HEADER HYDROLASE/HYDROLASE INHIBITOR 23-OCT-15 5EFJ TITLE CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 6 CATALYTIC TITLE 2 DOMAIN 2 IN COMPLEX WITH HC TOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: HDAC6 PROTEIN; COMPND 3 CHAIN: D; COMPND 4 FRAGMENT: CATALYTIC DOMAIN 2 (UNP RESIDUES 288-646); COMPND 5 SYNONYM: HISTONE DEACETYLASE 6; COMPND 6 EC: 3.5.1.98; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HC TOXIN; COMPND 10 CHAIN: F; COMPND 11 SYNONYM: TOXIN I SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: HDAC6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: BIPOLARIS ZEICOLA; SOURCE 10 ORGANISM_COMMON: HELMINTHOSPORIUM CARBONUM; SOURCE 11 ORGANISM_TAXID: 5017 KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.HAI,D.W.CHRISTIANSON REVDAT 7 15-NOV-23 5EFJ 1 LINK ATOM REVDAT 6 27-SEP-23 5EFJ 1 LINK REVDAT 5 25-DEC-19 5EFJ 1 REMARK REVDAT 4 13-SEP-17 5EFJ 1 REMARK REVDAT 3 07-SEP-16 5EFJ 1 JRNL REVDAT 2 10-AUG-16 5EFJ 1 JRNL REVDAT 1 27-JUL-16 5EFJ 0 JRNL AUTH Y.HAI,D.W.CHRISTIANSON JRNL TITL HISTONE DEACETYLASE 6 STRUCTURE AND MOLECULAR BASIS OF JRNL TITL 2 CATALYSIS AND INHIBITION. JRNL REF NAT.CHEM.BIOL. V. 12 741 2016 JRNL REFN ESSN 1552-4469 JRNL PMID 27454933 JRNL DOI 10.1038/NCHEMBIO.2134 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.3_1479 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 42818 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 2163 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 47.0895 - 4.2541 1.00 2954 144 0.1638 0.1706 REMARK 3 2 4.2541 - 3.3769 1.00 2815 149 0.1356 0.1493 REMARK 3 3 3.3769 - 2.9501 1.00 2776 162 0.1487 0.1973 REMARK 3 4 2.9501 - 2.6804 1.00 2744 151 0.1494 0.1575 REMARK 3 5 2.6804 - 2.4883 1.00 2779 139 0.1477 0.1770 REMARK 3 6 2.4883 - 2.3416 1.00 2720 144 0.1465 0.1567 REMARK 3 7 2.3416 - 2.2243 1.00 2736 157 0.1387 0.1684 REMARK 3 8 2.2243 - 2.1275 1.00 2713 152 0.1379 0.1484 REMARK 3 9 2.1275 - 2.0456 1.00 2724 144 0.1458 0.1619 REMARK 3 10 2.0456 - 1.9750 0.99 2698 137 0.1471 0.1882 REMARK 3 11 1.9750 - 1.9133 1.00 2713 121 0.1459 0.1779 REMARK 3 12 1.9133 - 1.8586 0.99 2698 175 0.1570 0.1834 REMARK 3 13 1.8586 - 1.8096 0.99 2669 138 0.1719 0.2156 REMARK 3 14 1.8096 - 1.7655 0.96 2612 144 0.1982 0.2023 REMARK 3 15 1.7655 - 1.7254 0.85 2304 106 0.2327 0.2688 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.270 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 : 0.011 2952 REMARK 3 ANGLE : 1.308 3999 REMARK 3 CHIRALITY : 0.062 435 REMARK 3 PLANARITY : 0.007 521 REMARK 3 DIHEDRAL : 13.231 1081 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 442 THROUGH 466 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.7352 29.9363 -17.5920 REMARK 3 T TENSOR REMARK 3 T11: 0.1280 T22: 0.0809 REMARK 3 T33: 0.0534 T12: -0.0071 REMARK 3 T13: 0.0252 T23: 0.0240 REMARK 3 L TENSOR REMARK 3 L11: 3.8847 L22: 4.3109 REMARK 3 L33: 1.3560 L12: 2.5444 REMARK 3 L13: 0.3813 L23: 0.1141 REMARK 3 S TENSOR REMARK 3 S11: -0.2156 S12: 0.2970 S13: 0.1794 REMARK 3 S21: -0.2499 S22: 0.1435 S23: -0.0629 REMARK 