PDB Short entry for 6B0Q HEADER TRANSCRIPTION/DNA 14-SEP-17 6B0Q TITLE ZINC FINGER DOMAIN OF WT1(-KTS FORM) WITH 13+1MER OLIGONUCLEOTIDE WITH TITLE 2 3' TRIPLET TGT COMPND MOL_ID: 1; COMPND 2 MOLECULE: WILMS TUMOR PROTEIN; COMPND 3 CHAIN: D, A; COMPND 4 SYNONYM: WT33; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(P*GP*CP*GP*TP*GP*GP*GP*AP*GP*TP*GP*TP*T)-3'); COMPND 8 CHAIN: E, B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(P*AP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3'); COMPND 12 CHAIN: F, C; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: WT1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS PROTEIN-DNA COMPLEX WILMS TUMOR SUPPRESSOR PROTEIN ZINC-FINGERS, KEYWDS 2 TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HORTON,X.CHENG REVDAT 4 13-MAR-24 6B0Q 1 REMARK REVDAT 3 16-MAY-18 6B0Q 1 JRNL REVDAT 2 17-JAN-18 6B0Q 1 JRNL REVDAT 1 03-JAN-18 6B0Q 0 JRNL AUTH D.WANG,J.R.HORTON,Y.ZHENG,R.M.BLUMENTHAL,X.ZHANG,X.CHENG JRNL TITL ROLE FOR FIRST ZINC FINGER OF WT1 IN DNA SEQUENCE JRNL TITL 2 SPECIFICITY: DENYS-DRASH SYNDROME-ASSOCIATED WT1 MUTANT IN JRNL TITL 3 ZF1 ENHANCES AFFINITY FOR A SUBSET OF WT1 BINDING SITES. JRNL REF NUCLEIC ACIDS RES. V. 46 3864 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 29294058 JRNL DOI 10.1093/NAR/GKX1274 REMARK 2 REMARK 2 RESOLUTION. 2.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 30219 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1509 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 38.8342 - 6.2058 0.99 2626 135 0.1806 0.1839 REMARK 3 2 6.2058 - 4.9289 1.00 2633 137 0.1676 0.1661 REMARK 3 3 4.9289 - 4.3067 1.00 2651 143 0.1723 0.1720 REMARK 3 4 4.3067 - 3.9134 1.00 2633 146 0.1928 0.2115 REMARK 3 5 3.9134 - 3.6331 1.00 2634 144 0.2120 0.2584 REMARK 3 6 3.6331 - 3.4190 0.98 2567 134 0.2471 0.3061 REMARK 3 7 3.4190 - 3.2479 0.95 2494 128 0.2901 0.3571 REMARK 3 8 3.2479 - 3.1066 0.98 2597 138 0.3014 0.2492 REMARK 3 9 3.1066 - 2.9870 1.00 2597 136 0.3348 0.3292 REMARK 3 10 2.9870 - 2.8840 1.00 2689 140 0.3299 0.4143 REMARK 3 11 2.8840 - 2.7938 0.99 2589 128 0.3390 0.3735 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.160 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 : 0.004 3289 REMARK 3 ANGLE : 0.479 4598 REMARK 3 CHIRALITY : 0.031 467 REMARK 3 PLANARITY : 0.003 407 REMARK 3 DIHEDRAL : 20.762 1759 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 319 THROUGH 347 ) REMARK 3 ORIGIN FOR THE GROUP (A): 84.4866 21.5915 -32.9613 REMARK 3 T TENSOR REMARK 3 T11: 0.5431 T22: 0.6882 REMARK 3 T33: 0.5412 T12: 0.1242 REMARK 3 T13: -0.1250 T23: -0.0192 REMARK 3 L TENSOR REMARK 3 L11: 2.0088 L22: 5.3753 REMARK 3 L33: 7.1764 L12: -0.4788 REMARK 3 L13: -0.6787 L23: 0.7260 REMARK 3 S TENSOR REMARK 3 S11: -0.7038 S12: -0.8052 S13: 1.1088 REMARK 3 S21: 0.7266 S22: 0.3770 S23: -0.0782 REMARK 3 S31: -0.9425 S32: -0.9007 S33: 0.3886 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 348 THROUGH 436 ) REMARK 3 ORIGIN FOR THE GROUP (A): 61.0605 9.7207 -2.2524 REMARK 3 T TENSOR REMARK 3 T11: 0.3882 T22: 0.1658 REMARK 3 T33: 0.2714 T12: 0.0160 REMARK 3 T13: -0.0219 T23: -0.0072 REMARK 3 L TENSOR REMARK 3 L11: 2.4737 L22: 4.1111 REMARK 3 L33: 4.0190 L12: 0.7616 REMARK 3 L13: -0.6561 L23: -2.1786 REMARK 3 S TENSOR REMARK 3 S11: 0.0013 S12: 0.0117 S13: -0.0692 REMARK 3 S21: -0.0031 S22: 0.1617 S23: 0.2067 REMARK 3 S31: 0.3474 S32: -0.2613 S33: -0.1216 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'E' AND (RESID 2 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 61.5826 7.7622 -7.4844 REMARK 3 T TENSOR REMARK 3 T11: 0.4634 T22: 0.2485 REMARK 3 T33: 0.2524 T12: -0.0147 REMARK 3 T13: 0.0154 T23: 0.0387 REMARK 3 L TENSOR REMARK 3 L11: 1.1120 L22: 1.9218 REMARK 3 L33: 2.1873 L12: -0.5733 REMARK 3 L13: -0.2420 L23: -0.0773 REMARK 3 S TENSOR REMARK 3 S11: -0.0012 S12: 0.1208 S13: -0.0853 REMARK 3 S21: 0.0112 S22: 0.1720 S23: 0.2710 REMARK 3 S31: 0.2528 S32: -0.3466 S33: -0.1561 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'F' AND (RESID 1 THROUGH 13 ) REMARK 3 ORIGIN FOR THE GROUP (A): 63.3535 8.9658 -7.4009 REMARK 3 T TENSOR REMARK 3 T11: 0.6724 T22: 0.3542 REMARK 3 T33: 0.3246 T12: -0.0684 REMARK 3 T13: 0.0562 T23: -0.0016 REMARK 3 L TENSOR REMARK 3 L11: 2.5174 L22: 2.3032 REMARK 3 L33: 6.8776 L12: -0.4056 REMARK 3 L13: -0.2797 L23: -0.7888 REMARK 3 S TENSOR REMARK 3 S11: -0.0075 S12: 0.0942 S13: 0.2604 REMARK 3 S21: -0.1875 S22: 0.5172 S23: 0.1194 REMARK 3 S31: -1.2866 S32: 0.0136 S33: -0.4604 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 319 THROUGH 346 ) REMARK 3 ORIGIN FOR THE GROUP (A): 52.6031 60.4911 0.3255 REMARK 3 T TENSOR REMARK 3 T11: 0.4399 T22: 0.4395 REMARK 3 T33: 0.4713 T12: 0.0569 REMARK 3 T13: 0.0926 T23: -0.0194 REMARK 3 L TENSOR REMARK 3 L11: 5.1377 L22: 4.6421 REMARK 3 L33: 4.3529 L12: 2.7456 REMARK 3 L13: -0.1088 L23: -1.4559 REMARK 3 S TENSOR REMARK 3 S11: 0.0332 S12: -0.7957 S13: 0.1268 REMARK 3 S21: -0.0263 S22: -0.2340 S23: 0.6867 REMARK 3 S31: -0.0044 S32: 0.3115 S33: 0.2116 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 347 THROUGH 437 ) REMARK 3 ORIGIN FOR THE GROUP (A): 50.4605 35.4466 -19.8952 REMARK 3 T TENSOR REMARK 3 T11: 0.3336 T22: 0.2782 REMARK 3 T33: 0.2965 T12: 0.0662 REMARK 3 T13: 0.0644 T23: 0.0428 REMARK 3 L TENSOR REMARK 3 L11: 2.8530 L22: 3.2545 REMARK 3 L33: 2.6527 L12: -0.4196 REMARK 3 L13: 1.3913 L23: -0.3730 REMARK 3 S TENSOR REMARK 3 S11: 