HEADER DNA BINDING PROTEIN/DNA 17-MAR-19 6JNL TITLE REF6 ZNF2-4-NAC004 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE REF6; COMPND 3 CHAIN: A; 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*CP*TP*GP*TP*TP*TP*TP*G)-3'); COMPND 10 CHAIN: D; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*A)-3'); COMPND 14 CHAIN: C; COMPND 15 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 6JNL 1 LINK REVDAT 2 15-MAY-19 6JNL 1 JRNL REVDAT 1 27-MAR-19 6JNL 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. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 15643 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 810 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1131 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.3530 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.3590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 739 REMARK 3 NUCLEIC ACID ATOMS : 465 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 24 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 65.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.53000 REMARK 3 B22 (A**2) : 0.53000 REMARK 3 B33 (A**2) : -1.06000 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): 0.155 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.155 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.140 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.888 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1312 ; 0.015 ; 0.016 REMARK 3 BOND LENGTHS OTHERS (A): 991 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1863 ; 1.963 ; 1.576 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2298 ; 1.468 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 88 ; 7.388 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 38 ;35.889 ;20.526 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 132 ;19.334 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;24.087 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 171 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1132 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 323 ; 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): 355 ; 5.633 ; 6.716 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 354 ; 5.632 ; 6.711 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 442 ; 7.172 ;10.038 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 443 ; 7.168 ;10.045 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 957 ; 6.142 ; 6.446 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 957 ; 6.122 ; 6.447 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1422 ; 7.871 ; 9.559 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1716 ; 9.529 ;56.078 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1717 ; 9.536 ;56.078 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 6JNL 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_1300011431. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : 18924 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 17.70 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 52.1600 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) : 0.59000 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: 4R2S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 3,350, 0.2 M NH4F, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 36.30150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 44.58000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.58000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.45225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.58000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 44.58000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 18.15075 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.58000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.58000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 54.45225 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 44.58000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.58000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 18.15075 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 36.30150 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 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 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 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 O3' DA C 11 P DA C 101 1.62 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 DT D 2 O5' - C5' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 DA C 9 O5' - P - OP2 ANGL. DEV. = -6.0 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 LYS A1271 -125.90 35.91 REMARK 500 CYS A1273 -81.04 -96.87 REMARK 500 ASP A1332 -1.08 73.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 DA C 101 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 CYS A1273 SG 119.2 REMARK 620 3 HIS A1286 NE2 114.4 108.1 REMARK 620 4 HIS A1290 NE2 93.2 128.3 90.5 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 CYS A1298 SG REMARK 620 2 CYS A1303 SG 111.8 REMARK 620 3 HIS A1316 NE2 102.0 118.4 REMARK 620 4 HIS A1320 NE2 111.4 103.9 109.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1298 O REMARK 620 2 TRP A1300 O 98.2 REMARK 620 3 CYS A1303 O 97.2 94.7 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 A1328 SG REMARK 620 2 CYS A1333 SG 107.2 REMARK 620 3 HIS A1346 NE2 106.7 106.2 REMARK 620 4 HIS A1352 ND1 105.3 112.7 118.1 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 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 MG A 1404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DA C 101 DBREF 6JNL A 1260 1360 UNP Q9STM3 REF6_ARATH 1260 1360 DBREF 6JNL D 1 12 PDB 6JNL 6JNL 1 12 DBREF 6JNL C 1 11 PDB 6JNL 6JNL 1 11 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 DC DT DG DT DT DT DT DG SEQRES 1 C 11 DC DA DA DA DA DC DA DG DA DG DA HET ZN A1401 1 HET ZN A1402 1 HET ZN A1403 1 HET MG A1404 1 HET GOL D 101 6 HET DA C 101 21 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM DA 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 ZN 3(ZN 2+) FORMUL 7 MG MG 2+ FORMUL 8 GOL C3 H8 O3 FORMUL 9 DA C10 H14 N5 O6 P FORMUL 10 HOH *24(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 SHEET 1 AA1 2 ASN A1266 ILE A1267 0 SHEET 2 AA1 2 ASN A1276 PHE A1277 -1 O PHE A1277 N ASN A1266 SHEET 1 AA2 2 LEU A1296 LYS A1297 0 SHEET 2 AA2 2 THR A1306 PHE A1307 -1 O PHE A1307 N LEU A1296 SHEET 1 AA3 2 TYR A1326 VAL A1327 0 SHEET 2 AA3 2 THR A1336 PHE A1337 -1 O PHE A1337 N TYR A1326 LINK SG CYS A1268 ZN ZN A1401 1555 1555 2.38 LINK SG CYS A1273 ZN ZN A1401 1555 1555 2.37 LINK NE2 HIS A1286 ZN ZN A1401 1555 1555 2.27 LINK NE2 HIS A1290 ZN ZN A1401 1555 1555 2.05 LINK SG CYS A1298 ZN ZN A1403 1555 1555 2.21 LINK O CYS A1298 MG MG A1404 1555 1555 2.57 LINK O TRP A1300 MG MG A1404 1555 1555 2.44 LINK SG CYS A1303 ZN ZN A1403 1555 1555 2.28 LINK O CYS A1303 MG MG A1404 1555 1555 2.84 LINK NE2 HIS A1316 ZN ZN A1403 1555 1555 2.04 LINK NE2 HIS A1320 ZN ZN A1403 1555 1555 2.05 LINK SG CYS A1328 ZN ZN A1402 1555 1555 2.28 LINK SG CYS A1333 ZN ZN A1402 1555 1555 2.32 LINK NE2 HIS A1346 ZN ZN A1402 1555 1555 2.17 LINK ND1 HIS A1352 ZN ZN A1402 1555 1555 2.19 SITE 1 AC1 4 CYS A1268 CYS A1273 HIS A1286 HIS A1290 SITE 1 AC2 4 CYS A1328 CYS A1333 HIS A1346 HIS A1352 SITE 1 AC3 4 CYS A1298 CYS A1303 HIS A1316 HIS A1320 SITE 1 AC4 3 CYS A1298 TRP A1300 CYS A1303 SITE 1 AC5 5 DG C 10 DA C 11 DT D 4 DC D 5 SITE 2 AC5 5 HOH D 201 SITE 1 AC6 6 PRO A1299 TRP A1300 LYS A1301 DA C 11 SITE 2 AC6 6 DT D 1 DT D 2 CRYST1 89.160 89.160 72.603 90.00 90.00 90.00 P 43 21 2 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 0.011216 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011216 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013774 0.00000