HEADER HYDROLASE/INHIBITOR 15-DEC-12 3ZG6 TITLE THE NOVEL DE-LONG CHAIN FATTY ACID FUNCTION OF HUMAN SIRT6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 1-296; COMPND 5 SYNONYM: REGULATORY PROTEIN SIR2 HOMOLOG 6, SIR2-LIKE PROTEIN 6, COMPND 6 SIRT6; COMPND 7 EC: 3.5.1.-, 2.4.2.31; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: PEPTIDE; COMPND 11 CHAIN: F; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28A; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE-INHIBITOR COMPLEX, SIRTUIN CLASS III, HDACS NAD DEPENDENT EXPDTA X-RAY DIFFRACTION AUTHOR Y.WANG,Q.HAO REVDAT 2 17-APR-13 3ZG6 1 JRNL REVDAT 1 03-APR-13 3ZG6 0 JRNL AUTH H.JIANG,S.KHAN,Y.WANG,G.CHARRON,B.HE,C.SEBASTIAN,J.DU,R.KIM, JRNL AUTH 2 E.GE,R.MOSTOSLAVSKY,H.C.HANG,Q.HAO,H.LIN JRNL TITL SIRT6 REGULATES TNF-ALPHA SECRETION THROUGH HYDROLYSIS OF JRNL TITL 2 LONG-CHAIN FATTY ACYL LYSINE JRNL REF NATURE V. 496 110 2013 JRNL REFN ISSN 0028-0836 JRNL PMID 23552949 JRNL DOI 10.1038/NATURE12038 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.02 REMARK 3 NUMBER OF REFLECTIONS : 23603 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) : 0.19343 REMARK 3 R VALUE (WORKING SET) : 0.19112 REMARK 3 FREE R VALUE : 0.23581 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 1268 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) : 2.204 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.261 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1695 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.238 REMARK 3 BIN FREE R VALUE SET COUNT : 90 REMARK 3 BIN FREE R VALUE : 0.274 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2366 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 73 REMARK 3 SOLVENT ATOMS : 150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.370 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00 REMARK 3 B22 (A**2) : 0.00 REMARK 3 B33 (A**2) : 0.01 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.190 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.176 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.124 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.882 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2493 ; 0.024 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3377 ; 2.207 ; 1.998 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 304 ; 6.636 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;35.747 ;22.157 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 411 ;18.552 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;22.970 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 372 ; 0.194 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1846 ; 0.011 ; 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): 1521 ; 1.339 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2445 ; 2.360 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 972 ; 3.457 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 932 ; 5.352 ; 4.500 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 : 1.40 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. REMARK 4 REMARK 4 3ZG6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-DEC-12. REMARK 100 THE PDBE ID CODE IS EBI-55133. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979073 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25066 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.20 REMARK 200 RESOLUTION RANGE LOW (A) : 40.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.7 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.8 REMARK 200 R MERGE (I) : 0.06 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 47.90 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.0 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.70 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 65.