HEADER HYDROLASE 20-JUL-17 5OJ7 TITLE SIRTUIN 4 ORTHOLOGUE FROM XENOPUS TROPICALIS IN COMPLEX WITH ADP- TITLE 2 RIBOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT PROTEIN DEACYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 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 BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: CODONPLUS KEYWDS SIRT4 DEACYLASE POSTTRANSLATIONAL MODIFICATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.PANNEK,C.STEEGBORN REVDAT 3 17-JAN-24 5OJ7 1 HETSYN ATOM REVDAT 2 24-JAN-18 5OJ7 1 SOURCE REVDAT 1 29-NOV-17 5OJ7 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. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 37316 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) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1964 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) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2705 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 142 REMARK 3 BIN FREE R VALUE : 0.2670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2257 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 59 REMARK 3 SOLVENT ATOMS : 261 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.30000 REMARK 3 B22 (A**2) : 0.66000 REMARK 3 B33 (A**2) : -0.35000 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): 0.076 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.079 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.059 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.184 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2410 ; 0.030 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2243 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3279 ; 2.608 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5153 ; 1.289 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 299 ; 6.657 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;38.197 ;23.391 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 382 ;13.990 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;18.838 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 355 ; 0.170 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2748 ; 0.015 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 598 ; 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): 1160 ; 2.319 ; 2.479 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1159 ; 2.311 ; 2.478 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1453 ; 3.351 ; 3.704 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1454 ; 3.352 ; 3.705 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1249 ; 3.570 ; 2.925 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1249 ; 3.569 ; 2.925 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1821 ; 5.303 ; 4.224 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2867 ; 7.158 ;21.504 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2867 ; 7.158 ;21.504 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 : 2 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 315 REMARK 3 ORIGIN FOR THE GROUP (A): 23.1585 15.1887 40.0645 REMARK 3 T TENSOR REMARK 3 T11: 0.0018 T22: 0.0235 REMARK 3 T33: 0.0188 T12: -0.0048 REMARK 3 T13: 0.0004 T23: 0.0025 REMARK 3 L TENSOR REMARK 3 L11: 0.5318 L22: 0.2595 REMARK 3 L33: 0.5315 L12: 0.1749 REMARK 3 L13: 0.3232 L23: 0.1202 REMARK 3 S TENSOR REMARK 3 S11: -0.0141 S12: -0.0006 S13: -0.0502 REMARK 3 S21: -0.0077 S22: -0.0225 S23: -0.0226 REMARK 3 S31: -0.0117 S32: -0.0044 S33: 0.0365 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 1 REMARK 3 ORIGIN FOR THE GROUP (A): 41.3721 31.9529 47.1162 REMARK 3 T TENSOR REMARK 3 T11: 0.0902 T22: 0.0537 REMARK 3 T33: 0.0809 T12: -0.0695 REMARK 3 T13: -0.0854 T23: 0.0659 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: -0.0000 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5OJ7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1200004969. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8-8.6 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) : 0.911656 REMARK 200 MONOCHROMATOR : SI111 CRYSTAL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39280 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6. REMARK 200 STARTING MODEL: 4TWI REMARK 200 REMARK 200 REMARK: DIAMOND-SHAPE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BICINE PH 8.0 17% PEG6000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 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 54.85000 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 54.85000 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 34.69500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.33000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.69500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.33000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 54.85000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.69500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.33000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 54.85000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.69500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.33000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 8.0 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 730 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 734 LIES ON A SPECIAL POSITION. 