HEADER SIGNALING PROTEIN 22-JUL-17 5OJN TITLE SIRTUIN 4 FROM XENOPUS TROPICALIS IN COMPLEX WITH THIOACETYL-ADP- TITLE 2 RIBOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT PROTEIN DEACYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SIRTUIN 4, REGULATORY PROTEIN SIR2 HOMOLOG; COMPND 5 EC: 3.5.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS TROPICALIS; SOURCE 3 ORGANISM_COMMON: WESTERN CLAWED FROG; SOURCE 4 ORGANISM_TAXID: 8364; SOURCE 5 GENE: SIRT4, TGAS015J14.1-001; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SIRTUIN, SIRT4, DEACYLASE, MITOCHONDRIA, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.PANNEK,C.STEEGBORN REVDAT 2 17-JAN-24 5OJN 1 REMARK REVDAT 1 29-NOV-17 5OJN 0 JRNL AUTH M.PANNEK,Z.SIMIC,M.FUSZARD,M.MELESHIN,D.ROTILI,A.MAI, JRNL AUTH 2 M.SCHUTKOWSKI,C.STEEGBORN JRNL TITL CRYSTAL STRUCTURES OF THE MITOCHONDRIAL DEACYLASE SIRTUIN 4 JRNL TITL 2 REVEAL ISOFORM-SPECIFIC ACYL RECOGNITION AND REGULATION JRNL TITL 3 FEATURES. JRNL REF NAT COMMUN V. 8 1513 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 29138502 JRNL DOI 10.1038/S41467-017-01701-2 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 25255 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1330 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1817 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2153 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 179 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.62000 REMARK 3 B22 (A**2) : 1.27000 REMARK 3 B33 (A**2) : -0.66000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.111 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.118 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.087 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.450 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2282 ; 0.029 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2040 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3110 ; 2.438 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4741 ; 1.260 ; 3.007 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 282 ; 6.371 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 107 ;38.154 ;23.178 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 369 ;14.372 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;14.717 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 341 ; 0.162 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2537 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 479 ; 0.002 ; 0.020 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): 1104 ; 2.752 ; 3.214 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1103 ; 2.753 ; 3.211 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1382 ; 3.728 ; 4.789 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1383 ; 3.727 ; 4.793 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1177 ; 4.309 ; 3.738 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1175 ; 4.313 ; 3.739 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1723 ; 6.428 ; 5.421 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2542 ; 7.856 ;38.833 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2543 ; 7.854 ;38.825 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 30 A 313 REMARK 3 ORIGIN FOR THE GROUP (A): 11.7105 22.3351 -15.0972 REMARK 3 T TENSOR REMARK 3 T11: 0.0062 T22: 0.0551 REMARK 3 T33: 0.0148 T12: -0.0109 REMARK 3 T13: 0.0017 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 0.3641 L22: 0.3592 REMARK 3 L33: 0.5823 L12: 0.1601 REMARK 3 L13: -0.4390 L23: -0.1169 REMARK 3 S TENSOR REMARK 3 S11: 0.0226 S12: -0.0179 S13: 0.0039 REMARK 3 S21: -0.0142 S22: -0.0337 S23: -0.0136 REMARK 3 S31: -0.0209 S32: -0.0242 S33: 0.0111 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5OJN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1200005902. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5-8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976250 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : SAGITALLY BENDED SI111-CRYSTAL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26585 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 1.04000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5OJ7 REMARK 200 REMARK 200 REMARK: DIAMONDS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M NA/K-TARTRATE 0.5% PEG5000MME REMARK 280 0.1 M TRIS, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K 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 54.77500 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 54.77500 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 34.48500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.44000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.48500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.44000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 54.77500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.48500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.44000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 54.77500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.48500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.44000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 503 LIES ON A SPECIAL POSITION. 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 GLN A 194 REMARK 465 ALA A 195 REMARK 465 HIS A 196 REMARK 465 GLY A 197 REMARK 465 LEU A 198 REMARK 465 ALA A 199 REMARK 465 PRO A 200 REMARK 465 ASP A 201 REMARK 465 GLY A 202 REMARK 465 ASP A 203 REMARK 465 VAL A 204 REMARK 465 PHE A 205 REMARK 465 ASP A 314 REMARK 465 GLN A 315 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 OE2 GLU A 93 O HOH A 501 2.15 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 647 O HOH A 647 3654 2.10 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 GLU A 67 CD GLU A 67 OE2 0.073 REMARK 500 TRP A 130 CB TRP A 130 CG -0.163 REMARK 500 GLU A 182 CD GLU A 182 OE1 0.067 REMARK 500 GLU A 182 CD GLU A 182 OE2 0.080 REMARK 500 SER A 212 CA SER A 212 CB 0.100 REMARK 500 ASP A 213 C ASP A 213 O 0.123 REMARK 500 SER A 266 CB SER A 266 OG -0.081 REMARK 500 CYS A 303 CB CYS A 303 SG -0.098 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 59 CG - SD - CE ANGL. DEV. = -20.2 DEGREES REMARK 500 ARG A 83 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 83 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 87 NE - CZ - NH1 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 87 NE - CZ - NH2 ANGL. DEV. = 6.9 DEGREES REMARK 500 PRO A 88 C - N - CA ANGL. DEV. = -9.9 DEGREES REMARK 500 ARG A 132 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 290 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 290 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 302 NE - CZ - NH1 ANGL. DEV. = 3.2 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 VAL A 78 -31.20 -139.99 REMARK 500 SER A 212 -62.35 -20.47 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 A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 168 SG REMARK 620 2 CYS A 171 SG 111.3 REMARK 620 3 CYS A 219 SG 105.6 110.4 REMARK 620 4 CYS A 222 SG 99.3 113.0 116.4 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 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9X8 A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5OJO RELATED DB: PDB REMARK 900 RELATED ID: 5OJ7 RELATED DB: PDB DBREF 5OJN A 32 315 UNP Q28CB4 