HEADER GENE REGULATION 02-NOV-18 6IP4 TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA JMJ13 CATALYTIC DOMAIN IN TITLE 2 COMPLEX WITH NOG AND AN H3K27ME3 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARABIDOPSIS JMJ13; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 90-578; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HISTONE H3.2; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 25-36; COMPND 10 SYNONYM: HISTONE H3.1; COMPND 11 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSUMO; 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 HISTONE MODIFICATION, FLOWERING, EPIGENETICS, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR H.HU,J.DU REVDAT 2 22-NOV-23 6IP4 1 LINK REVDAT 1 10-APR-19 6IP4 0 JRNL AUTH S.ZHENG,H.HU,H.REN,Z.YANG,Q.QIU,W.QI,X.LIU,X.CHEN,X.CUI, JRNL AUTH 2 S.LI,B.ZHOU,D.SUN,X.CAO,J.DU JRNL TITL THE ARABIDOPSIS H3K27ME3 DEMETHYLASE JUMONJI 13 IS A JRNL TITL 2 TEMPERATURE AND PHOTOPERIOD DEPENDENT FLOWERING REPRESSOR. JRNL REF NAT COMMUN V. 10 1303 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 30899015 JRNL DOI 10.1038/S41467-019-09310-X REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 33189 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1681 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 49.3757 - 5.9455 0.88 2709 145 0.2228 0.2413 REMARK 3 2 5.9455 - 4.7203 0.91 2627 140 0.1970 0.2197 REMARK 3 3 4.7203 - 4.1239 0.92 2610 151 0.1699 0.2136 REMARK 3 4 4.1239 - 3.7470 0.93 2610 160 0.1887 0.2127 REMARK 3 5 3.7470 - 3.4785 0.94 2611 141 0.2114 0.3024 REMARK 3 6 3.4785 - 3.2735 0.94 2617 139 0.2305 0.2960 REMARK 3 7 3.2735 - 3.1096 0.94 2632 125 0.2388 0.2825 REMARK 3 8 3.1096 - 2.9742 0.94 2613 133 0.2467 0.2691 REMARK 3 9 2.9742 - 2.8598 0.95 2616 140 0.2527 0.2883 REMARK 3 10 2.8598 - 2.7611 0.95 2636 134 0.2752 0.3203 REMARK 3 11 2.7611 - 2.6748 0.95 2613 136 0.2834 0.2985 REMARK 3 12 2.6748 - 2.5983 0.95 2614 137 0.2796 0.3015 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.500 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 : 0.010 3925 REMARK 3 ANGLE : 1.302 5323 REMARK 3 CHIRALITY : 0.083 573 REMARK 3 PLANARITY : 0.009 672 REMARK 3 DIHEDRAL : 25.571 1422 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 93 THROUGH 186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.6267 45.0074 140.6084 REMARK 3 T TENSOR REMARK 3 T11: 0.7517 T22: 0.4650 REMARK 3 T33: 0.7389 T12: 0.4094 REMARK 3 T13: 0.0031 T23: 0.0019 REMARK 3 L TENSOR REMARK 3 L11: 2.7649 L22: 3.9448 REMARK 3 L33: 3.8760 L12: -0.1840 REMARK 3 L13: -0.4220 L23: -0.0468 REMARK 3 S TENSOR REMARK 3 S11: -0.2222 S12: -0.3662 S13: 0.0676 REMARK 3 S21: 0.3149 S22: 0.2098 S23: -0.2132 REMARK 3 S31: 0.1713 S32: 0.2995 S33: -0.0086 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 187 THROUGH 333 ) REMARK 3 ORIGIN FOR THE GROUP (A): 44.0859 44.9932 142.2435 REMARK 3 T TENSOR REMARK 3 T11: 0.7618 T22: 0.6095 REMARK 3 T33: 0.7939 T12: 0.3938 REMARK 3 T13: -0.0523 T23: -0.0491 REMARK 3 L TENSOR REMARK 3 L11: 1.9207 L22: 4.5453 REMARK 3 L33: 2.1900 L12: -1.3661 REMARK 3 L13: -0.3249 L23: 0.7841 REMARK 3 S