PDB Short entry for 5KL3 HEADER TRANSCRIPTION/DNA 23-JUN-16 5KL3 TITLE WILMS TUMOR PROTEIN (WT1) ZNF2-4 Q369H IN COMPLEX WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: WILMS TUMOR PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: WT33; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*T)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*TP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 VARIANT: -KTS; SOURCE 6 GENE: WT1; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) RIL-CODON PLUS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PGEX-6P-1; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PXC1305; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630 KEYWDS WILMS TUMOR PROTEIN, WT1, ZINC FINGER, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.HASHIMOTO,X.CHENG REVDAT 6 27-SEP-23 5KL3 1 REMARK REVDAT 5 25-DEC-19 5KL3 1 REMARK REVDAT 4 27-SEP-17 5KL3 1 REMARK REVDAT 3 14-DEC-16 5KL3 1 JRNL REVDAT 2 21-SEP-16 5KL3 1 JRNL REVDAT 1 14-SEP-16 5KL3 0 JRNL AUTH H.HASHIMOTO,X.ZHANG,Y.ZHENG,G.G.WILSON,X.CHENG JRNL TITL DENYS-DRASH SYNDROME ASSOCIATED WT1 GLUTAMINE 369 MUTANTS JRNL TITL 2 HAVE ALTERED SEQUENCE-PREFERENCES AND ALTERED RESPONSES TO JRNL TITL 3 EPIGENETIC MODIFICATIONS. JRNL REF NUCLEIC ACIDS RES. V. 44 10165 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 27596598 JRNL DOI 10.1093/NAR/GKW766 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2257: ???) 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.7 REMARK 3 NUMBER OF REFLECTIONS : 27162 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1361 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 29.2294 - 3.1214 0.99 2990 135 0.1411 0.1446 REMARK 3 2 3.1214 - 2.4780 1.00 2981 137 0.1692 0.1884 REMARK 3 3 2.4780 - 2.1649 1.00 2932 162 0.1542 0.1962 REMARK 3 4 2.1649 - 1.9670 1.00 2903 181 0.1701 0.1880 REMARK 3 5 1.9670 - 1.8260 1.00 2904 176 0.1734 0.2198 REMARK 3 6 1.8260 - 1.7184 0.98 2883 156 0.1793 0.2005 REMARK 3 7 1.7184 - 1.6323 0.92 2686 145 0.1938 0.1987 REMARK 3 8 1.6323 - 1.5613 0.79 2338 108 0.2068 0.2822 REMARK 3 9 1.5613 - 1.5012 0.65 1961 62 0.2305 0.3202 REMARK 3 10 1.5012 - 1.4494 0.43 1223 99 0.2777 0.2890 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.250 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 : 0.009 1313 REMARK 3 ANGLE : 1.133 1846 REMARK 3 CHIRALITY : 0.069 191 REMARK 3 PLANARITY : 0.010 161 REMARK 3 DIHEDRAL : 22.014 544 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 351 THROUGH 360 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.5781-261.8593 -64.5254 REMARK 3 T TENSOR REMARK 3 T11: 0.2680 T22: 0.2795 REMARK 3 T33: 0.3408 T12: -0.0280 REMARK 3 T13: 0.0644 T23: -0.0407 REMARK 3 L TENSOR REMARK 3 L11: 6.4020 L22: 5.1637 REMARK 3 L33: 8.6613 L12: 2.2383 REMARK 3 L13: 1.6767 L23: 5.1801 REMARK 3 S TENSOR REMARK 3 S11: -0.2732 S12: 0.0693 S13: -0.9743 REMARK 3 S21: -0.3439 S22: 0.1662 S23: -1.1099 REMARK 3 S31: -0.0991 S32: 0.4302 S33: -0.2159 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 361 THROUGH 366 ) REMARK 3 ORIGIN FOR THE GROUP (A): -41.0823-267.6762 -64.1097 REMARK 3 T TENSOR REMARK 3 T11: 0.3286 T22: 0.2923 REMARK 3 T33: 0.4205 T12: 0.0387 REMARK 3 T13: -0.0088 T23: -0.0302 REMARK 3 L TENSOR REMARK 3 L11: 6.1590 L22: 5.0780 REMARK 3 L33: 8.6180 L12: 5.5395 REMARK 3 L13: 6.7864 L23: 6.1511 REMARK 3 S TENSOR REMARK 3 S11: 0.2593 S12: 0.2875 S13: -1.5704 REMARK 3 S21: 0.0288 S22: 0.4103 S23: -1.1362 REMARK 3 S31: 0.5805 S32: 0.5932 S33: -0.5392 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 367 THROUGH 378 ) REMARK 3 ORIGIN FOR THE GROUP (A): -46.7977-260.5730 -62.7407 REMARK 3 T TENSOR REMARK 3 T11: 0.2733 T22: 0.1969 REMARK 3 T33: 0.1583 T12: 0.0068 REMARK 3 T13: 0.0184 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 3.6722 L22: 6.1526 REMARK 3 L33: 7.9193 L12: 3.9024 REMARK 3 L13: 2.7611 L23: 6.2958 REMARK 3 S TENSOR REMARK 3 S11: -0.0720 S12: 0.0963 S13: -0.1432 REMARK 3 S21: 0.0021 S22: 0.1867 S23: -0.2084 REMARK 3 S31: 0.0254 S32: 0.2235 S33: -0.0759 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 379 THROUGH 406 ) REMARK 3 ORIGIN FOR THE GROUP (A): -61.8157-257.0362 -55.3444 REMARK 3 T TENSOR REMARK 3 T11: 0.1602 T22: 0.1068 REMARK 3 T33: 0.0960 T12: 0.0134 REMARK 3 T13: -0.0310 T23: 0.0121 REMARK 3 L TENSOR REMARK 3 L11: 5.5660 L22: 3.6518 REMARK 3 L33: 2.8267 L12: 0.0782 REMARK 3 L13: -2.9406 L23: -0.3012 REMARK 3 S TENSOR REMARK 3 S11: 0.0130 S12: 0.1214 S13: 0.2057 REMARK 3 S21: -0.0630 S22: 0.0749 S23: 0.3619 REMARK 3 S31: -0.0887 S32: -0.0379 S33: -0.0857 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 407 THROUGH 424 ) REMARK 3 ORIGIN FOR THE GROUP (A): -69.9744-275.4396 -45.1545 REMARK 3 T TENSOR REMARK 3 T11: 0.2120 T22: 0.1857 REMARK 3 T33: 0.1476 T12: 0.0105 REMARK 3 T13: -0.0116 T23: -0.0166 REMARK 3 L TENSOR REMARK 3 L11: 4.9154 L22: 3.6349 REMARK 3 L33: 4.4821 L12: 2.1491 REMARK 3 L13: -1.7056 L23: -1.3433 REMARK 3 S TENSOR REMARK 3 S11: -0.1369 S12: -0.1615 S13: 0.0153 REMARK 3 S21: -0.1728 S22: -0.1274 S23: 0.5415 REMARK 3 S31: 0.0447 S32: -0.3783 S33: 0.1666 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 425 THROUGH 437 ) REMARK 3 ORIGIN FOR THE GROUP (A): -61.6764-278.0428 -43.2893 REMARK 3 T TENSOR REMARK 3 T11: 0.3425 T22: 0.1768 REMARK 3 T33: 0.1492 T12: 0.0054 REMARK 3 T13: 0.0028 T23: -0.0071 REMARK 3 L TENSOR REMARK 3 L11: 2.6659 L22: 5.3805 REMARK 3 L33: 2.4216 L12: 3.6716 REMARK 3 L13: -2.4544 L23: -3.5139 REMARK 3 S TENSOR REMARK 3 S11: -0.1339 S12: -0.1527 S13: -0.1384 REMARK 3 S21: -0.0040 S22: -0.0534 S23: -0.4224 REMARK 3 S31: 0.0636 S32: 0.0522 S33: 0.0854 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -55.1574-268.2969 -54.6526 REMARK 3 T TENSOR REMARK 3 T11: 0.2610 T22: 0.1506 REMARK 3 T33: 0.1051 T12: 0.0027 REMARK 3 T13: -0.0186 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 1.2457 