Q28CB4_XENTR 32 315 SEQADV 5OJN HIS A 30 UNP Q28CB4 EXPRESSION TAG SEQADV 5OJN MET A 31 UNP Q28CB4 EXPRESSION TAG SEQRES 1 A 286 HIS MET VAL PRO ALA CYS PRO PRO PRO ASN PRO HIS GLN SEQRES 2 A 286 VAL GLU GLN LEU GLN ASP PHE VAL SER GLN SER GLN ARG SEQRES 3 A 286 LEU PHE VAL MET THR GLY ALA GLY ILE SER THR GLU SER SEQRES 4 A 286 GLY ILE PRO ASP TYR ARG SER GLU GLY VAL GLY LEU TYR SEQRES 5 A 286 SER ARG THR GLU ARG ARG PRO ILE GLN HIS SER GLU PHE SEQRES 6 A 286 VAL GLN SER GLN ALA ALA ARG ARG ARG TYR TRP ALA ARG SEQRES 7 A 286 ASN PHE VAL GLY TRP PRO SER PHE SER SER HIS GLU PRO SEQRES 8 A 286 ASN SER ALA HIS VAL ASN LEU CYS LYS TRP GLU ARG ALA SEQRES 9 A 286 GLY ARG LEU HIS TRP LEU VAL THR GLN ASN VAL ASP ALA SEQRES 10 A 286 LEU HIS THR LYS ALA GLY GLN CYS ARG LEU SER GLU LEU SEQRES 11 A 286 HIS GLY CYS THR HIS ARG VAL ILE CYS LEU GLY CYS GLN SEQRES 12 A 286 THR VAL THR LYS ARG SER GLU LEU GLN GLU ARG PHE LEU SEQRES 13 A 286 ASN LEU ASN PRO SER TRP ASN GLU GLN ALA HIS GLY LEU SEQRES 14 A 286 ALA PRO ASP GLY ASP VAL PHE LEU THR ASP GLU GLN VAL SEQRES 15 A 286 SER ASP PHE GLN VAL PRO ALA CYS THR LYS CYS GLY GLY SEQRES 16 A 286 ILE LEU LYS PRO GLN VAL THR PHE PHE GLY ASP THR VAL SEQRES 17 A 286 ASN ARG GLY PHE VAL PHE SER ILE TYR GLU GLN MET LYS SEQRES 18 A 286 GLN ALA ASP ALA MET LEU ILE VAL GLY SER SER LEU GLN SEQRES 19 A 286 VAL TYR SER GLY TYR ARG PHE ALA LEU ASN ALA LYS GLU SEQRES 20 A 286 LEU HIS LEU PRO ILE ALA ILE LEU ASN ILE GLY PRO THR SEQRES 21 A 286 ARG ALA ASP HIS LEU ALA LYS VAL LYS VAL SER ALA ARG SEQRES 22 A 286 CYS GLY ASP VAL LEU PRO HIS ILE LEU LEU GLN ASP GLN HET ZN A 401 1 HET 9X8 A 402 39 HETNAM ZN ZINC ION HETNAM 9X8 THIOACETYL-ADP-RIBOSE FORMUL 2 ZN ZN 2+ FORMUL 3 9X8 C17 H25 N5 O14 P2 S FORMUL 4 HOH *179(H2 O) HELIX 1 AA1 ASN A 39 GLN A 52 1 14 HELIX 2 AA2 ALA A 62 GLY A 69 5 8 HELIX 3 AA3 GLY A 79 THR A 84 1 6 HELIX 4 AA4 GLN A 90 SER A 97 1 8 HELIX 5 AA5 SER A 97 SER A 116 1 20 HELIX 6 AA6 ASN A 121 ALA A 133 1 13 HELIX 7 AA7 ALA A 146 GLY A 152 1 7 HELIX 8 AA8 ARG A 177 ASN A 188 1 12 HELIX 9 AA9 PRO A 189 ASN A 192 5 4 HELIX 10 AB1 THR A 207 SER A 212 1 6 HELIX 11 AB2 ASN A 238 LYS A 250 1 13 HELIX 12 AB3 VAL A 264 LEU A 277 1 14 HELIX 13 AB4 ALA A 291 ALA A 295 5 5 HELIX 14 AB5 ARG A 302 LEU A 307 1 6 HELIX 15 AB6 PRO A 308 ILE A 310 5 3 SHEET 1 AA1 6 LEU A 156 GLU A 158 0 SHEET 2 AA1 6 LEU A 136 THR A 141 1 N LEU A 139 O SER A 157 SHEET 3 AA1 6 LEU A 56 THR A 60 1 N VAL A 58 O VAL A 140 SHEET 4 AA1 6 ALA A 254 VAL A 258 1 O VAL A 258 N MET A 59 SHEET 5 AA1 6 ILE A 281 LEU A 284 1 O LEU A 284 N ILE A 257 SHEET 6 AA1 6 VAL A 297 VAL A 299 1 O VAL A 299 N ILE A 283 SHEET 1 AA2 3 VAL A 174 LYS A 176 0 SHEET 2 AA2 3 GLY A 161 CYS A 168 -1 N VAL A 166 O THR A 175 SHEET 3 AA2 3 LEU A 226 VAL A 230 -1 O LYS A 227 N ILE A 167 SSBOND 1 CYS A 154 CYS A 154 1555 3554 2.04 LINK SG CYS A 168 ZN ZN A 401 1555 1555 2.32 LINK SG CYS A 171 ZN ZN A 401 1555 1555 2.29 LINK SG CYS A 219 ZN ZN A 401 1555 1555 2.34 LINK SG CYS A 222 ZN ZN A 401 1555 1555 2.32 SITE 1 AC1 4 CYS A 168 CYS A 171 CYS A 219 CYS A 222 SITE 1 AC2 28 PRO A 33 GLY A 61 ALA A 62 GLY A 63 SITE 2 AC2 28 THR A 66 GLU A 67 ASP A 72 TYR A 73 SITE 3 AC2 28 ARG A 74 SER A 75 TYR A 81 GLN A 142 SITE 4 AC2 28 HIS A 160 THR A 231 GLY A 259 SER A 260 SITE 5 AC2 28 SER A 261 VAL A 264 ASN A 285 ILE A 286 SITE 6 AC2 28 GLY A 287 ALA A 301 ARG A 302 CYS A 303 SITE 7 AC2 28 HOH A 515 HOH A 525 HOH A 556 HOH A 585 CRYST1 68.970 74.880 109.550 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 0.014499 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013355 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009128 0.00000