HEADER DNA BINDING PROTEIN/DNA 17-MAR-19 6JNM TITLE REF6 ZNF2-4-NAC004-MC3 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE REF6; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: JUMONJI DOMAIN-CONTAINING PROTEIN 12,LYSINE-SPECIFIC HISTONE COMPND 5 DEMETHYLASE REF6,PROTEIN RELATIVE OF EARLY FLOWERING 6; COMPND 6 EC: 1.14.11.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*TP*TP*CP*TP*(5CM)P*TP*GP*TP*TP*TP*TP*G)-3'); COMPND 10 CHAIN: D, F; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: 5CM; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*A)-3'); COMPND 15 CHAIN: C, E; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: REF6, JMJ12, PKDM9A, AT3G48430, T29H11_50; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS REF6, ZINC FINGER, 5MC, DNA COMPLEX, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Q.Q.YAO,B.X.WU,J.B.MA REVDAT 3 22-NOV-23 6JNM 1 REMARK REVDAT 2 15-MAY-19 6JNM 1 JRNL REVDAT 1 27-MAR-19 6JNM 0 JRNL AUTH Q.QIU,H.MEI,X.DENG,K.HE,B.WU,Q.YAO,J.ZHANG,F.LU,J.MA,X.CAO JRNL TITL DNA METHYLATION REPELS TARGETING OF ARABIDOPSIS REF6. JRNL REF NAT COMMUN V. 10 2063 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31048693 JRNL DOI 10.1038/S41467-019-10026-1 REMARK 2 REMARK 2 RESOLUTION. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 31212 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1666 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 963 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 38.47 REMARK 3 BIN R VALUE (WORKING SET) : 0.2820 REMARK 3 BIN FREE R VALUE SET COUNT : 40 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1478 REMARK 3 NUCLEIC ACID ATOMS : 974 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 168 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.23000 REMARK 3 B22 (A**2) : -0.23000 REMARK 3 B33 (A**2) : 0.46000 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): 0.152 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.141 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.905 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2622 ; 0.024 ; 0.016 REMARK 3 BOND LENGTHS OTHERS (A): 1924 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3736 ; 2.092 ; 1.600 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4484 ; 1.410 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 176 ; 6.535 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 76 ;35.586 ;20.526 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 264 ;18.738 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;19.956 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 340 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2242 ; 0.016 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 592 ; 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): 710 ; 2.722 ; 2.820 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 709 ; 2.713 ; 2.815 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 884 ; 3.927 ; 4.192 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 885 ; 3.926 ; 4.197 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1912 ; 3.362 ; 2.745 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1913 ; 3.361 ; 2.745 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2853 ; 4.837 ; 4.033 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3412 ; 6.350 ;27.721 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3381 ; 6.356 ;27.603 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 : 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 6JNM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1300011433. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35297 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.2410 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.02000 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 REMARK 200 STARTING MODEL: 6JNL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 3,350, 0.03 M CITRATE ACID, REMARK 280 0.07 M BIS-TRIS PROPANE PH 7.