3 S31: -0.1675 S32: 0.0598 S33: 0.0289 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 467 THROUGH 557 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.9665 33.1578 -12.2348 REMARK 3 T TENSOR REMARK 3 T11: 0.1011 T22: 0.0787 REMARK 3 T33: 0.1122 T12: 0.0112 REMARK 3 T13: -0.0144 T23: 0.0180 REMARK 3 L TENSOR REMARK 3 L11: 1.4100 L22: 1.1126 REMARK 3 L33: 0.8487 L12: 0.2122 REMARK 3 L13: 0.0999 L23: -0.0842 REMARK 3 S TENSOR REMARK 3 S11: -0.0416 S12: 0.0532 S13: 0.2847 REMARK 3 S21: -0.1012 S22: 0.0269 S23: 0.0473 REMARK 3 S31: -0.1564 S32: -0.0409 S33: 0.0008 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 558 THROUGH 656 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.6203 24.9182 1.5048 REMARK 3 T TENSOR REMARK 3 T11: 0.0717 T22: 0.0827 REMARK 3 T33: 0.0744 T12: 0.0052 REMARK 3 T13: 0.0059 T23: -0.0135 REMARK 3 L TENSOR REMARK 3 L11: 1.1959 L22: 0.6660 REMARK 3 L33: 1.2623 L12: -0.0129 REMARK 3 L13: 0.2481 L23: -0.3143 REMARK 3 S TENSOR REMARK 3 S11: 0.0006 S12: -0.1689 S13: 0.0668 REMARK 3 S21: 0.0705 S22: 0.0129 S23: 0.0179 REMARK 3 S31: -0.0964 S32: -0.1139 S33: -0.0120 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 657 THROUGH 684 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.5272 12.8045 5.6542 REMARK 3 T TENSOR REMARK 3 T11: 0.0747 T22: 0.0837 REMARK 3 T33: 0.0565 T12: -0.0094 REMARK 3 T13: -0.0183 T23: 0.0337 REMARK 3 L TENSOR REMARK 3 L11: 2.1821 L22: 2.5835 REMARK 3 L33: 2.7467 L12: -0.8195 REMARK 3 L13: -0.5294 L23: 0.9182 REMARK 3 S TENSOR REMARK 3 S11: 0.0052 S12: -0.1840 S13: -0.0570 REMARK 3 S21: 0.0788 S22: 0.0622 S23: -0.0880 REMARK 3 S31: 0.1917 S32: 0.0623 S33: -0.0346 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 685 THROUGH 746 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.5447 13.7927 -4.4011 REMARK 3 T TENSOR REMARK 3 T11: 0.0833 T22: 0.0707 REMARK 3 T33: 0.0676 T12: -0.0121 REMARK 3 T13: -0.0180 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 1.4542 L22: 1.0152 REMARK 3 L33: 1.4383 L12: 0.2580 REMARK 3 L13: -0.2569 L23: -0.2438 REMARK 3 S TENSOR REMARK 3 S11: 0.0125 S12: -0.0313 S13: -0.0776 REMARK 3 S21: -0.0271 S22: 0.0331 S23: 0.0130 REMARK 3 S31: 0.1451 S32: -0.0602 S33: -0.0286 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 747 THROUGH 776 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.1139 8.3044 -12.0532 REMARK 3 T TENSOR REMARK 3 T11: 0.1682 T22: 0.1057 REMARK 3 T33: 0.1469 T12: 0.0046 REMARK 3 T13: -0.0150 T23: -0.0162 REMARK 3 L TENSOR REMARK 3 L11: 0.0828 L22: 0.4559 REMARK 3 L33: 0.8329 L12: -0.1002 REMARK 3 L13: 0.0838 L23: -0.3419 REMARK 3 S TENSOR REMARK 3 S11: 0.0364 S12: 0.0435 S13: -0.3074 REMARK 3 S21: -0.0981 S22: 0.0059 S23: -0.1161 REMARK 3 S31: 0.2547 S32: 0.1302 S33: -0.0403 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 777 THROUGH 798 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.0838 9.7994 14.2810 REMARK 3 T TENSOR REMARK 3 T11: 0.1545 T22: 0.1334 REMARK 3 T33: 0.0803 T12: -0.0334 REMARK 3 T13: -0.0347 T23: 0.0490 REMARK 3 L TENSOR REMARK 3 L11: 3.8630 L22: 