HEADER GENE REGULATION 15-OCT-17 5YKO TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA JMJ14 CATALYTIC DOMAIN IN TITLE 2 COMPLEX WITH NOG AND H3K4ME3 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE LYSINE-SPECIFIC DEMETHYLASE JMJ14; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: JUMONJI DOMAIN-CONTAINING PROTEIN 14,JUMONJI DOMAIN- COMPND 5 CONTAINING PROTEIN 4,LYSINE-SPECIFIC HISTONE DEMETHYLASE JMJ14, COMPND 6 PROTEIN JUMONJI 14; COMPND 7 EC: 1.14.11.-; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: H3(1-10)K4ME3 PEPTIDE; COMPND 12 CHAIN: P; COMPND 13 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: JMJ14, JMJ4, PKDM7B, AT4G20400, F9F13.50; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-SUMO; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 14 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 15 ORGANISM_TAXID: 3702 KEYWDS JMJ14, JUMONJI DOMAIN, C5HC2 ZINC FINGER, H3K4ME3 DEMETHYLASE, GENE KEYWDS 2 REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR Z.YANG,J.DU REVDAT 3 22-NOV-23 5YKO 1 REMARK REVDAT 2 28-FEB-18 5YKO 1 JRNL REVDAT 1 27-DEC-17 5YKO 0 JRNL AUTH Z.YANG,Q.QIU,W.CHEN,B.JIA,X.CHEN,H.HU,K.HE,X.DENG,S.LI, JRNL AUTH 2 W.A.TAO,X.CAO,J.DU JRNL TITL STRUCTURE OF THE ARABIDOPSIS JMJ14-H3K4ME3 COMPLEX PROVIDES JRNL TITL 2 INSIGHT INTO THE SUBSTRATE SPECIFICITY OF KDM5 SUBFAMILY JRNL TITL 3 HISTONE DEMETHYLASES. JRNL REF PLANT CELL V. 30 167 2018 JRNL REFN ESSN 1532-298X JRNL PMID 29233856 JRNL DOI 10.1105/TPC.17.00666 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 17179 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 864 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 39.3416 - 5.2663 0.99 2843 159 0.1928 0.2206 REMARK 3 2 5.2663 - 4.1815 1.00 2759 126 0.1678 0.1883 REMARK 3 3 4.1815 - 3.6534 1.00 2731 132 0.1891 0.2330 REMARK 3 4 3.6534 - 3.3195 1.00 2684 152 0.2208 0.2799 REMARK 3 5 3.3195 - 3.0817 0.99 2661 140 0.2471 0.3036 REMARK 3 6 3.0817 - 2.9001 0.98 2637 155 0.2705 0.3010 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 4138 REMARK 3 ANGLE : 0.939 5600 REMARK 3 CHIRALITY : 0.049 578 REMARK 3 PLANARITY : 0.004 722 REMARK 3 DIHEDRAL : 14.986 1531 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 42 THROUGH 245 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.9924 -21.4412 -13.3707 REMARK 3 T TENSOR REMARK 3 T11: 0.2505 T22: 0.2057 REMARK 3 T33: 0.3387 T12: 0.0752 REMARK 3 T13: 0.0042 T23: -0.0471 REMARK 3 L TENSOR REMARK 3 L11: 2.8181 L22: 2.1838 REMARK 3 L33: 2.1558 L12: 1.1258 REMARK 3 L13: -0.4618 L23: -0.0608 REMARK 3 S TENSOR REMARK 3 S11: -0.1128 S12: 0.1611 S13: -0.0933 REMARK 3 S21: -0.1441 S22: 0.0200 S23: -0.0350 REMARK 3 S31: 0.1448 S32: -0.1869 S33: 0.1002 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 246 THROUGH 478 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.1114 -5.8300 -12.1966 REMARK 3 T TENSOR REMARK 3 T11: 0.2509 T22: 