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 36.16500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.24750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 18.08250 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, F, E 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 LEU A 1260 REMARK 465 MET A 1261 REMARK 465 LEU A 1262 REMARK 465 HIS A 1263 REMARK 465 LYS A 1264 REMARK 465 VAL A 1354 REMARK 465 LYS A 1355 REMARK 465 LYS A 1356 REMARK 465 THR A 1357 REMARK 465 ASN A 1358 REMARK 465 LYS A 1359 REMARK 465 ARG A 1360 REMARK 465 LEU B 1260 REMARK 465 MET B 1261 REMARK 465 LEU B 1262 REMARK 465 HIS B 1263 REMARK 465 LYS B 1264 REMARK 465 VAL B 1354 REMARK 465 LYS B 1355 REMARK 465 LYS B 1356 REMARK 465 THR B 1357 REMARK 465 ASN B 1358 REMARK 465 LYS B 1359 REMARK 465 ARG B 1360 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 SG CYS B 1273 ZN ZN B 1401 1.57 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 B 1502 O HOH F 111 4465 1.95 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 DT D 4 P DT D 4 OP1 -0.105 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 CYS A1268 CA - CB - SG ANGL. DEV. = 8.7 DEGREES REMARK 500 CYS A1273 CA - CB - SG ANGL. DEV. = 15.2 DEGREES REMARK 500 CYS A1328 CA - CB - SG ANGL. DEV. = 8.2 DEGREES REMARK 500 CYS A1333 CA - CB - SG ANGL. DEV. = 9.4 DEGREES REMARK 500 ARG A1338 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A1345 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A1348 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A1348 NE - CZ - NH2 ANGL. DEV. = 4.5 DEGREES REMARK 500 DG D 7 O5' - P - OP1 ANGL. DEV. = 7.3 DEGREES REMARK 500 CYS B1273 CA - CB - SG ANGL. DEV. = 19.2 DEGREES REMARK 500 SER B1312 N - CA - CB ANGL. DEV. = 9.0 DEGREES REMARK 500 CYS B1328 CA - CB - SG ANGL. DEV. = 9.3 DEGREES REMARK 500 CYS B1333 CA - CB - SG ANGL. DEV. = 11.1 DEGREES REMARK 500 ARG B1348 NE - CZ - NH2 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT F 6 O5' - P - OP2 ANGL. DEV. = 13.4 DEGREES REMARK 500 DG F 7 O5' - P - OP1 ANGL. DEV. = 7.7 DEGREES REMARK 500 DG E 10 O4' - C1' - N9 ANGL. DEV. = 2.0 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 ASN A1266 63.59 65.87 REMARK 500 CYS A1273 -72.30 -103.31 REMARK 500 CYS B1273 -83.59 -100.30 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 A1401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1268 SG REMARK 620 2 HIS A1286 NE2 116.5 REMARK 620 3 HIS A1290 NE2 114.1 112.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1298 SG REMARK 620 2 CYS A1303 SG 113.3 REMARK 620 3 HIS A1316 NE2 105.6 113.6 REMARK 620 4 HIS A1320 NE2 109.4 110.0 104.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1346 NE2 REMARK 620 2 HIS A1352 ND1 112.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1268 SG REMARK 620 2 HIS B1286 NE2 109.4 REMARK 620 3 HIS B1290 NE2 119.3 114.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1298 SG REMARK 620 2 CYS B1303 SG 116.4 REMARK 620 3 HIS B1316 NE2 107.0 113.3 REMARK 620 4 HIS B1320 NE2 108.4 107.7 103.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B1346 NE2 REMARK 620 2 HIS B1352 ND1 111.9 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 ZN A 1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 1402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 1403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide DT F 4 and 5CM F REMARK 800 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide 5CM F 5 and DT F REMARK 800 6 DBREF 6JNM A 1260 1360 UNP Q9STM3 REF6_ARATH 1260 1360 DBREF 6JNM D 1 12 PDB 6JNM 6JNM 1 12 DBREF 6JNM C 1 12 PDB 6JNM 6JNM 1 12 DBREF 6JNM B 1260 1360 UNP Q9STM3 REF6_ARATH 1260 1360 DBREF 6JNM F 1 12 PDB 6JNM 6JNM 1 12 DBREF 6JNM E 1 12 PDB 6JNM 6JNM 1 12 SEQRES 1 A 101 LEU MET LEU HIS LYS ARG ASN ILE CYS PRO ILE LYS GLY SEQRES 2 A 101 CYS GLY LYS ASN PHE PHE SER HIS LYS TYR LEU VAL GLN SEQRES 3 A 101 HIS GLN ARG VAL HIS SER ASP ASP ARG PRO LEU LYS CYS SEQRES 4 A 101 PRO TRP LYS GLY CYS LYS MET THR PHE LYS TRP ALA TRP SEQRES 5 A 101 SER ARG THR GLU HIS ILE ARG VAL HIS THR GLY ALA ARG SEQRES 6 A 101 PRO TYR VAL CYS ALA GLU PRO ASP CYS GLY GLN THR PHE SEQRES 7 A 101 ARG PHE VAL