0.1428 S12: -0.0827 S13: -0.1859 REMARK 3 S21: 0.0084 S22: 0.0371 S23: 0.1771 REMARK 3 S31: 0.0588 S32: -0.3130 S33: -0.1737 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 2 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.7921 37.1232 -13.7818 REMARK 3 T TENSOR REMARK 3 T11: 0.4003 T22: 0.4874 REMARK 3 T33: 0.3107 T12: 0.1112 REMARK 3 T13: -0.0262 T23: 0.0836 REMARK 3 L TENSOR REMARK 3 L11: 1.4666 L22: 2.2713 REMARK 3 L33: 1.9462 L12: -0.6803 REMARK 3 L13: 0.4874 L23: 0.0466 REMARK 3 S TENSOR REMARK 3 S11: 0.1928 S12: -0.2109 S13: -0.1659 REMARK 3 S21: 0.0458 S22: 0.0729 S23: 0.1887 REMARK 3 S31: -0.3001 S32: -0.7425 S33: -0.2255 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 2 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 51.5751 37.2597 -14.4322 REMARK 3 T TENSOR REMARK 3 T11: 0.4988 T22: 0.4589 REMARK 3 T33: 0.3588 T12: 0.1129 REMARK 3 T13: -0.0462 T23: 0.0760 REMARK 3 L TENSOR REMARK 3 L11: 1.2018 L22: 0.3389 REMARK 3 L33: 6.7675 L12: -0.5700 REMARK 3 L13: -0.6443 L23: 0.4080 REMARK 3 S TENSOR REMARK 3 S11: 0.4398 S12: 0.1358 S13: 0.1324 REMARK 3 S21: 0.0135 S22: 0.3524 S23: -0.0219 REMARK 3 S31: 0.3244 S32: -0.2561 S33: -0.7547 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 6B0Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1000229812. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-17 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 : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30219 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.790 REMARK 200 RESOLUTION RANGE LOW (A) : 38.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.82200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350 0.2M LITHIUM SULFATE 0.1M REMARK 280 BIS-TRIS, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-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 -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 0.00000 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 0.00000 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 21.08600 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 21.08600 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 21.08600 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: 4690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F 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: 5050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 ARG D 437 REMARK 465 DA E 1 REMARK 465 DT F 0 REMARK 465 DA B 1 REMARK 465 DT C 1 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 HIS D 319 CG ND1 CD2 CE1 NE2 REMARK 470 TYR D 327 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN D 331 CG OD1 ND2 REMARK 470 LYS D 332 CG CD CE NZ REMARK 470 LYS D 346 CG CD CE