0.2407 REMARK 3 T33: 0.2600 T12: 0.0178 REMARK 3 T13: 0.0122 T23: 0.0055 REMARK 3 L TENSOR REMARK 3 L11: 1.6463 L22: 2.0402 REMARK 3 L33: 0.7543 L12: 0.2976 REMARK 3 L13: 0.0010 L23: 0.0233 REMARK 3 S TENSOR REMARK 3 S11: -0.0699 S12: 0.0960 S13: 0.1474 REMARK 3 S21: -0.2497 S22: -0.0377 S23: -0.0001 REMARK 3 S31: -0.1347 S32: -0.0637 S33: 0.1165 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 479 THROUGH 588 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.3937 21.6898 -10.2328 REMARK 3 T TENSOR REMARK 3 T11: 0.4133 T22: 0.3019 REMARK 3 T33: 0.3482 T12: -0.0169 REMARK 3 T13: 0.0023 T23: 0.0442 REMARK 3 L TENSOR REMARK 3 L11: 6.3579 L22: 3.2524 REMARK 3 L33: 2.3274 L12: -1.6056 REMARK 3 L13: -0.3142 L23: 0.6379 REMARK 3 S TENSOR REMARK 3 S11: 0.1459 S12: -0.0412 S13: 0.1849 REMARK 3 S21: 0.0135 S22: -0.2113 S23: 0.2715 REMARK 3 S31: -0.3244 S32: -0.3781 S33: 0.0640 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'P' AND (RESID 1 THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.7535 -3.2110 -8.2088 REMARK 3 T TENSOR REMARK 3 T11: 1.0191 T22: 0.8789 REMARK 3 T33: 1.4309 T12: 0.1435 REMARK 3 T13: 0.0944 T23: -0.3300 REMARK 3 L TENSOR REMARK 3 L11: 6.0401 L22: 8.0646 REMARK 3 L33: 7.3795 L12: 0.4850 REMARK 3 L13: -0.7937 L23: 3.7893 REMARK 3 S TENSOR REMARK 3 S11: -0.0097 S12: 0.5242 S13: -0.3411 REMARK 3 S21: -0.7017 S22: -0.1400 S23: -0.2459 REMARK 3 S31: 0.6271 S32: -0.6964 S33: 0.2328 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5YKO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1300005450. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17462 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.16100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.77600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5YKN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NA2SO4, 20% PEG 3350, 0.1M BIS REMARK 280 -TRIS PROPANE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 34.31950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.70250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.05650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.70250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.31950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.05650 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P 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 SER A 34 REMARK 465 SER A 35 REMARK 465 SER A 36 REMARK 465 PRO A 37 REMARK 465 LYS A 38 REMARK 465 ILE A 39 REMARK 465 THR A 40 REMARK 465 ALA A 41 REMARK 465 GLU A 125 REMARK 465 PRO A 126 REMARK 465 ILE A 127 REMARK 465 LYS A 128 REMARK 465 LYS A 129 REMARK 465 SER A 130 REMARK 465 THR A 131 REMARK 465 LYS A 132 REMARK 465 THR A 133 REMARK 465 LYS A 134 REMARK 465 LYS A 135 REMARK 465 ARG A 136 REMARK 465 LYS A 137 REMARK 465 ARG A 138 REMARK 465 ARG A 139 REMARK 465 ARG A 140 REMARK 465 ILE A 141 REMARK 465 SER A 142 REMARK 465 