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 52.44550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 30.27942 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 77.16400 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 52.44550 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 30.27942 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 77.16400 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 52.44550 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 30.27942 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 77.16400 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 52.44550 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 30.27942 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 77.16400 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 52.44550 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 30.27942 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 77.16400 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 52.44550 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 30.27942 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 77.16400 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 60.55885 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 154.32800 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 60.55885 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 154.32800 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 60.55885 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 154.32800 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 60.55885 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 154.32800 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 60.55885 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 154.32800 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 60.55885 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 154.32800 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: 3640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F 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 MET A -1 REMARK 465 SER A 0 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 ARG A 88 CZ NH1 NH2 REMARK 470 LYS A 158 NZ REMARK 470 VAL A 166 CG1 CG2 REMARK 470 ALA A 167 O REMARK 470 ARG A 176 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 270 OE1 OE2 REMARK 470 ASP A 275 OD2 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 PRO A 24 O GLU A 27 2.05 REMARK 500 NE ARG A 88 O HOH A 2048 2.09 REMARK 500 CE MYK F 9 O HOH A 2146 2.15 REMARK 500 NZ MYK F 9 O HOH A 2146 2.04 REMARK 500 CB SER F 10 O HOH F 2003 2.19 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 TYR A 10 CE2 TYR A 10 CZ -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 VAL A 152 CG1 - CB - CG2 ANGL. DEV. = 10.2 DEGREES REMARK 500 ARG A 162 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 162 NE - CZ - NH2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 218 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 246 NE - CZ - NH1 ANGL. DEV. = 7.4 DEGREES REMARK 500 ARG A 246 NE - CZ - NH2 ANGL. DEV. = -8.2 DEGREES REMARK 500 ARG A 251 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 251 NE - CZ - NH2 ANGL. DEV. = -4.5 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 ALA A 4 -87.04 89.37 REMARK 500 LEU A 28 -69.90 130.08 REMARK 500 ASN A 238 139.03 -170.63 REMARK 500 PRO A 241 160.79 -45.01 REMARK 500 THR F 6 144.06 -32.33 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 4 23.0 L L OUTSIDE RANGE REMARK 500 THR A 92 19.7 L L OUTSIDE RANGE REMARK 500 THR A 144 24.9 L L OUTSIDE RANGE REMARK 500 THR F 6 24.6 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL 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 ZN A1295 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 139 SG REMARK 620 2 CYS A 142 SG 110.7 REMARK 620 3 CYS A 164 SG 102.9 107.5 REMARK 620 4 CYS A 175 SG 98.2 121.7 114.