TENSOR REMARK 3 S11: -0.4377 S12: -0.5633 S13: 0.1065 REMARK 3 S21: 0.5637 S22: 0.4297 S23: -0.4094 REMARK 3 S31: 0.1111 S32: 0.1149 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 334 THROUGH 358 ) REMARK 3 ORIGIN FOR THE GROUP (A): 64.9583 49.7549 139.7602 REMARK 3 T TENSOR REMARK 3 T11: 1.2891 T22: 1.3490 REMARK 3 T33: 1.9854 T12: 0.3888 REMARK 3 T13: -0.1006 T23: -0.2082 REMARK 3 L TENSOR REMARK 3 L11: 5.6292 L22: 2.0639 REMARK 3 L33: 8.9404 L12: 0.7911 REMARK 3 L13: -6.9266 L23: -0.6444 REMARK 3 S TENSOR REMARK 3 S11: 1.1792 S12: -0.9915 S13: 0.9276 REMARK 3 S21: -0.2894 S22: -0.4121 S23: -2.1896 REMARK 3 S31: -0.5661 S32: 2.1187 S33: -0.5782 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 359 THROUGH 421 ) REMARK 3 ORIGIN FOR THE GROUP (A): 48.5343 43.2432 132.9766 REMARK 3 T TENSOR REMARK 3 T11: 0.7379 T22: 0.4286 REMARK 3 T33: 0.8706 T12: 0.2950 REMARK 3 T13: 0.0202 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 2.7655 L22: 3.7376 REMARK 3 L33: 2.5401 L12: -1.9387 REMARK 3 L13: 0.1941 L23: 0.2358 REMARK 3 S TENSOR REMARK 3 S11: -0.0318 S12: -0.0225 S13: 0.3592 REMARK 3 S21: -0.2547 S22: 0.1048 S23: -0.6922 REMARK 3 S31: -0.0799 S32: 0.1988 S33: -0.0790 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 422 THROUGH 453 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.9908 21.6332 125.7246 REMARK 3 T TENSOR REMARK 3 T11: 0.8864 T22: 0.4168 REMARK 3 T33: 0.9545 T12: 0.2154 REMARK 3 T13: 0.1296 T23: -0.0612 REMARK 3 L TENSOR REMARK 3 L11: 1.9249 L22: 5.9618 REMARK 3 L33: 2.1617 L12: -1.9063 REMARK 3 L13: -1.1138 L23: -1.1025 REMARK 3 S TENSOR REMARK 3 S11: -0.1403 S12: 0.2573 S13: -0.4487 REMARK 3 S21: 0.0137 S22: 0.1120 S23: 0.4280 REMARK 3 S31: 0.8150 S32: -0.0110 S33: 0.0501 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 454 THROUGH 563 ) REMARK 3 ORIGIN FOR THE GROUP (A): 61.1446 14.1821 127.0798 REMARK 3 T TENSOR REMARK 3 T11: 1.0098 T22: 0.2931 REMARK 3 T33: 0.8614 T12: 0.1696 REMARK 3 T13: 0.1521 T23: -0.0087 REMARK 3 L TENSOR REMARK 3 L11: 3.5871 L22: 2.3675 REMARK 3 L33: 2.9646 L12: -0.7827 REMARK 3 L13: 0.9716 L23: 0.1453 REMARK 3 S TENSOR REMARK 3 S11: -0.4253 S12: -0.0686 S13: -0.1160 REMARK 3 S21: 0.1049 S22: 0.0757 S23: -0.2678 REMARK 3 S31: -0.2389 S32: 0.0150 S33: 0.3413 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SF FILE CONTAINS FRIEDEL PAIRS UNDER REMARK 3 I/F_MINUS AND I/F_PLUS COLUMNS. REMARK 4 REMARK 4 6IP4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1300009663. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-17 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) : 0.97776 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 : 33189 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 (%) : 93.2 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.9300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.86800 REMARK 200 R SYM FOR SHELL (I) : 0.86800 REMARK 200 FOR SHELL : 1.970 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: 6IP0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES, PH 6.5, 8% DIOXANE, AND 1.6M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 