LYS A 143 REMARK 465 ILE A 144 REMARK 465 GLY A 145 REMARK 465 TYR A 146 REMARK 465 THR A 147 REMARK 465 ARG A 148 REMARK 465 ARG A 149 REMARK 465 LYS A 150 REMARK 465 ARG A 151 REMARK 465 ASP A 152 REMARK 465 SER A 153 REMARK 465 GLY A 154 REMARK 465 CYS A 155 REMARK 465 ASP A 156 REMARK 465 THR A 157 REMARK 465 ALA A 158 REMARK 465 SER A 159 REMARK 465 SER A 160 REMARK 465 GLY A 161 REMARK 465 SER A 162 REMARK 465 SER A 163 REMARK 465 ASP A 164 REMARK 465 SER A 165 REMARK 465 GLU A 166 REMARK 465 GLY A 167 REMARK 465 LYS A 168 REMARK 465 SER A 196 REMARK 465 GLU A 197 REMARK 465 ASP A 198 REMARK 465 HIS A 199 REMARK 465 PRO A 200 REMARK 465 GLY A 201 REMARK 465 SER A 202 REMARK 465 LYS A 203 REMARK 465 ALA A 204 REMARK 465 SER A 205 REMARK 465 GLU A 206 REMARK 465 ASN A 207 REMARK 465 LYS A 208 REMARK 465 LYS A 209 REMARK 465 PHE A 210 REMARK 465 LYS A 211 REMARK 465 CYS A 589 REMARK 465 ARG A 590 REMARK 465 ASP A 591 REMARK 465 GLN A 592 REMARK 465 TYR A 593 REMARK 465 PRO A 594 REMARK 465 SER A 595 REMARK 465 GLN A 596 REMARK 465 HIS A 597 REMARK 465 ARG P 8 REMARK 465 LYS P 9 REMARK 465 SER P 10 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 LYS A 104 CG CD CE NZ 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 PRO A 257 150.17 -46.32 REMARK 500 SER A 475 -179.98 -176.09 REMARK 500 GLU A 476 -7.46 -56.13 REMARK 500 ASP A 500 -55.70 72.19 REMARK 500 LYS A 514 -57.12 76.36 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 NI A 800 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 309 NE2 REMARK 620 2 GLU A 311 OE1 120.4 REMARK 620 3 HIS A 397 NE2 98.0 95.1 REMARK 620 4 OGA A 803 O2' 85.8 139.0 113.1 REMARK 620 5 OGA A 803 O1 154.1 78.9 97.1 68.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 519 SG REMARK 620 2 CYS A 522 SG 140.5 REMARK 620 3 CYS A 542 SG 110.9 107.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 533 SG REMARK 620 2 CYS A 535 SG 89.3 REMARK 620 3 CYS A 550 SG 141.9 96.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OGA A 803 DBREF 5YKO A 35 597 UNP Q8GUI6 JMJ14_ARATH 35 597 DBREF 5YKO P 1 10 UNP P59226 H32_ARATH 2 11 SEQADV 5YKO SER A 34 UNP Q8GUI6 EXPRESSION TAG SEQADV 5YKO ALA A 180 UNP Q8GUI6 GLU 180 ENGINEERED MUTATION SEQADV 5YKO ALA A 181 UNP Q8GUI6 GLU 181 ENGINEERED MUTATION SEQRES 1 A 564 SER SER SER PRO LYS ILE THR ALA ARG TRP ASN PRO SER SEQRES 2 A 564 GLU ALA CYS ARG PRO LEU VAL ASP ASP ALA PRO ILE PHE SEQRES 3 A 564 TYR PRO THR ASN GLU ASP PHE ASP ASP PRO LEU GLY TYR SEQRES 4 A 564 ILE GLU LYS LEU ARG SER LYS ALA GLU SER TYR GLY ILE SEQRES 5 A 564 CYS ARG ILE VAL PRO PRO VAL ALA TRP ARG PRO PRO CYS SEQRES 6 A 564 PRO LEU LYS GLU LYS LYS ILE TRP GLU ASN SER LYS PHE SEQRES 7 A 564 PRO THR ARG ILE GLN PHE ILE ASP LEU LEU GLN ASN ARG SEQRES 8 A 564 GLU PRO ILE LYS LYS SER THR LYS THR LYS LYS ARG LYS SEQRES 9 A 564 ARG ARG ARG ILE SER LYS ILE GLY TYR THR ARG ARG LYS SEQRES 10 A 564 ARG ASP