1.4335 REMARK 3 L33: 2.2365 L12: -0.9869 REMARK 3 L13: -0.6518 L23: 0.6397 REMARK 3 S TENSOR REMARK 3 S11: 0.0192 S12: -0.3481 S13: -0.3148 REMARK 3 S21: 0.1736 S22: -0.0243 S23: -0.0029 REMARK 3 S31: 0.3280 S32: -0.0753 S33: -0.0227 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 5EFJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00003 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42871 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 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 (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.15100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.44200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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: PDB ENTRY 5EEK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM NITRATE, 20% PEG3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 41.76500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.07200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.76500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.07200 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: 1980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, 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 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 N NO3 D2005 LIES ON A SPECIAL POSITION. REMARK 375 O1 NO3 D2005 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE HC TOXIN IS PEPTIDE-LIKE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: HC TOXIN REMARK 400 CHAIN: F REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 D 435 REMARK 465 ASN D 436 REMARK 465 ALA D 437 REMARK 465 GLY D 438 REMARK 465 GLY D 439 REMARK 465 SER D 440 REMARK 465 SER D 441 REMARK 465 ASP D 770 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 771 CG ND1 CD2 CE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O3 NO3 D 2006 O HOH D 2101 2.06 REMARK 500 O HOH D 2112 O HOH D 2195 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 5OM F 1 C DPR F 2 N 0.119 REMARK 500 DPR F 2 CD DPR F 2 N -0.190 REMARK 500 DPR F 2 CA DPR F 2 C -0.145 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 ASP D 460 89.02 -153.32 REMARK 500 THR D 600 -91.92 -131.53 REMARK 500 TYR D 637 -52.09 -128.40 REMARK 500 LEU D 685 -63.27 -126.33 REMARK 500 GLN D 716 33.90 -140.56 REMARK 500 GLU D 742 -112.43 -112.61 REMARK 500 LEU D 772 15.10 -62.85 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 K D2002 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP D 610 O REMARK 620 2 ASP D 610 OD1 70.4 REMARK 620 3 ASP D 612 O 99.1 94.8 REMARK 620 4 HIS D 614 O 162.8 92.9 77.6 REMARK 620 5 SER D 633 OG 85.9 111.5 153.3 104.8 REMARK 620 6 LEU D 634 O 79.3 143.3 69.7 114.5 85.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D2001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP D 612 OD1 REMARK 620 2 HIS D 614 ND1 106.0 REMARK 620 3 ASP D 705 OD2 113.1 100.6 REMARK 620 4 5OM F 1 O01 135.7 105.7 90.