NZ REMARK 470 THR D 348 OG1 CG2 REMARK 470 LYS D 386 CG CD CE NZ REMARK 470 SER D 417 OG REMARK 470 GLN D 419 CG CD OE1 NE2 REMARK 470 HIS A 319 CG ND1 CD2 CE1 NE2 REMARK 470 MET A 320 CG SD CE REMARK 470 THR A 348 OG1 CG2 REMARK 470 GLU A 350 CG CD OE1 OE2 REMARK 470 GLU A 361 CG CD OE1 OE2 REMARK 470 GLU A 408 CG CD OE1 OE2 REMARK 470 ARG A 414 CG CD NE CZ NH1 NH2 REMARK 470 SER A 417 OG REMARK 470 GLN A 419 CG CD OE1 NE2 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 A 351 78.26 -116.69 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 D 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 325 SG REMARK 620 2 CYS D 330 SG 121.1 REMARK 620 3 HIS D 343 NE2 118.2 72.2 REMARK 620 4 HIS D 347 NE2 111.1 111.6 117.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 355 SG REMARK 620 2 CYS D 360 SG 114.3 REMARK 620 3 HIS D 373 NE2 106.8 102.1 REMARK 620 4 HIS D 377 NE2 108.8 119.1 104.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 385 SG REMARK 620 2 CYS D 388 SG 116.4 REMARK 620 3 HIS D 401 NE2 109.2 89.0 REMARK 620 4 HIS D 405 NE2 126.3 98.4 111.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 413 SG REMARK 620 2 CYS D 418 SG 104.4 REMARK 620 3 HIS D 431 NE2 113.6 114.5 REMARK 620 4 HIS D 435 NE2 119.8 119.3 84.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 325 SG REMARK 620 2 CYS A 330 SG 121.0 REMARK 620 3 HIS A 343 NE2 105.0 87.1 REMARK 620 4 HIS A 347 NE2 108.1 123.1 107.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 355 SG REMARK 620 2 CYS A 360 SG 106.8 REMARK 620 3 HIS A 373 NE2 103.4 113.7 REMARK 620 4 HIS A 377 NE2 109.6 117.8 104.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 385 SG REMARK 620 2 CYS A 388 SG 118.0 REMARK 620 3 HIS A 401 NE2 115.2 88.9 REMARK 620 4 HIS A 405 NE2 135.6 97.9 89.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 413 SG REMARK 620 2 CYS A 418 SG 113.1 REMARK 620 3 HIS A 431 NE2 104.9 109.8 REMARK 620 4 HIS A 435 NE2 119.1 119.5 84.7 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 D 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 D 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 508 DBREF 6B0Q D 321 437 UNP P19544 WT1_HUMAN 304 420 DBREF 6B0Q E 1 14 PDB 6B0Q 6B0Q 1 14 DBREF 6B0Q F 0 13 PDB 6B0Q 6B0Q 0 13 DBREF 6B0Q A 321 437 UNP P19544 WT1_HUMAN 304 420 DBREF 6B0Q B 1 14 PDB 6B0Q 6B0Q 1 14 DBREF 6B0Q C 1 14 PDB 6B0Q 6B0Q 1 14 SEQADV 6B0Q HIS D 319 UNP P19544 EXPRESSION TAG SEQADV 6B0Q MET D 320 UNP P19544 EXPRESSION TAG SEQADV 6B0Q HIS A 319 UNP P19544 EXPRESSION TAG SEQADV 6B0Q MET A 320 UNP P19544 EXPRESSION TAG SEQRES 1 D 119 HIS MET ARG PRO PHE MET CYS ALA TYR PRO GLY CYS ASN SEQRES 2 D 119 LYS ARG TYR PHE LYS LEU SER HIS LEU GLN MET HIS SER SEQRES 