153.76133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 76.88067 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 153.76133 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 76.88067 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 153.76133 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 76.88067 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 153.76133 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 76.88067 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: 2730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -100.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 S SO4 A 607 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 SER A 89 REMARK 465 GLU A 90 REMARK 465 THR A 91 REMARK 465 ASP A 92 REMARK 465 ASP A 564 REMARK 465 LEU A 565 REMARK 465 ILE A 566 REMARK 465 THR A 567 REMARK 465 THR A 568 REMARK 465 ASP A 569 REMARK 465 GLU A 570 REMARK 465 ASP A 571 REMARK 465 LEU A 572 REMARK 465 TYR A 573 REMARK 465 LYS A 574 REMARK 465 TYR A 575 REMARK 465 PRO A 576 REMARK 465 SER A 577 REMARK 465 SER A 578 REMARK 465 THR B 32 REMARK 465 GLY B 33 REMARK 465 GLY B 34 REMARK 465 VAL B 35 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 PRO B 30 C - N - CD ANGL. DEV. = -15.8 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 GLU A 114 -130.91 50.63 REMARK 500 ARG A 166 111.90 -160.68 REMARK 500 ALA A 168 133.33 -32.66 REMARK 500 CYS A 203 -10.00 68.11 REMARK 500 CYS A 223 19.53 -147.53 REMARK 500 GLU A 295 -168.21 73.15 REMARK 500 LYS A 446 -2.85 80.43 REMARK 500 LEU A 450 -83.95 -117.89 REMARK 500 LEU A 502 -69.89 -105.33 REMARK 500 LYS A 504 13.97 88.37 REMARK 500 TYR A 517 4.66 81.81 REMARK 500 ASN A 545 33.39 -95.16 REMARK 500 ARG B 26 177.83 178.90 REMARK 500 M3L B 27 -157.56 -94.34 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 601 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 293 NE2 REMARK 620 2 GLU A 295 OE2 108.5 REMARK 620 3 HIS A 388 NE2 79.1 113.2 REMARK 620 4 OGA A 604 O1 146.8 104.7 89.4 REMARK 620 5 OGA A 604 O2' 83.9 113.6 133.1 81.6 REMARK 620 6 HOH A 705 O 98.6 58.4 170.3 97.4 55.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 500 SG REMARK 620 2 CYS A 503 SG 94.2 REMARK 620 3 CYS A 522 SG 112.4 103.2 REMARK 620 4 HIS A 525 NE2 104.5 121.8 118.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 603 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 514 SG REMARK 620 2 CYS A 516 SG 109.6 REMARK 620 3 HIS A 519 ND1 102.3 93.5 REMARK 620 4 CYS A 534 SG 105.7 130.7 111.4 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 NI A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OGA A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 609 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 610 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 611 DBREF 6IP4 A 90 578 UNP F4KIX0 F4KIX0_ARATH 90 578 DBREF 6IP4 B 24 35 UNP P59226 H32_ARATH 25 36 SEQADV 6IP4 SER A 89 UNP F4KIX0 EXPRESSION TAG SEQRES 1 A 490 SER GLU THR ASP ASP LEU LYS TRP THR GLU ARG LEU PRO SEQRES 2 A 490 GLU CYS PRO VAL TYR ARG PRO THR LYS GLU GLU PHE GLU SEQRES 3 A 490 ASP PRO LEU