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K D2003 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE D 623 O REMARK 620 2 ASP D 626 O 77.0 REMARK 620 3 VAL D 629 O 119.3 77.8 REMARK 620 4 TYR D 662 O 155.1 118.3 84.6 REMARK 620 5 HOH D2179 O 82.5 88.8 150.1 78.5 REMARK 620 6 HOH D2219 O 70.3 146.7 123.8 90.8 81.2 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5EDU RELATED DB: PDB REMARK 900 RELATED ID: 5EEF RELATED DB: PDB REMARK 900 RELATED ID: 5EEI RELATED DB: PDB REMARK 900 RELATED ID: 5EEK RELATED DB: PDB REMARK 900 RELATED ID: 5EEM RELATED DB: PDB REMARK 900 RELATED ID: 5EEN RELATED DB: PDB REMARK 900 RELATED ID: 5EF7 RELATED DB: PDB REMARK 900 RELATED ID: 5EF8 RELATED DB: PDB REMARK 900 RELATED ID: 5EFB RELATED DB: PDB REMARK 900 RELATED ID: 5EFG RELATED DB: PDB REMARK 900 RELATED ID: 5EFH RELATED DB: PDB REMARK 900 RELATED ID: 5EFK RELATED DB: PDB REMARK 900 RELATED ID: 5EFN RELATED DB: PDB DBREF 5EFJ D 440 798 UNP A7YT55 A7YT55_DANRE 288 646 DBREF 5EFJ F 1 4 PDB 5EFJ 5EFJ 1 4 SEQADV 5EFJ SER D 435 UNP A7YT55 EXPRESSION TAG SEQADV 5EFJ ASN D 436 UNP A7YT55 EXPRESSION TAG SEQADV 5EFJ ALA D 437 UNP A7YT55 EXPRESSION TAG SEQADV 5EFJ GLY D 438 UNP A7YT55 EXPRESSION TAG SEQADV 5EFJ GLY D 439 UNP A7YT55 EXPRESSION TAG SEQRES 1 D 364 SER ASN ALA GLY GLY SER SER PRO ILE THR GLY LEU VAL SEQRES 2 D 364 TYR ASP GLN ARG MET MET LEU HIS HIS ASN MET TRP ASP SEQRES 3 D 364 SER HIS HIS PRO GLU LEU PRO GLN ARG ILE SER ARG ILE SEQRES 4 D 364 PHE SER ARG HIS GLU GLU LEU ARG LEU LEU SER ARG CYS SEQRES 5 D 364 HIS ARG ILE PRO ALA ARG LEU ALA THR GLU GLU GLU LEU SEQRES 6 D 364 ALA LEU CYS HIS SER SER LYS HIS ILE SER ILE ILE LYS SEQRES 7 D 364 SER SER GLU HIS MET LYS PRO ARG ASP LEU ASN ARG LEU SEQRES 8 D 364 GLY ASP GLU TYR ASN SER ILE PHE ILE SER ASN GLU SER SEQRES 9 D 364 TYR THR CYS ALA LEU LEU ALA ALA GLY SER CYS PHE ASN SEQRES 10 D 364 SER ALA GLN ALA ILE LEU THR GLY GLN VAL ARG ASN ALA SEQRES 11 D 364 VAL ALA ILE VAL ARG PRO PRO GLY HIS HIS ALA GLU LYS SEQRES 12 D 364 ASP THR ALA CYS GLY PHE CYS PHE PHE ASN THR ALA ALA SEQRES 13 D 364 LEU THR ALA ARG TYR ALA GLN SER ILE THR ARG GLU SER SEQRES 14 D 364 LEU ARG VAL LEU ILE VAL ASP TRP ASP VAL HIS HIS GLY SEQRES 15 D 364 ASN GLY THR GLN HIS ILE PHE GLU GLU ASP ASP SER VAL SEQRES 16 D 364 LEU TYR ILE SER LEU HIS ARG TYR GLU ASP GLY ALA PHE SEQRES 17 D 364 PHE PRO ASN SER GLU ASP ALA ASN TYR ASP LYS VAL GLY SEQRES 18 D 364 LEU GLY LYS GLY ARG GLY TYR ASN VAL ASN ILE PRO TRP SEQRES 19 D 364 ASN GLY GLY LYS MET GLY ASP PRO GLU TYR MET ALA ALA SEQRES 20 D 364 PHE HIS HIS LEU VAL MET PRO ILE ALA ARG GLU PHE ALA SEQRES 21 D 364 PRO GLU LEU VAL LEU VAL SER ALA GLY PHE ASP ALA ALA SEQRES 22 D 364 ARG GLY ASP PRO LEU GLY GLY PHE GLN VAL THR PRO GLU SEQRES 23 D 364 GLY TYR ALA HIS LEU THR HIS GLN LEU MET SER LEU ALA SEQRES 24 D 364 ALA GLY ARG VAL LEU ILE ILE LEU GLU GLY GLY TYR ASN SEQRES 25 D 364 LEU THR SER ILE SER GLU SER MET SER MET CYS THR SER SEQRES 26 D 364 MET LEU LEU GLY ASP SER PRO PRO SER LEU ASP HIS LEU SEQRES 27 D 364 THR PRO LEU LYS THR SER ALA THR VAL SER ILE ASN ASN SEQRES 28 D 364 VAL LEU ARG ALA HIS ALA PRO PHE TRP SER SER LEU ARG SEQRES 1 F 4 5OM