SER ASP PHE SER ARG HIS LYS ARG LYS THR SEQRES 8 A 101 GLY HIS SER VAL LYS LYS THR ASN LYS ARG SEQRES 1 D 12 DT DT DC DT 5CM DT DG DT DT DT DT DG SEQRES 1 C 12 DC DA DA DA DA DC DA DG DA DG DA DA SEQRES 1 B 101 LEU MET LEU HIS LYS ARG ASN ILE CYS PRO ILE LYS GLY SEQRES 2 B 101 CYS GLY LYS ASN PHE PHE SER HIS LYS TYR LEU VAL GLN SEQRES 3 B 101 HIS GLN ARG VAL HIS SER ASP ASP ARG PRO LEU LYS CYS SEQRES 4 B 101 PRO TRP LYS GLY CYS LYS MET THR PHE LYS TRP ALA TRP SEQRES 5 B 101 SER ARG THR GLU HIS ILE ARG VAL HIS THR GLY ALA ARG SEQRES 6 B 101 PRO TYR VAL CYS ALA GLU PRO ASP CYS GLY GLN THR PHE SEQRES 7 B 101 ARG PHE VAL SER ASP PHE SER ARG HIS LYS ARG LYS THR SEQRES 8 B 101 GLY HIS SER VAL LYS LYS THR ASN LYS ARG SEQRES 1 F 12 DT DT DC DT 5CM DT DG DT DT DT DT DG SEQRES 1 E 12 DC DA DA DA DA DC DA DG DA DG DA DA HET 5CM D 5 33 HET 5CM F 5 33 HET ZN A1401 1 HET ZN A1402 1 HET ZN A1403 1 HET ZN B1401 1 HET ZN B1402 1 HET ZN B1403 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM ZN ZINC ION FORMUL 2 5CM 2(C10 H16 N3 O7 P) FORMUL 7 ZN 6(ZN 2+) FORMUL 13 HOH *168(H2 O) HELIX 1 AA1 SER A 1279 GLN A 1287 1 9 HELIX 2 AA2 ARG A 1288 SER A 1291 5 4 HELIX 3 AA3 TRP A 1309 GLY A 1322 1 14 HELIX 4 AA4 PHE A 1339 GLY A 1351 1 13 HELIX 5 AA5 SER B 1279 GLN B 1287 1 9 HELIX 6 AA6 ARG B 1288 SER B 1291 5 4 HELIX 7 AA7 TRP B 1309 GLY B 1322 1 14 HELIX 8 AA8 PHE B 1339 GLY B 1351 1 13 SHEET 1 AA1 2 LEU A1296 LYS A1297 0 SHEET 2 AA1 2 THR A1306 PHE A1307 -1 O PHE A1307 N LEU A1296 SHEET 1 AA2 2 TYR A1326 VAL A1327 0 SHEET 2 AA2 2 THR A1336 PHE A1337 -1 O PHE A1337 N TYR A1326 SHEET 1 AA3 2 LEU B1296 LYS B1297 0 SHEET 2 AA3 2 THR B1306 PHE B1307 -1 O PHE B1307 N LEU B1296 SHEET 1 AA4 2 TYR B1326 VAL B1327 0 SHEET 2 AA4 2 THR B1336 PHE B1337 -1 O PHE B1337 N TYR B1326 SSBOND 1 CYS A 1268 CYS A 1273 1555 1555 2.54 SSBOND 2 CYS A 1328 CYS A 1333 1555 1555 2.43 SSBOND 3 CYS B 1268 CYS B 1273 1555 1555 2.45 SSBOND 4 CYS B 1328 CYS B 1333 1555 1555 2.42 LINK O3' DT D 4 P 5CM D 5 1555 1555 1.57 LINK O3' 5CM D 5 P DT D 6 1555 1555 1.65 LINK O3' DT F 4 P 5CM F 5 1555 1555 1.57 LINK O3' 5CM F 5 P DT F 6 1555 1555 1.61 LINK SG CYS A1268 ZN ZN A1401 1555 1555 2.00 LINK NE2 HIS A1286 ZN ZN A1401 1555 1555 2.04 LINK NE2 HIS A1290 ZN ZN A1401 1555 1555 1.85 LINK SG CYS A1298 ZN ZN A1402 1555 1555 2.26 LINK SG CYS A1303 ZN ZN A1402 1555 1555 2.22 LINK NE2 HIS A1316 ZN ZN A1402 1555 1555 2.15 LINK NE2 HIS A1320 ZN ZN A1402 1555 1555 2.02 LINK NE2 HIS A1346 ZN ZN A1403 1555 1555 1.98 LINK ND1 HIS A1352 ZN ZN A1403 1555 1555 2.34 LINK SG CYS B1268 ZN ZN B1401 1555 1555 2.23 LINK NE2 HIS B1286 ZN ZN B1401 1555 1555 2.00 LINK NE2 HIS B1290 ZN ZN B1401 1555 1555 1.91 LINK SG CYS B1298 ZN ZN B1402 1555 1555 2.25 LINK SG CYS B1303 ZN ZN B1402 1555 1555 2.21 LINK NE2 HIS B1316 ZN ZN B1402 1555 1555 2.11 LINK NE2 HIS B1320 ZN ZN B1402 1555 1555 2.06 LINK NE2 HIS B1346 ZN ZN B1403 1555 1555 2.01 LINK ND1 HIS B1352 ZN ZN B1403 1555 1555 2.23 SITE 1 AC1 4 CYS A1268 CYS A1273 HIS A1286 HIS A1290 SITE 1 AC2 4 CYS A1298 CYS A1303 HIS A1316 HIS A1320 SITE 1 AC3 4 CYS A1328 CYS A1333 HIS A1346 HIS A1352 SITE 1 AC4 4 CYS B1268 CYS B1273 HIS B1286 HIS B1290 SITE 1 AC5 4 CYS B1298 CYS B1303 HIS B1316 HIS B1320 SITE 1 AC6 4 CYS B1328 CYS B1333 HIS B1346 HIS B1352 SITE 1 AC7 20 ARG B1294 PHE B1307 SER B1312 GLU B1315 SITE 2 AC7 20 HIS B1316 PHE B1339 HOH B1511 HOH B1525 SITE 3 AC7 20 HOH B1527 DA E 7 DG E 8 DA E 9 SITE 4 AC7 20 DG E 10 DC F 3 DT F 6 HOH F 104 SITE 5 AC7 20 HOH F 107 HOH F 110 HOH F 117 HOH F 119 SITE 1 AC8 23 TYR B1282 VAL B1289 ARG B1294 PHE B1307 SITE 2 AC8 23 TRP B1309 TRP B1311 SER B1312 GLU B1315 SITE 3 AC8 23 HOH B1516 HOH B1527 DC E 6 DA E 7 SITE 4 AC8 23 DG E 8 DA E 9 DT F 4 DG F 7 SITE 5 AC8 23 HOH F 101 HOH F 106 HOH F 107 HOH F 110 SITE 6 AC8 23 HOH F 114 HOH F 117 HOH F 119 CRYST1 88.516 88.516 72.330 90.00 90.00 90.00 P 43 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 0.011297 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011297 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013826 0.00000