THR TYR LEU GLN LYS ILE PHE PRO GLU ALA SEQRES 4 A 490 SER LYS TYR GLY ILE CYS LYS ILE VAL SER PRO LEU THR SEQRES 5 A 490 ALA THR VAL PRO ALA GLY ALA VAL LEU MET LYS GLU LYS SEQRES 6 A 490 SER ASN PHE LYS PHE THR THR ARG VAL GLN PRO LEU ARG SEQRES 7 A 490 LEU ALA GLU TRP ASP SER ASP ASP LYS VAL THR PHE PHE SEQRES 8 A 490 MET SER GLY ARG THR TYR THR PHE ARG ASP TYR GLU LYS SEQRES 9 A 490 MET ALA ASN LYS VAL PHE ALA ARG ARG TYR CYS SER GLY SEQRES 10 A 490 GLY SER LEU PRO ASP SER PHE LEU GLU LYS GLU PHE TRP SEQRES 11 A 490 LYS GLU ILE ALA CYS GLY LYS THR GLU THR VAL GLU TYR SEQRES 12 A 490 ALA CYS ASP VAL ASP GLY SER ALA PHE SER SER ALA PRO SEQRES 13 A 490 GLY ASP PRO LEU GLY SER SER LYS TRP ASN LEU ASN LYS SEQRES 14 A 490 VAL SER ARG LEU PRO LYS SER THR LEU ARG LEU LEU GLU SEQRES 15 A 490 THR SER ILE PRO GLY VAL THR GLU PRO MET LEU TYR ILE SEQRES 16 A 490 GLY MET LEU PHE SER MET PHE ALA TRP HIS VAL GLU ASP SEQRES 17 A 490 HIS TYR LEU TYR SER ILE ASN TYR GLN HIS CYS GLY ALA SEQRES 18 A 490 SER LYS THR TRP TYR GLY ILE PRO GLY SER ALA ALA LEU SEQRES 19 A 490 LYS PHE GLU LYS VAL VAL LYS GLU CYS VAL TYR ASN ASP SEQRES 20 A 490 ASP ILE LEU SER THR ASN GLY GLU ASP GLY ALA PHE ASP SEQRES 21 A 490 VAL LEU LEU GLY LYS THR THR ILE PHE PRO PRO LYS THR SEQRES 22 A 490 LEU LEU ASP HIS ASN VAL PRO VAL TYR LYS ALA VAL GLN SEQRES 23 A 490 LYS PRO GLY GLU PHE VAL VAL THR PHE PRO ARG ALA TYR SEQRES 24 A 490 HIS ALA GLY PHE SER HIS GLY PHE ASN CYS GLY GLU ALA SEQRES 25 A 490 VAL ASN PHE ALA MET GLY ASP TRP PHE PRO PHE GLY ALA SEQRES 26 A 490 ILE ALA SER CYS ARG TYR ALA HIS LEU ASN ARG VAL PRO SEQRES 27 A 490 LEU LEU PRO HIS GLU GLU LEU ILE CYS LYS GLU ALA MET SEQRES 28 A 490 LEU LEU ASN SER SER SER LYS SER GLU ASN LEU ASP LEU SEQRES 29 A 490 THR PRO THR GLU LEU SER GLY GLN ARG SER ILE LYS THR SEQRES 30 A 490 ALA PHE VAL HIS LEU ILE ARG PHE LEU HIS LEU ALA ARG SEQRES 31 A 490 TRP SER LEU MET LYS SER GLY LEU CYS THR GLY LEU VAL SEQRES 32 A 490 SER ASN THR TYR GLY THR ILE VAL CYS SER LEU CYS LYS SEQRES 33 A 490 ARG ASP CYS TYR LEU ALA PHE ILE ASN CYS GLU CYS TYR SEQRES 34 A 490 SER HIS PRO VAL CYS LEU ARG HIS ASP VAL LYS LYS LEU SEQRES 35 A 490 ASP LEU PRO CYS GLY THR THR HIS THR LEU TYR LEU ARG SEQRES 36 A 490 ASP ASN ILE GLU ASP MET GLU ALA ALA ALA MET LYS PHE SEQRES 37 A 490 GLU LYS GLU ASP GLY VAL SER ASP LEU ILE THR THR ASP SEQRES 38 A 490 GLU ASP LEU TYR LYS TYR PRO SER SER SEQRES 1 B 12 ALA ALA ARG M3L SER ALA PRO ALA THR GLY GLY VAL MODRES 6IP4 M3L B 27 LYS MODIFIED RESIDUE HET M3L B 27 12 HET NI A 601 1 HET ZN A 602 1 HET ZN A 603 1 HET OGA A 604 10 HET SO4 A 605 5 HET SO4 A 606 5 HET SO4 A 607 5 HET SO4 A 608 5 HET SO4 A 609 5 HET SO4 A 610 5 HET SO4 A 611 5 HETNAM M3L N-TRIMETHYLLYSINE HETNAM NI NICKEL (II) ION HETNAM ZN ZINC ION HETNAM OGA N-OXALYLGLYCINE HETNAM SO4 SULFATE ION 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 FORMUL 7 SO4 7(O4 S 2-) FORMUL 14 HOH *57(H2 O) HELIX 1 AA1 LEU A 94 LEU A 100 1 7 HELIX 2 AA2 THR A 109 GLU A 114 1 6 HELIX 3 AA3 ASP A 115 SER A 128 1 14 HELIX 4 AA4 PRO A 144 LYS A 151 1 8 HELIX 5 AA5 ASP A 171 MET A 180 1 10 HELIX 6 AA6 