DPR ALA DAL HET 5OM F 1 15 HET DPR F 2 7 HET DAL F 4 5 HET ZN D2001 1 HET K D2002 1 HET K D2003 1 HET GOL D2004 6 HET NO3 D2005 4 HET NO3 D2006 4 HET EDO D2007 4 HET EDO D2008 4 HET EDO D2009 4 HETNAM 5OM (2S)-2-AMINO-8,8-DIHYDROXY-8-[(2S)-OXIRAN-2-YL]OCTANOIC HETNAM 2 5OM ACID HETNAM DPR D-PROLINE HETNAM DAL D-ALANINE HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM GOL GLYCEROL HETNAM NO3 NITRATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 5OM C10 H19 N O5 FORMUL 2 DPR C5 H9 N O2 FORMUL 2 DAL C3 H7 N O2 FORMUL 3 ZN ZN 2+ FORMUL 4 K 2(K 1+) FORMUL 6 GOL C3 H8 O3 FORMUL 7 NO3 2(N O3 1-) FORMUL 9 EDO 3(C2 H6 O2) FORMUL 12 HOH *293(H2 O) HELIX 1 AA1 GLN D 450 HIS D 455 5 6 HELIX 2 AA2 PRO D 467 LEU D 480 1 14 HELIX 3 AA3 LEU D 482 CYS D 486 5 5 HELIX 4 AA4 THR D 495 ALA D 500 1 6 HELIX 5 AA5 SER D 504 SER D 514 1 11 HELIX 6 AA6 GLU D 515 MET D 517 5 3 HELIX 7 AA7 LYS D 518 GLU D 528 1 11 HELIX 8 AA8 GLU D 537 THR D 558 1 22 HELIX 9 AA9 ASN D 587 ILE D 599 1 13 HELIX 10 AB1 GLY D 616 PHE D 623 1 8 HELIX 11 AB2 GLU D 638 ALA D 641 5 4 HELIX 12 AB3 SER D 646 ASN D 650 5 5 HELIX 13 AB4 LEU D 656 ARG D 660 5 5 HELIX 14 AB5 GLY D 674 LEU D 685 1 12 HELIX 15 AB6 LEU D 685 ALA D 694 1 10 HELIX 16 AB7 THR D 718 MET D 730 1 13 HELIX 17 AB8 SER D 731 GLY D 735 5 5 HELIX 18 AB9 ASN D 746 LEU D 762 1 17 HELIX 19 AC1 LYS D 776 ALA D 791 1 16 HELIX 20 AC2 TRP D 794 ARG D 798 5 5 SHEET 1 AA1 8 HIS D 487 ARG D 488 0 SHEET 2 AA1 8 THR D 444 TYR D 448 1 N THR D 444 O HIS D 487 SHEET 3 AA1 8 ASN D 563 ILE D 567 1 O ASN D 563 N GLY D 445 SHEET 4 AA1 8 VAL D 737 LEU D 741 1 O ILE D 739 N ALA D 566 SHEET 5 AA1 8 LEU D 697 ALA D 702 1 N VAL D 700 O LEU D 738 SHEET 6 AA1 8 VAL D 606 ASP D 610 1 N LEU D 607 O LEU D 699 SHEET 7 AA1 8 VAL D 629 ARG D 636 1 O ILE D 632 N ASP D 610 SHEET 8 AA1 8 ASN D 663 TRP D 668 1 O VAL D 664 N TYR D 631 LINK C 5OM F 1 N DPR F 2 1555 1555 1.46 LINK N 5OM F 1 C DAL F 4 1555 1555 1.43 LINK C DPR F 2 N ALA F 3 1555 1555 1.45 LINK C ALA F 3 N DAL F 4 1555 1555 1.44 LINK O ASP D 610 K K D2002 1555 1555 2.78 LINK OD1 ASP D 610 K K D2002 1555 1555 2.73 LINK OD1 ASP D 612 ZN ZN D2001 1555 1555 2.02 LINK O ASP D 612 K K D2002 1555 1555 2.59 LINK ND1 HIS D 614 ZN ZN D2001 1555 1555 2.08 LINK O HIS D 614 K K D2002 1555 1555 2.74 LINK O PHE D 623 K K D2003 1555 1555 2.68 LINK O ASP D 626 K K D2003 1555 1555 2.94 LINK O VAL D 629 K K D2003 1555 1555 2.67 LINK OG SER D 633 K K D2002 1555 1555 2.70 LINK O LEU D 634 K K D2002 1555 1555 2.67 LINK O TYR D 662 K K D2003 1555 1555 2.79 LINK OD2 ASP D 705 ZN ZN D2001 1555 1555 1.96 LINK ZN ZN D2001 O01 5OM F 1 1555 1555 2.00 LINK K K D2003 O HOH D2179 1555 1555 2.60 LINK K K D2003 O HOH D2219 1555 1555 2.94 CISPEP 1 ARG D 569 PRO D 570 0 -3.30 CISPEP 2 PHE D 643 PRO D 644 0 8.18 CISPEP 3 ALA F 3 DAL F 4 0 0.32 CRYST1 83.530 94.144 51.476 90.00 90.00 90.00 P 21 21 2 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 0.011972 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010622 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019427 0.00000