3 D 119 ARG LYS HIS THR GLY GLU LYS PRO TYR GLN CYS ASP PHE SEQRES 4 D 119 LYS ASP CYS GLU ARG ARG PHE SER ARG SER ASP GLN LEU SEQRES 5 D 119 LYS ARG HIS GLN ARG ARG HIS THR GLY VAL LYS PRO PHE SEQRES 6 D 119 GLN CYS LYS THR CYS GLN ARG LYS PHE SER ARG SER ASP SEQRES 7 D 119 HIS LEU LYS THR HIS THR ARG THR HIS THR GLY GLU LYS SEQRES 8 D 119 PRO PHE SER CYS ARG TRP PRO SER CYS GLN LYS LYS PHE SEQRES 9 D 119 ALA ARG SER ASP GLU LEU VAL ARG HIS HIS ASN MET HIS SEQRES 10 D 119 GLN ARG SEQRES 1 E 14 DA DG DC DG DT DG DG DG DA DG DT DG DT SEQRES 2 E 14 DT SEQRES 1 F 14 DT DA DA DC DA DC DT DC DC DC DA DC DG SEQRES 2 F 14 DC SEQRES 1 A 119 HIS MET ARG PRO PHE MET CYS ALA TYR PRO GLY CYS ASN SEQRES 2 A 119 LYS ARG TYR PHE LYS LEU SER HIS LEU GLN MET HIS SER SEQRES 3 A 119 ARG LYS HIS THR GLY GLU LYS PRO TYR GLN CYS ASP PHE SEQRES 4 A 119 LYS ASP CYS GLU ARG ARG PHE SER ARG SER ASP GLN LEU SEQRES 5 A 119 LYS ARG HIS GLN ARG ARG HIS THR GLY VAL LYS PRO PHE SEQRES 6 A 119 GLN CYS LYS THR CYS GLN ARG LYS PHE SER ARG SER ASP SEQRES 7 A 119 HIS LEU LYS THR HIS THR ARG THR HIS THR GLY GLU LYS SEQRES 8 A 119 PRO PHE SER CYS ARG TRP PRO SER CYS GLN LYS LYS PHE SEQRES 9 A 119 ALA ARG SER ASP GLU LEU VAL ARG HIS HIS ASN MET HIS SEQRES 10 A 119 GLN ARG SEQRES 1 B 14 DA DG DC DG DT DG DG DG DA DG DT DG DT SEQRES 2 B 14 DT SEQRES 1 C 14 DT DA DA DC DA DC DT DC DC DC DA DC DG SEQRES 2 C 14 DC HET ZN D 501 1 HET ZN D 502 1 HET ZN D 503 1 HET ZN D 504 1 HET SO4 D 505 5 HET SO4 D 506 5 HET SO4 D 507 5 HET SO4 D 508 5 HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 1 HET ZN A 504 1 HET SO4 A 505 5 HET SO4 A 506 5 HET SO4 A 507 5 HET SO4 A 508 5 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 7 ZN 8(ZN 2+) FORMUL 11 SO4 8(O4 S 2-) FORMUL 23 HOH *30(H2 O) HELIX 1 AA1 LYS D 336 ARG D 345 1 10 HELIX 2 AA2 ARG D 366 GLN D 374 1 9 HELIX 3 AA3 GLN D 374 GLY D 379 1 6 HELIX 4 AA4 ARG D 394 GLY D 407 1 14 HELIX 5 AA5 ARG D 424 HIS D 435 1 12 HELIX 6 AA6 LYS A 336 ARG A 345 1 10 HELIX 7 AA7 ARG A 366 GLN A 374 1 9 HELIX 8 AA8 GLN A 374 GLY A 379 1 6 HELIX 9 AA9 ARG A 394 GLY A 407 1 14 HELIX 10 AB1 ARG A 424 GLN A 436 1 13 SHEET 1 AA1 2 PHE D 323 MET D 324 0 SHEET 2 AA1 2 ARG D 333 TYR D 334 -1 O TYR D 334 N PHE D 323 SHEET 1 AA2 2 TYR D 353 GLN D 354 0 SHEET 2 AA2 2 ARG D 363 PHE D 364 -1 O PHE D 364 N TYR D 353 SHEET 1 AA3 2 PHE D 383 GLN D 384 0 SHEET 2 AA3 2 LYS D 391 PHE D 392 -1 O PHE D 392 N PHE D 383 SHEET 1 AA4 2 PHE D 411 SER D 412 0 SHEET 2 AA4 2 LYS D 421 PHE D 422 -1 O PHE D 422 N PHE D 411 SHEET 1 AA5 2 PHE A 323 MET A 324 0 SHEET 2 AA5 2 ARG A 333 TYR A 334 -1 O TYR A 334 N PHE A 323 SHEET 1 AA6 2 TYR A 353 GLN A 354 0 SHEET 2 AA6 2 ARG A 363 PHE A 364 -1 O PHE A 