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1295 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE APR A1296 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1298 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1299 DBREF 3ZG6 A -1 294 UNP Q8N6T7 SIR6_HUMAN 1 296 DBREF 3ZG6 F 4 15 PDB 3ZG6 3ZG6 4 15 SEQADV 3ZG6 MET A 1 UNP Q8N6T7 VAL 3 CONFLICT SEQRES 1 A 296 MET SER MET ASN TYR ALA ALA GLY LEU SER PRO TYR ALA SEQRES 2 A 296 ASP LYS GLY LYS CYS GLY LEU PRO GLU ILE PHE ASP PRO SEQRES 3 A 296 PRO GLU GLU LEU GLU ARG LYS VAL TRP GLU LEU ALA ARG SEQRES 4 A 296 LEU VAL TRP GLN SER SER SER VAL VAL PHE HIS THR GLY SEQRES 5 A 296 ALA GLY ILE SER THR ALA SER GLY ILE PRO ASP PHE ARG SEQRES 6 A 296 GLY PRO HIS GLY VAL TRP THR MET GLU GLU ARG GLY LEU SEQRES 7 A 296 ALA PRO LYS PHE ASP THR THR PHE GLU SER ALA ARG PRO SEQRES 8 A 296 THR GLN THR HIS MET ALA LEU VAL GLN LEU GLU ARG VAL SEQRES 9 A 296 GLY LEU LEU ARG PHE LEU VAL SER GLN ASN VAL ASP GLY SEQRES 10 A 296 LEU HIS VAL ARG SER GLY PHE PRO ARG ASP LYS LEU ALA SEQRES 11 A 296 GLU LEU HIS GLY ASN MET PHE VAL GLU GLU CYS ALA LYS SEQRES 12 A 296 CYS LYS THR GLN TYR VAL ARG ASP THR VAL VAL GLY THR SEQRES 13 A 296 MET GLY LEU LYS ALA THR GLY ARG LEU CYS THR VAL ALA SEQRES 14 A 296 LYS ALA ARG GLY LEU ARG ALA CYS ARG GLY GLU LEU ARG SEQRES 15 A 296 ASP THR ILE LEU ASP TRP GLU ASP SER LEU PRO ASP ARG SEQRES 16 A 296 ASP LEU ALA LEU ALA ASP GLU ALA SER ARG ASN ALA ASP SEQRES 17 A 296 LEU SER ILE THR LEU GLY THR SER LEU GLN ILE ARG PRO SEQRES 18 A 296 SER GLY ASN LEU PRO LEU ALA THR LYS ARG ARG GLY GLY SEQRES 19 A 296 ARG LEU VAL ILE VAL ASN LEU GLN PRO THR LYS HIS ASP SEQRES 20 A 296 ARG HIS ALA ASP LEU ARG ILE HIS GLY TYR VAL ASP GLU SEQRES 21 A 296 VAL MET THR ARG LEU MET LYS HIS LEU GLY LEU GLU ILE SEQRES 22 A 296 PRO ALA TRP ASP GLY PRO ARG VAL LEU GLU ARG ALA LEU SEQRES 23 A 296 PRO PRO LEU PRO ARG PRO PRO THR PRO LYS SEQRES 1 F 12 LYS GLN THR ALA ARG MYK SER THR GLY GLY TRP TRP MODRES 3ZG6 MYK F 9 LYS N~6~-TETRADECANOYL-L-LYSINE HET ZN A1295 1 HET APR A1296 36 HET MYK F 9 24 HET GOL A1298 6 HET GOL A1299 6 HETNAM MYK N~6~-TETRADECANOYL-L-LYSINE HETNAM APR ADENOSINE-5-DIPHOSPHORIBOSE HETNAM GOL GLYCEROL HETNAM ZN ZINC ION HETSYN MYK N6-MYRISTOYL LYSINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MYK C20 H40 N2 O3 FORMUL 4 APR C15 H23 N5 O14 P2 FORMUL 5 GOL 2(C3 H8 O3) FORMUL 6 ZN ZN 2+ FORMUL 7 HOH *150(H2 O) HELIX 1 1 PRO A 25 SER A 42 1 18 HELIX 2 2 ALA A 51 GLY A 58 5 8 HELIX 3 3 GLY A 67 ARG A 74 1 8 HELIX 4 4 THR A 90 VAL A 102 1 13 HELIX 5 5 GLY A 115 SER A 120 1 6 HELIX 6 6 PRO A 123 ASP A 125 5 3 HELIX 7 7 PRO A 191 ALA A 205 1 15 HELIX 8 8 ASN A 222 THR A 227 1 6 HELIX 9 9 LYS A 228 GLY A 231 5 4 HELIX 10 10 HIS A 244 ALA A 248 5 5 HELIX 11 11 TYR A 255 GLY A 268 1 14 SHEET 1 AA 6 LEU A 127 GLU A 129 0 SHEET 2 AA 6 PHE A 107 SER A 110 1 O LEU A 108 N ALA A 128 SHEET 3 AA 6 VAL A 45 THR A 49 1 O PHE A 47 N VAL A 109 SHEET 4 AA 6 LEU A 207 LEU A 211 1 O LEU A 207 N VAL A 46 SHEET 5 AA 6 ARG A 233 VAL A 237 1 O ARG A 233 N SER A 208 SHEET 6 AA 6 LEU A 250 ILE A 252 1 O LEU A 250 N ILE A 236 SHEET 1 AB 4 GLN A 145 VAL A 147 0 SHEET 2 AB 4 VAL A 136 CYS A 139 -1 O GLU A 137 N TYR A 146 SHEET 3 AB 4 GLU A 178 ASP A 181 -1 O ARG A 180 N GLU A 138 SHEET 4 AB 4 ALA A 159 LEU A 163 -1 N THR A 160 O LEU A 179 LINK ZN ZN A1295 SG CYS A 139 1555 1555 2.42 LINK ZN ZN A1295 SG CYS A 175 1555 1555 2.39 LINK ZN ZN A1295 SG CYS A 164 1555 1555 2.22 LINK ZN ZN A1295 SG CYS A 142 1555 1555 2.21 LINK N MYK F 9 C ARG F 8 1555 1555 1.33 LINK C MYK F 9 N SER F 10 1555 1555 1.34 CISPEP 1 TYR A 3 ALA A 4 0 -22.15 CISPEP 2 ARG A 218 PRO A 219 0 -1.62 SITE 1 AC1 4 CYS A 139 CYS A 142 CYS A 164 CYS A 175 SITE 1 AC2 27 GLY A 50 ALA A 51 GLY A 52 THR A 55 SITE 2 AC2 27 ASP A 61 PHE A 62 ARG A 63 TRP A 69 SITE 3 AC2 27 GLN A 111 HIS A 131 GLY A 212 THR A 213 SITE 4 AC2 27 SER A 214 ILE A 217 ASN A 238 LEU A 239 SITE 5 AC2 27 GLN A 240 GLY A 254 TYR A 255 VAL A 256 SITE 6 AC2 27 GOL A1299 HOH A2019 HOH A2033 HOH A2041 SITE 7 AC2 27 HOH A2061 HOH A2145 HOH A2146 SITE 1 AC3 5 GLU A 187 HIS A 244 ARG A 246 HIS A 247 SITE 2 AC3 5 TRP F 15 SITE 1 AC4 8 GLU A 20 THR A 55 ASP A 61 PRO A 65 SITE 2 AC4 8 APR A1296 HOH A2018 HOH A2019 HOH A2040 CRYST1 104.891 104.891 231.492 90.00 90.00 120.00 H 3 2 18 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 0.009534 0.005504 0.000000 0.00000 SCALE2 0.000000 0.011009 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004320 0.00000