHEET 4 AB12 ARG A 161 VAL A 171 -1 O ARG A 161 N LEU A 133 SHEET 5 AB12 ALA A 200 ALA A 204 1 O VAL A 201 N ILE A 166 SHEET 6 AB12 GLY A 393 TYR A 404 -1 O ARG A 400 N ALA A 204 SHEET 7 AB12 ALA A 213 SER A 221 -1 O ALA A 213 N TYR A 401 SHEET 8 AB12 VAL A 374 VAL A 378 -1 O CYS A 375 N ARG A 220 SHEET 9 AB12 LEU A 340 ALA A 351 1 O ALA A 344 N ASN A 376 SHEET 10 AB12 LYS A 318 VAL A 332 -1 O PHE A 322 N ALA A 350 SHEET 11 AB12 VAL A 308 ASN A 315 -1 O PHE A 309 N PHE A 325 SHEET 12 AB12 LEU A 264 GLU A 266 -1 O ARG A 265 N VAL A 312 SHEET 1 AC11 PHE A 56 TRP A 59 0 SHEET 2 AC11 HIS A 111 ARG A 116 -1 O ALA A 113 N TRP A 59 SHEET 3 AC11 LEU A 122 ARG A 134 -1 N LEU A 123 O VAL A 114 SHEET 4 AC11 ARG A 161 VAL A 171 -1 O ARG A 161 N LEU A 133 SHEET 5 AC11 ALA A 200 ALA A 204 1 O VAL A 201 N ILE A 166 SHEET 6 AC11 GLY A 393 TYR A 404 -1 O ARG A 400 N ALA A 204 SHEET 7 AC11 ALA A 213 SER A 221 -1 O ALA A 213 N TYR A 401 SHEET 8 AC11 VAL A 374 VAL A 378 -1 O CYS A 375 N ARG A 220 SHEET 9 AC11 LEU A 340 ALA A 351 1 O ALA A 344 N ASN A 376 SHEET 10 AC11 LYS A 318 VAL A 332 -1 O PHE A 322 N ALA A 350 SHEET 11 AC11 PHE A 88 PHE A 90 -1 O ARG A 89 N THR A 331 SHEET 1 AD 2 GLY A 289 PRO A 290 0 SHEET 2 AD 2 LEU A 122 ARG A 134 -1 O ARG A 134 N GLY A 289 LINK O2A MYA A1422 MG MG A1423 1555 1555 2.80 LINK MG MG A1423 O LEU A 175 1555 1555 2.72 CISPEP 1 PRO A 209 THR A 210 0 -20.63 SITE 1 AC1 36 HIS A 12 ALA A 13 PHE A 14 TRP A 15 SITE 2 AC1 36 ASN A 79 VAL A 81 PHE A 168 LEU A 169 SITE 3 AC1 36 CYS A 170 VAL A 171 ARG A 176 GLU A 177 SITE 4 AC1 36 LYS A 178 ARG A 179 LEU A 180 ALA A 181 SITE 5 AC1 36 PRO A 182 THR A 189 VAL A 192 TRP A 198 SITE 6 AC1 36 TYR A 202 THR A 203 LEU A 208 TYR A 404 SITE 7 AC1 36 MG A1423 JJ1 A1424 HOH A2004 HOH A2328 SITE 8 AC1 36 HOH A2333 HOH A2575 HOH A2576 HOH A2577 SITE 9 AC1 36 HOH A2578 HOH A2579 HOH A2580 HOH A2582 SITE 1 AC2 6 LEU A 175 GLU A 177 LYS A 178 ARG A 179 SITE 2 AC2 6 LEU A 180 MYA A1422 SITE 1 AC3 23 TYR A 80 ASP A 83 ASP A 84 ASP A 85 SITE 2 AC3 23 ASN A 167 THR A 203 TYR A 217 HIS A 219 SITE 3 AC3 23 PHE A 232 SER A 233 TYR A 253 ALA A 394 SITE 4 AC3 23 GLY A 395 ASP A 396 GLY A 397 MYA A1422 SITE 5 AC3 23 DMS A1425 DMS A1426 HOH A2185 HOH A2189 SITE 6 AC3 23 HOH A2317 HOH A2534 HOH A2554 SITE 1 AC4 5 PHE A 88 PHE A 90 SER A 330 JJ1 A1424 SITE 2 AC4 5 HOH A2508 SITE 1 AC5 7 PHE A 90 TYR A 92 TYR A 217 TYR A 345 SITE 2 AC5 7 MET A 420 JJ1 A1424 HOH A2508 CRYST1 48.641 91.056 53.596 90.00 113.98 90.00 P 1 21 1 2 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 0.020559 0.000000 0.009145 0.00000 SCALE2 0.000000 0.010982 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020421 0.00000