SER GLY CYS ASP THR ALA SER SER GLY SER SER SEQRES 11 A 564 ASP SER GLU GLY LYS PHE GLY PHE GLN THR GLY PRO ASP SEQRES 12 A 564 PHE THR LEU ALA ALA PHE GLN LYS TYR ASP GLU TYR PHE SEQRES 13 A 564 LYS GLU CYS TYR PHE GLN SER GLU ASP HIS PRO GLY SER SEQRES 14 A 564 LYS ALA SER GLU ASN LYS LYS PHE LYS PRO LYS VAL LYS SEQRES 15 A 564 ASP LEU GLU GLY GLU TYR TRP ARG ILE VAL GLU GLN ALA SEQRES 16 A 564 THR ASP GLU VAL GLU VAL TYR TYR GLY ALA ASP LEU GLU SEQRES 17 A 564 THR LYS LYS PHE GLY SER GLY PHE PRO LYS TYR LYS PRO SEQRES 18 A 564 GLY TYR PRO ILE SER GLU ALA ASP GLN TYR SER GLN CYS SEQRES 19 A 564 GLY TRP ASN LEU ASN ASN LEU SER ARG LEU PRO GLY SER SEQRES 20 A 564 VAL LEU ALA PHE GLU SER CYS ASP ILE SER GLY VAL ILE SEQRES 21 A 564 VAL PRO TRP LEU TYR VAL GLY MET CYS PHE SER THR PHE SEQRES 22 A 564 CYS TRP HIS VAL GLU ASP HIS HIS LEU TYR SER MET ASN SEQRES 23 A 564 TYR LEU HIS THR GLY ASP PRO LYS VAL TRP TYR GLY ILE SEQRES 24 A 564 PRO GLY ASN HIS ALA GLU SER PHE GLU ASN VAL MET LYS SEQRES 25 A 564 LYS ARG LEU PRO ASP LEU PHE GLU GLU GLN PRO ASP LEU SEQRES 26 A 564 LEU HIS GLN LEU VAL THR GLN LEU SER PRO ARG ILE LEU SEQRES 27 A 564 LYS GLU GLU GLY VAL PRO VAL TYR ARG ALA VAL GLN ARG SEQRES 28 A 564 SER GLY GLU PHE ILE LEU THR PHE PRO LYS ALA TYR HIS SEQRES 29 A 564 SER GLY PHE ASN CYS GLY PHE ASN CYS ALA GLU ALA VAL SEQRES 30 A 564 ASN VAL ALA PRO VAL ASP TRP LEU VAL HIS GLY GLN ASN SEQRES 31 A 564 ALA VAL GLU GLY TYR SER LYS GLN ARG ARG LYS SER SER SEQRES 32 A 564 LEU SER HIS ASP LYS LEU LEU LEU GLY ALA ALA MET GLU SEQRES 33 A 564 ALA THR TYR CYS LEU TRP GLU LEU SER LEU SER LYS LYS SEQRES 34 A 564 LYS THR PRO VAL ILE ALA ARG TRP LYS ARG VAL CYS SER SEQRES 35 A 564 GLU ASP GLY LEU LEU THR LYS ALA VAL LYS LYS ARG VAL SEQRES 36 A 564 GLN MET GLU GLU GLU ARG LEU ASN HIS LEU GLN ASP GLY SEQRES 37 A 564 PHE SER LEU ARG LYS MET GLU GLY ASP PHE ASP ASN LYS SEQRES 38 A 564 ARG GLU ARG GLU CYS PHE LEU CYS PHE TYR ASP LEU HIS SEQRES 39 A 564 MET SER ALA SER SER CYS LYS CYS SER PRO ASN ARG PHE SEQRES 40 A 564 ALA CYS LEU ILE HIS ALA LYS ASP LEU CYS SER CYS GLU SEQRES 41 A 564 SER LYS ASP ARG TYR ILE LEU ILE ARG HIS THR LEU ASP SEQRES 42 A 564 GLU LEU TRP ALA LEU VAL ARG ALA LEU GLU GLY ASP LEU SEQRES 43 A 564 ASP ALA ILE ASP LEU TRP ALA SER LYS CYS ARG ASP GLN SEQRES 44 A 564 TYR PRO SER GLN HIS SEQRES 1 P 10 ALA ARG THR M3L GLN THR ALA ARG LYS SER MODRES 5YKO M3L P 4 LYS MODIFIED RESIDUE HET M3L P 4 12 HET NI A 800 1 HET ZN A 801 1 HET ZN A 802 1 HET OGA A 803 10 HETNAM M3L N-TRIMETHYLLYSINE HETNAM NI NICKEL (II) ION HETNAM ZN ZINC ION HETNAM OGA N-OXALYLGLYCINE FORMUL 2 M3L C9 H21 N2 O2 1+ FORMUL 3 NI NI 2+ FORMUL 4 ZN 2(ZN 2+) FORMUL 6 OGA C4 H5 N O5 HELIX 1 AA1 ASN A 44 ALA A 48 5 5 HELIX 2 AA2 THR A 62 ASP A 68 1 7 HELIX 3 AA3 ASP A 68 GLU A 81 1 14 HELIX 4 AA4 CYS A 98 LYS A 101 5 4 HELIX 5 AA5 GLU A 102 GLU A 107 1 6 HELIX 6 AA6 ASP A 119 LEU A 121 5 3 