364 N TYR A 353 SHEET 1 AA7 2 PHE A 383 GLN A 384 0 SHEET 2 AA7 2 LYS A 391 PHE A 392 -1 O PHE A 392 N PHE A 383 SHEET 1 AA8 2 PHE A 411 SER A 412 0 SHEET 2 AA8 2 LYS A 421 PHE A 422 -1 O PHE A 422 N PHE A 411 LINK SG CYS D 325 ZN ZN D 501 1555 1555 2.34 LINK SG CYS D 330 ZN ZN D 501 1555 1555 2.29 LINK NE2 HIS D 343 ZN ZN D 501 1555 1555 2.04 LINK NE2 HIS D 347 ZN ZN D 501 1555 1555 2.04 LINK SG CYS D 355 ZN ZN D 502 1555 1555 2.32 LINK SG CYS D 360 ZN ZN D 502 1555 1555 2.26 LINK NE2 HIS D 373 ZN ZN D 502 1555 1555 2.03 LINK NE2 HIS D 377 ZN ZN D 502 1555 1555 2.02 LINK SG CYS D 385 ZN ZN D 503 1555 1555 2.33 LINK SG CYS D 388 ZN ZN D 503 1555 1555 2.27 LINK NE2 HIS D 401 ZN ZN D 503 1555 1555 2.03 LINK NE2 HIS D 405 ZN ZN D 503 1555 1555 2.03 LINK SG CYS D 413 ZN ZN D 504 1555 1555 2.32 LINK SG CYS D 418 ZN ZN D 504 1555 1555 2.32 LINK NE2 HIS D 431 ZN ZN D 504 1555 1555 2.03 LINK NE2 HIS D 435 ZN ZN D 504 1555 1555 2.03 LINK SG CYS A 325 ZN ZN A 501 1555 1555 2.37 LINK SG CYS A 330 ZN ZN A 501 1555 1555 2.35 LINK NE2 HIS A 343 ZN ZN A 501 1555 1555 2.03 LINK NE2 HIS A 347 ZN ZN A 501 1555 1555 2.05 LINK SG CYS A 355 ZN ZN A 502 1555 1555 2.29 LINK SG CYS A 360 ZN ZN A 502 1555 1555 2.28 LINK NE2 HIS A 373 ZN ZN A 502 1555 1555 2.04 LINK NE2 HIS A 377 ZN ZN A 502 1555 1555 2.03 LINK SG CYS A 385 ZN ZN A 503 1555 1555 2.30 LINK SG CYS A 388 ZN ZN A 503 1555 1555 2.29 LINK NE2 HIS A 401 ZN ZN A 503 1555 1555 2.03 LINK NE2 HIS A 405 ZN ZN A 503 1555 1555 2.03 LINK SG CYS A 413 ZN ZN A 504 1555 1555 2.31 LINK SG CYS A 418 ZN ZN A 504 1555 1555 2.26 LINK NE2 HIS A 431 ZN ZN A 504 1555 1555 2.03 LINK NE2 HIS A 435 ZN ZN A 504 1555 1555 2.03 SITE 1 AC1 4 CYS D 325 CYS D 330 HIS D 343 HIS D 347 SITE 1 AC2 4 CYS D 355 CYS D 360 HIS D 373 HIS D 377 SITE 1 AC3 4 CYS D 385 CYS D 388 HIS D 401 HIS D 405 SITE 1 AC4 4 CYS D 413 CYS D 418 HIS D 431 HIS D 435 SITE 1 AC5 4 ARG A 321 LYS A 332 ARG A 333 ARG D 362 SITE 1 AC6 4 TYR D 334 PHE D 335 LYS D 336 HIS D 339 SITE 1 AC7 4 ARG A 437 LYS D 336 LEU D 337 SER D 338 SITE 1 AC8 1 ARG D 390 SITE 1 AC9 4 CYS A 325 CYS A 330 HIS A 343 HIS A 347 SITE 1 AD1 4 CYS A 355 CYS A 360 HIS A 373 HIS A 377 SITE 1 AD2 4 CYS A 385 CYS A 388 HIS A 401 HIS A 405 SITE 1 AD3 4 CYS A 413 CYS A 418 HIS A 431 HIS A 435 SITE 1 AD4 2 ARG A 362 ARG A 376 SITE 1 AD5 4 TYR A 334 PHE A 335 LYS A 336 HIS A 339 SITE 1 AD6 6 LYS A 332 TYR A 334 HIS A 343 LYS A 346 SITE 2 AD6 6 GLU D 350 LYS D 351 SITE 1 AD7 1 ARG A 390 CRYST1 161.664 161.664 42.172 90.00 90.00 120.00 P 63 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 0.006186 0.003571 0.000000 0.00000 SCALE2 0.000000 0.007143 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023712 0.00000