PHE A 187 CYS A 203 1 17 HELIX 7 AA7 PRO A 209 GLY A 224 1 16 HELIX 8 AA8 ASN A 254 SER A 259 1 6 HELIX 9 AA9 SER A 264 LEU A 269 5 6 HELIX 10 AB1 PRO A 317 SER A 319 5 3 HELIX 11 AB2 ALA A 320 ASN A 334 1 15 HELIX 12 AB3 ALA A 346 GLY A 352 1 7 HELIX 13 AB4 PRO A 358 HIS A 365 1 8 HELIX 14 AB5 MET A 405 ASP A 407 5 3 HELIX 15 AB6 TRP A 408 LEU A 422 1 15 HELIX 16 AB7 PRO A 429 ASN A 442 1 14 HELIX 17 AB8 THR A 453 GLY A 485 1 33 HELIX 18 AB9 ASP A 526 LEU A 530 5 5 HELIX 19 AC1 ASN A 545 GLU A 559 1 15 SHEET 1 AA1 8 VAL A 105 TYR A 106 0 SHEET 2 AA1 8 ILE A 132 VAL A 136 1 O LYS A 134 N TYR A 106 SHEET 3 AA1 8 GLU A 378 THR A 382 -1 O PHE A 379 N ILE A 135 SHEET 4 AA1 8 TYR A 300 GLY A 308 -1 N ASN A 303 O VAL A 380 SHEET 5 AA1 8 ASN A 396 PHE A 403 -1 O GLU A 399 N TYR A 304 SHEET 6 AA1 8 MET A 280 GLY A 284 -1 N TYR A 282 O GLY A 398 SHEET 7 AA1 8 THR A 228 VAL A 235 -1 N VAL A 235 O LEU A 281 SHEET 8 AA1 8 ARG A 161 PRO A 164 -1 N GLN A 163 O VAL A 229 SHEET 1 AA2 2 LYS A 157 THR A 159 0 SHEET 2 AA2 2 THR A 184 THR A 186 -1 O TYR A 185 N PHE A 158 SHEET 1 AA3 4 MET A 289 HIS A 293 0 SHEET 2 AA3 4 HIS A 388 SER A 392 -1 O GLY A 390 N PHE A 290 SHEET 3 AA3 4 LYS A 311 GLY A 315 -1 N TYR A 314 O ALA A 389 SHEET 4 AA3 4 TYR A 370 GLN A 374 -1 O GLN A 374 N LYS A 311 SHEET 1 AA4 3 CYS A 487 ASN A 493 0 SHEET 2 AA4 3 HIS A 538 ARG A 543 1 O LEU A 540 N VAL A 491 SHEET 3 AA4 3 ALA A 510 ASN A 513 -1 N PHE A 511 O TYR A 541 SHEET 1 AA5 2 ILE A 498 VAL A 499 0 SHEET 2 AA5 2 ASP A 506 CYS A 507 -1 O CYS A 507 N ILE A 498 LINK C ARG B 26 N M3L B 27 1555 1555 1.34 LINK C M3L B 27 N SER B 28 1555 1555 1.34 LINK NE2 HIS A 293 NI NI A 601 1555 1555 2.17 LINK OE2 GLU A 295 NI NI A 601 1555 1555 2.13 LINK NE2 HIS A 388 NI NI A 601 1555 1555 2.30 LINK SG CYS A 500 ZN ZN A 602 1555 1555 2.22 LINK SG CYS A 503 ZN ZN A 602 1555 1555 2.59 LINK SG CYS A 514 ZN ZN A 603 1555 1555 2.38 LINK SG CYS A 516 ZN ZN A 603 1555 1555 2.29 LINK ND1 HIS A 519 ZN ZN A 603 1555 1555 2.08 LINK SG CYS A 522 ZN ZN A 602 1555 1555 2.22 LINK NE2 HIS A 525 ZN ZN A 602 1555 1555 2.31 LINK SG CYS A 534 ZN ZN A 603 1555 1555 2.13 LINK NI NI A 601 O1 OGA A 604 1555 1555 1.97 LINK NI NI A 601 O2' OGA A 604 1555 1555 2.16 LINK NI NI A 601 O HOH A 705 1555 1555 2.77 SITE 1 AC1 5 HIS A 293 GLU A 295 HIS A 388 OGA A 604 SITE 2 AC1 5 HOH A 705 SITE 1 AC2 4 CYS A 500 CYS A 503 CYS A 522 HIS A 525 SITE 1 AC3 4 CYS A 514 CYS A 516 HIS A 519 CYS A 534 SITE 1 AC4 10 TYR A 231 TYR A 282 PHE A 290 HIS A 293 SITE 2 AC4 10 GLU A 295 SER A 301 ASN A 303 HIS A 388 SITE 3 AC4 10 NI A 601 HOH A 705 SITE 1 AC5 5 THR A 488 SER A 492 LEU A 542 ARG A 543 SITE 2 AC5 5 ASP A 544 SITE 1 AC6 3 LEU A 427 LEU A 428 PRO A 429 SITE 1 AC7 1 LYS A 196 SITE 1 AC8 2 LYS A 153 SER A 154 SITE 1 AC9 1 ILE A 414 SITE 1 AD1 2 HIS A 525 ASP A 526 SITE 1 AD2 4 ARG A 188 LYS A 192 LYS A 196 ARG A 200 CRYST1 128.794 128.794 230.642 90.00 90.00 120.00 P 62 2 2 12 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 0.007764 0.004483 0.000000 0.00000 SCALE2 0.000000 0.008965 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004336 0.00000