L22: 1.3202 REMARK 3 L33: 0.8345 L12: 0.4691 REMARK 3 L13: 0.5242 L23: -0.6184 REMARK 3 S TENSOR REMARK 3 S11: 0.0459 S12: 0.0093 S13: -0.0245 REMARK 3 S21: 0.1049 S22: 0.0898 S23: -0.0797 REMARK 3 S31: 0.2560 S32: -0.0549 S33: -0.0894 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -55.9087-268.5544 -56.5158 REMARK 3 T TENSOR REMARK 3 T11: 0.3036 T22: 0.1791 REMARK 3 T33: 0.1330 T12: 0.0171 REMARK 3 T13: 0.0100 T23: -0.0287 REMARK 3 L TENSOR REMARK 3 L11: 1.6979 L22: 1.8012 REMARK 3 L33: 5.7168 L12: 0.5948 REMARK 3 L13: 0.3930 L23: 0.1857 REMARK 3 S TENSOR REMARK 3 S11: 0.1349 S12: -0.1111 S13: -0.0196 REMARK 3 S21: -0.0545 S22: 0.2025 S23: -0.0046 REMARK 3 S31: 0.1453 S32: -0.2909 S33: -0.3151 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 5KL3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000222095. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 1.000 REMARK 200 MONOCHROMATOR : SI (111) 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 : 27228 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.449 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 43.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.61000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 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: 4R2R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% (W/V) PEG 3350, 4% (V/V) REMARK 280 TACSIMATE, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 37.61150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.03450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 37.61150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.03450 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 GLY A 345 REMARK 465 PRO A 346 REMARK 465 LEU A 347 REMARK 465 GLY A 348 REMARK 465 SER A 349 REMARK 465 GLU A 350 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 ARG A 437 CG CD NE CZ NH1 NH2 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 OE1 GLN A 436 O HOH A 601 2.02 REMARK 500 OP2 DC C 5 O HOH C 101 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC C 5 O3' DC C 5 C3' -0.036 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 DC B 3 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT B 5 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC C 3 O4' - C1' - N1 ANGL. DEV. = 2.1 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 GLN A 436 142.48 -174.45 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 A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 355 SG REMARK 620 2 CYS A 360 SG 113.0 REMARK 620 3 HIS A 373 NE2 110.1 107.9 REMARK 620 4 HIS A 377 NE2 109.1 114.3 101.9 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 113.2 REMARK 620 3 HIS A 401 NE2 110.3 106.6 REMARK 620 4 HIS A 405 NE2 106.8 115.2 104.5 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 114.7 REMARK 620 3 HIS A 431 NE2 105.9 114.4 REMARK 620 4 HIS A 435 NE2 107.0 117.9 94.7 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 EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KL2 RELATED DB: PDB REMARK 900 RELATED ID: 5KL4 RELATED DB: PDB REMARK 900 RELATED ID: 5KL5 RELATED DB: PDB REMARK 900 RELATED ID: 5KL6 RELATED DB: PDB REMARK 900 RELATED ID: 5KL7 RELATED DB: PDB DBREF 5KL3 A 350 437 UNP P19544 WT1_HUMAN 333 420 DBREF 5KL3 B 1 11 PDB 5KL3 5KL3 1 11 DBREF 5KL3 C 1 11 PDB 5KL3 5KL3 1 11 SEQADV 5KL3 GLY A 345 UNP P19544 EXPRESSION TAG SEQADV 5KL3 PRO A 346 UNP P19544 EXPRESSION TAG SEQADV 5KL3 LEU A 347 UNP P19544 EXPRESSION TAG SEQADV 5KL3 GLY A 348 UNP P19544 EXPRESSION TAG SEQADV 5KL3 SER A 349 UNP P19544 EXPRESSION TAG SEQADV 5KL3 HIS A 369 UNP P19544 GLN 352 ENGINEERED MUTATION SEQRES 1 A 93 GLY PRO LEU GLY SER GLU LYS PRO TYR GLN CYS ASP PHE SEQRES 2 A 93 LYS ASP CYS GLU ARG ARG PHE SER ARG SER ASP HIS LEU SEQRES 3 A 93 LYS ARG HIS GLN ARG ARG HIS THR GLY VAL LYS PRO PHE SEQRES 4 A 93 GLN CYS LYS THR CYS GLN ARG LYS PHE SER ARG SER ASP SEQRES 5 A 93 HIS LEU LYS THR HIS THR ARG THR HIS THR GLY GLU LYS SEQRES 6 A 93 PRO PHE SER CYS ARG TRP PRO SER CYS GLN LYS LYS PHE SEQRES 7 A 93 ALA ARG SER ASP GLU LEU VAL ARG HIS HIS ASN MET HIS SEQRES 8 A 93 GLN ARG SEQRES 1 B 11 DA DG DC DG DT DG DG DG DA DG DT SEQRES 1 C 11 DT DA DC DT DC DC DC DA DC DG DC HET EDO A 501 10 HET ZN A 502 1 HET ZN A 503 1 HET ZN A 504 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM ZN ZINC ION HETSYN EDO ETHYLENE GLYCOL FORMUL 4 EDO C2 H6 O2 FORMUL 5 ZN 3(ZN 2+) FORMUL 8 HOH *180(H2 O) HELIX 1 AA1 ARG A 366 GLY A 379 1 14 HELIX 2 AA2 ARG A 394 THR A 402 1 9 HELIX 3 AA3 THR A 402 GLY A 407 1 6 HELIX 4 AA4 ARG A 424 GLN A 436 1 13 SHEET 1 AA1 2 TYR A 353 GLN A 354 0 SHEET 2 AA1 2 ARG A 363 PHE A 364 -1 O PHE A 364 N TYR A 353 SHEET 1 AA2 2 PHE A 383 GLN A 384 0 SHEET 2 AA2 2 LYS A 391 PHE A 392 -1 O PHE A 392 N PHE A 383 SHEET 1 AA3 2 PHE A 411 SER A 412 0 SHEET 2 AA3 2 LYS A 421 PHE A 422 -1 O PHE A 422 N PHE A 411 LINK SG CYS A 355 ZN ZN A 502 1555 1555 2.28 LINK SG CYS A 360 ZN ZN A 502 1555 1555 2.26 LINK NE2 HIS A 373 ZN ZN A 502 1555 1555 2.05 LINK NE2 HIS A 377 ZN ZN A 502 1555 1555 2.03 LINK SG CYS A 385 ZN ZN A 503 1555 1555 2.31 LINK SG CYS A 388 ZN ZN A 503 1555 1555 2.28 LINK NE2 HIS A 401 ZN ZN A 503 1555 1555 2.07 LINK NE2 HIS A 405 ZN ZN A 503 1555 1555 2.03 LINK SG CYS A 413 ZN ZN A 504 1555 1555 2.25 LINK SG CYS A 418 ZN ZN A 504 1555 1555 2.31 LINK NE2 HIS A 431 ZN ZN A 504 1555 1555 2.03 LINK NE2 HIS A 435 ZN ZN A 504 1555 1555 2.04 SITE 1 AC1 6 ARG A 366 ASP A 368 HIS A 369 HOH A 639 SITE 2 AC1 6 DA B 9 DC C 3 SITE 1 AC2 4 CYS A 355 CYS A 360 HIS A 373 HIS A 377 SITE 1 AC3 4 CYS A 385 CYS A 388 HIS A 401 HIS A 405 SITE 1 AC4 4 CYS A 413 CYS A 418 HIS A 431 HIS A 435 CRYST1 75.223 66.069 35.646 90.00 91.75 90.00 C 1 2 1 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 0.013294 0.000000 0.000406 0.00000 SCALE2 0.000000 0.015136 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028067 0.00000