PDB Short entry for 3PEY HEADER HYDROLASE/RNA 27-OCT-10 3PEY TITLE S. CEREVISIAE DBP5 BOUND TO RNA AND ADP BEF3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT RNA HELICASE DBP5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEAD BOX PROTEIN 5, HELICASE CA5/6, RIBONUCLEIC ACID- COMPND 5 TRAFFICKING PROTEIN 8; COMPND 6 EC: 3.6.4.13; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: DBP5, RAT8, YOR046C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES KEYWDS RECA, DEAD-BOX, ATPASE, HELICASE, MRNA-EXPORT, NUCLEAR PORE, KEYWDS 2 HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.MONTPETIT,N.D.THOMSEN,K.J.HELMKE,M.A.SEELIGER,J.M.BERGER,K.WEIS REVDAT 4 21-FEB-24 3PEY 1 REMARK SEQADV LINK REVDAT 3 08-NOV-17 3PEY 1 REMARK REVDAT 2 27-APR-11 3PEY 1 JRNL REVDAT 1 23-MAR-11 3PEY 0 JRNL AUTH B.MONTPETIT,N.D.THOMSEN,K.J.HELMKE,M.A.SEELIGER,J.M.BERGER, JRNL AUTH 2 K.WEIS JRNL TITL A CONSERVED MECHANISM OF DEAD-BOX ATPASE ACTIVATION BY JRNL TITL 2 NUCLEOPORINS AND INSP(6) IN MRNA EXPORT. JRNL REF NATURE V. 472 238 2011 JRNL REFN ISSN 0028-0836 JRNL PMID 21441902 JRNL DOI 10.1038/NATURE09862 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.4_486 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 75947 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 3757 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 45.4905 - 4.2019 0.99 3045 160 0.1724 0.1826 REMARK 3 2 4.2019 - 3.3355 1.00 2949 157 0.1324 0.1392 REMARK 3 3 3.3355 - 2.9140 1.00 2892 149 0.1528 0.1633 REMARK 3 4 2.9140 - 2.6476 1.00 2868 156 0.1623 0.1771 REMARK 3 5 2.6476 - 2.4578 0.99 2859 149 0.1588 0.1795 REMARK 3 6 2.4578 - 2.3129 1.00 2853 152 0.1525 0.1604 REMARK 3 7 2.3129 - 2.1971 1.00 2849 148 0.1438 0.1790 REMARK 3 8 2.1971 - 2.1015 0.99 2825 143 0.1611 0.1952 REMARK 3 9 2.1015 - 2.0206 0.98 2790 152 0.1636 0.1642 REMARK 3 10 2.0206 - 1.9508 0.98 2787 155 0.1546 0.1792 REMARK 3 11 1.9508 - 1.8898 0.98 2782 143 0.1465 0.1734 REMARK 3 12 1.8898 - 1.8358 0.97 2735 151 0.1487 0.1833 REMARK 3 13 1.8358 - 1.7875 0.98 2767 143 0.1415 0.1514 REMARK 3 14 1.7875 - 1.7439 0.98 2763 146 0.1437 0.1802 REMARK 3 15 1.7439 - 1.7042 0.98 2775 143 0.1486 0.1884 REMARK 3 16 1.7042 - 1.6680 0.98 2753 144 0.1512 0.1862 REMARK 3 17 1.6680 - 1.6346 0.98 2753 139 0.1533 0.1764 REMARK 3 18 1.6346 - 1.6037 0.98 2768 143 0.1612 0.1954 REMARK 3 19 1.6037 - 1.5751 0.98 2763 147 0.1648 0.1910 REMARK 3 20 1.5751 - 1.5484 0.98 2728 148 0.1756 0.2263 REMARK 3 21 1.5484 - 1.5234 0.97 2743 145 0.1803 0.2356 REMARK 3 22 1.5234 - 1.5000 0.93 2609 131 0.2023 0.2718 REMARK 3 23 1.5000 - 1.4779 0.87 2473 121 0.2147 0.2263 REMARK 3 24 1.4779 - 1.4571 0.83 2336 116 0.2364 0.2580 REMARK 3 25 1.4571 - 1.4374 0.75 2110 105 0.2556 0.2684 REMARK 3 26 1.4374 - 1.4187 0.68 1907 93 0.2679 0.2798 REMARK 3 27 1.4187 - 1.4010 0.61 1708 78 0.2976 0.3405 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 36.23 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.45480 REMARK 3 B22 (A**2) : 4.83080 REMARK 3 B33 (A**2) : -2.37600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.016 3588 REMARK 3 ANGLE : 1.516 4894 REMARK 3 CHIRALITY : 0.094 570 REMARK 3 PLANARITY : 0.009 617 REMARK 3 DIHEDRAL : 15.638 1450 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESSEQ 90:295 REMARK 3 ORIGIN FOR THE GROUP (A): -3.4702 -9.0128 41.4606 REMARK 3 T TENSOR REMARK 3 T11: 0.0605 T22: 0.0546 REMARK 3 T33: 0.0554 T12: -0.0020 REMARK 3 T13: -0.0008 T23: 0.0149 REMARK 3 L TENSOR REMARK 3 L11: 0.3967 L22: 0.3722 REMARK 3 L33: 0.2696 L12: -0.0434 REMARK 3 L13: -0.2050 L23: -0.0116 REMARK 3 S TENSOR REMARK 3 S11: 0.0032 S12: -0.0844 S13: -0.0132 REMARK 3 S21: 0.0279 S22: -0.0081 S23: -0.0114 REMARK 3 S31: 0.0087 S32: 0.0067 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND RESSEQ 296:481 REMARK 3 ORIGIN FOR THE GROUP (A): -5.4034 -13.9884 13.3600 REMARK 3 T TENSOR REMARK 3 T11: 0.0622 T22: 0.0601 REMARK 3 T33: 0.0622 T12: -0.0117 REMARK 3 T13: 0.0071 T23: -0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.1415 L22: 0.4493 REMARK 3 L33: 0.6498 L12: -0.0485 REMARK 3 L13: -0.0474 L23: -0.1170 REMARK 3 S TENSOR REMARK 3 S11: -0.0229 S12: 0.0578 S13: -0.0179 REMARK 3 S21: -0.0441 S22: 0.0072 S23: -0.0234 REMARK 3 S31: 0.0196 S32: -0.0045 