HELIX 7 AA7 THR A 178 GLN A 195 1 18 HELIX 8 AA8 LYS A 213 GLN A 227 1 15 HELIX 9 AA9 THR A 242 GLY A 246 1 5 HELIX 10 AB1 SER A 259 CYS A 267 1 9 HELIX 11 AB2 ASN A 270 SER A 275 1 6 HELIX 12 AB3 SER A 280 GLU A 285 5 6 HELIX 13 AB4 GLU A 311 LEU A 315 5 5 HELIX 14 AB5 PRO A 333 ASN A 335 5 3 HELIX 15 AB6 HIS A 336 LEU A 348 1 13 HELIX 16 AB7 LEU A 348 GLN A 355 1 8 HELIX 17 AB8 ASP A 357 LEU A 362 5 6 HELIX 18 AB9 SER A 367 GLU A 374 1 8 HELIX 19 AC1 PRO A 414 ASP A 416 5 3 HELIX 20 AC2 TRP A 417 ARG A 432 1 16 HELIX 21 AC3 SER A 438 LEU A 459 1 22 HELIX 22 AC4 THR A 464 VAL A 473 1 10 HELIX 23 AC5 GLY A 478 HIS A 497 1 20 HELIX 24 AC6 GLU A 508 ASP A 512 5 5 HELIX 25 AC7 GLU A 553 LYS A 555 5 3 HELIX 26 AC8 THR A 564 GLU A 576 1 13 HELIX 27 AC9 ASP A 578 ALA A 586 1 9 SHEET 1 AA1 5 ASP A 54 ASP A 55 0 SHEET 2 AA1 5 TYR A 379 GLN A 383 1 O ARG A 380 N ASP A 54 SHEET 3 AA1 5 LYS A 327 GLY A 331 -1 N TRP A 329 O ALA A 381 SHEET 4 AA1 5 HIS A 397 ASN A 401 -1 O SER A 398 N TYR A 330 SHEET 5 AA1 5 THR A 305 HIS A 309 -1 N PHE A 306 O GLY A 399 SHEET 1 AA2 9 ILE A 58 PHE A 59 0 SHEET 2 AA2 9 ILE A 85 ILE A 88 1 O ARG A 87 N PHE A 59 SHEET 3 AA2 9 PHE A 388 THR A 391 -1 O PHE A 388 N ILE A 88 SHEET 4 AA2 9 TYR A 316 GLY A 324 -1 N SER A 317 O THR A 391 SHEET 5 AA2 9 ASN A 405 VAL A 412 -1 O VAL A 410 N MET A 318 SHEET 6 AA2 9 TRP A 296 GLY A 300 -1 N TRP A 296 O ALA A 409 SHEET 7 AA2 9 GLU A 233 GLU A 241 -1 N LEU A 240 O LEU A 297 SHEET 8 AA2 9 ARG A 114 PHE A 117 -1 N GLN A 116 O VAL A 234 SHEET 9 AA2 9 GLN A 172 THR A 173 -1 O GLN A 172 N ILE A 115 SHEET 1 AA3 3 SER A 503 LYS A 506 0 SHEET 2 AA3 3 ARG A 557 ILE A 561 1 O ILE A 559 N ARG A 505 SHEET 3 AA3 3 SER A 529 CYS A 533 -1 N SER A 532 O TYR A 558 LINK C THR P 3 N M3L P 4 1555 1555 1.33 LINK C M3L P 4 N GLN P 5 1555 1555 1.32 LINK NE2 HIS A 309 NI NI A 800 1555 1555 2.07 LINK OE1 GLU A 311 NI NI A 800 1555 1555 2.01 LINK NE2 HIS A 397 NI NI A 800 1555 1555 2.29 LINK SG CYS A 519 ZN ZN A 801 1555 1555 2.34 LINK SG CYS A 522 ZN ZN A 801 1555 1555 2.40 LINK SG CYS A 533 ZN ZN A 802 1555 1555 2.53 LINK SG CYS A 535 ZN ZN A 802 1555 1555 2.37 LINK SG CYS A 542 ZN ZN A 801 1555 1555 2.36 LINK SG CYS A 550 ZN ZN A 802 1555 1555 2.49 LINK NI NI A 800 O2' OGA A 803 1555 1555 2.24 LINK NI NI A 800 O1 OGA A 803 1555 1555 2.46 SITE 1 AC1 4 HIS A 309 GLU A 311 HIS A 397 OGA A 803 SITE 1 AC2 4 CYS A 519 CYS A 522 CYS A 542 HIS A 545 SITE 1 AC3 4 CYS A 533 CYS A 535 CYS A 550 CYS A 552 SITE 1 AC4 13 TYR A 236 TYR A 298 PHE A 306 HIS A 309 SITE 2 AC4 13 GLU A 311 SER A 317 ASN A 319 LYS A 327 SITE 3 AC4 13 TRP A 329 HIS A 397 ALA A 409 NI A 800 SITE 4 AC4 13 M3L P 4 CRYST1 68.639 100.113 109.405 90.00 90.00 90.00 P 21 21 21 4 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 0.014569 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009989 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009140 0.00000