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 559 O HOH A 597 1.11 REMARK 500 OG SER A 117 O HOH A 501 1.95 REMARK 500 O1 EDO A 403 O HOH A 502 2.17 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 44 CD GLU A 44 OE2 -0.083 REMARK 500 CYS A 128 CA CYS A 128 CB -0.111 REMARK 500 TRP A 130 CB TRP A 130 CG -0.128 REMARK 500 GLU A 247 CD GLU A 247 OE2 -0.079 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 ASP A 72 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 GLU A 85 N - CA - CB ANGL. DEV. = 10.9 DEGREES REMARK 500 GLU A 182 OE1 - CD - OE2 ANGL. DEV. = -7.3 DEGREES REMARK 500 LEU A 198 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 ASP A 235 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 TYR A 268 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 LEU A 272 CB - CG - CD2 ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG A 290 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 290 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 302 NE - CZ - NH1 ANGL. DEV. = 3.8 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 ASP A 314 130.10 -31.28 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 A 760 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A 761 DISTANCE = 6.84 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 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 168 SG REMARK 620 2 CYS A 171 SG 112.9 REMARK 620 3 CYS A 219 SG 103.9 109.2 REMARK 620 4 CYS A 222 SG 101.4 114.1 114.6 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 AR6 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 407 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5OJO RELATED DB: PDB REMARK 900 RELATED ID: 5OJN RELATED DB: PDB DBREF 5OJ7 A 32 315 UNP Q28CB4 Q28CB4_XENTR 32 315 SEQADV 5OJ7 HIS A 30 UNP Q28CB4 EXPRESSION TAG SEQADV 5OJ7 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 AR6 A 401 36 HET ZN A 402 1 HET EDO A 403 4 HET EDO A 404 4 HET EDO A 405 4 HET EDO A 406 4 HET GOL A 407 6 HETNAM AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY- HETNAM 2 AR6 OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5- HETNAM 3 AR6 TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN HETNAM 4 AR6 PHOSPHATE HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETSYN AR6 ADENOSINE-5-DIPHOSPHORIBOSE HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 AR6 C15 H23 N5 O14 P2 FORMUL 3 ZN ZN 2+ FORMUL 4 EDO 4(C2 H6 O2) FORMUL 8 GOL C3 H8 O3 FORMUL 9 HOH *261(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 117 1 21 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 ASN A 238 LYS A 250 1 13 HELIX 10 AB1 VAL A 264 LEU A 277 1 14 HELIX 11 AB2 ALA A 291 ALA A 295 5 5 HELIX 12 AB3 ARG A 302 LEU A 307 1 6 HELIX 13 AB4 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 THR A 141 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 3655 2.41 LINK SG CYS A 168 ZN ZN A 402 1555 1555 2.34 LINK SG CYS A 171 ZN ZN A 402 1555 1555 2.27 LINK SG CYS A 219 ZN ZN A 402 1555 1555 2.31 LINK SG CYS A 222 ZN ZN A 402 1555 1555 2.32 SITE 1 AC1 30 PRO A 33 GLY A 61 ALA A 62 GLY A 63 SITE 2 AC1 30 THR A 66 GLU A 67 ASP A 72 TYR A 73 SITE 3 AC1 30 ARG A 74 SER A 75 GLN A 142 HIS A 160 SITE 4 AC1 30 GLY A 259 SER A 260 SER A 261 VAL A 264 SITE 5 AC1 30 ASN A 285 ILE A 286 GLY A 287 ALA A 301 SITE 6 AC1 30 ARG A 302 CYS A 303 GOL A 407 HOH A 520 SITE 7 AC1 30 HOH A 546 HOH A 557 HOH A 559 HOH A 575 SITE 8 AC1 30 HOH A 600 HOH A 657 SITE 1 AC2 4 CYS A 168 CYS A 171 CYS A 219 CYS A 222 SITE 1 AC3 9 GLY A 161 GLN A 229 VAL A 230 THR A 231 SITE 2 AC3 9 HOH A 502 HOH A 514 HOH A 565 HOH A 584 SITE 3 AC3 9 HOH A 630 SITE 1 AC4 5 ARG A 103 TYR A 104 ASP A 203 HOH A 547 SITE 2 AC4 5 HOH A 581 SITE 1 AC5 4 PHE A 241 HOH A 504 HOH A 605 HOH A 621 SITE 1 AC6 5 SER A 157 PHE A 241 SER A 244 HOH A 607 SITE 2 AC6 5 HOH A 621 SITE 1 AC7 9 HIS A 160 THR A 231 PHE A 232 PHE A 233 SITE 2 AC7 9 ASP A 235 VAL A 264 SER A 266 AR6 A 401 SITE 3 AC7 9 HOH A 582 CRYST1 69.390 74.660 109.700 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 0.014411 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013394 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009116 0.00000