S33: -0.0050 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND RESSEQ 1000:1002 REMARK 3 ORIGIN FOR THE GROUP (A): 3.2363 -5.3798 29.1381 REMARK 3 T TENSOR REMARK 3 T11: 0.0880 T22: 0.0725 REMARK 3 T33: 0.1027 T12: -0.0005 REMARK 3 T13: 0.0037 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.0064 L22: 0.0036 REMARK 3 L33: 0.0009 L12: 0.0048 REMARK 3 L13: 0.0024 L23: 0.0018 REMARK 3 S TENSOR REMARK 3 S11: 0.0361 S12: -0.0148 S13: -0.0382 REMARK 3 S21: 0.0313 S22: 0.0376 S23: -0.0289 REMARK 3 S31: -0.0111 S32: -0.0366 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): -15.2172 -22.2870 29.5945 REMARK 3 T TENSOR REMARK 3 T11: 0.1226 T22: 0.1286 REMARK 3 T33: 0.1414 T12: -0.0239 REMARK 3 T13: 0.0142 T23: 0.0115 REMARK 3 L TENSOR REMARK 3 L11: 0.0123 L22: 0.0096 REMARK 3 L33: 0.0041 L12: 0.0102 REMARK 3 L13: -0.0006 L23: 0.0017 REMARK 3 S TENSOR REMARK 3 S11: -0.0554 S12: -0.0557 S13: -0.1113 REMARK 3 S21: 0.0466 S22: 0.0391 S23: 0.1135 REMARK 3 S31: 0.0993 S32: -0.2526 S33: 0.0000 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 3PEY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000062295. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.116 REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76028 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.43500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 200 MM MGNO3, 10 MM REMARK 280 HEPES PH 7.5, 100 MM NACL, 1MM DTT, 0.5 MM IP6, 5 MM MGCL2, 1 MM REMARK 280 ADP, 3 MM BECL2, 15 MM NAF, 5% GLYCEROL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 21.06800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.26200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.10300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.26200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.06800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.10300 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: 3570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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 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 88 REMARK 465 ALA A 89 REMARK 465 MET A 90 REMARK 465 ASP A 482 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 U B 6 C5' C4' O4' C3' O3' C2' O2' REMARK 470 U B 6 C1' N1 C2 O2 N3 C4 O4 REMARK 470 U B 6 C5 C6 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 ASN A 313 -179.61 -174.50 REMARK 500 ASP A 468 76.22 -154.47 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 MG A1003 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 264 OD1 REMARK 620 2 HOH A1117 O 92.8 REMARK 620 3 HOH A1125 O 77.3 99.0 REMARK 620 4 HOH A1148 O 172.0 83.3 96.5 REMARK 620 5 HOH A1320 O 90.9 175.7 84.0 93.3 REMARK 620 6 HOH A1356 O 108.5 84.1 173.4 78.0 92.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1003 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 264 OD1 REMARK 620 2 HOH A1117 O 83.0 REMARK 620 3 HOH A1125 O 91.8 173.3 REMARK 620 4 HOH A1147 O 93.1 96.9 87.7 REMARK 620 5 HOH A1228 O 94.3 86.7 89.4 172.1 REMARK 620 6 HOH A1234 O 174.0 91.5 93.8 85.0 87.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A1000 O2B REMARK 620 2 HOH A1010 O 96.6 REMARK 620 3 HOH A1095 O 91.6 85.2 REMARK 620 4 HOH A1096 O 176.8 85.9 86.5 REMARK 620 5 HOH A1481 O 89.4 174.0 94.5 88.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BEF A1002 BE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A1000 O1B REMARK 620 2 BEF A1002 F1 98.8 REMARK 620 3 BEF A1002 F2 103.3 117.1 REMARK 620 4 BEF A1002 F3 103.8 115.9 114.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1004 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1200 O REMARK 620 2 HOH A1215 O 165.6 REMARK 620 3 HOH A1349 O 101.5 81.9 REMARK 620 4 HOH A1403 O 93.9 100.2 88.6 REMARK 620 5 HOH A1477 O 81.2 84.5 96.7 173.4 REMARK 620 6 HOH A1483 O 96.9 81.6 160.9 84.9 91.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEF A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1008 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 B 1009 DBREF 3PEY A 91 482 UNP P20449 DBP5_YEAST 91 482 DBREF 3PEY B 1 6 PDB 3PEY 3PEY 1 6 SEQADV 3PEY GLY A 88 UNP P20449 EXPRESSION TAG SEQADV 3PEY ALA A 89 UNP P20449 EXPRESSION TAG SEQADV 3PEY MET A 90 UNP P20449 EXPRESSION TAG SEQRES 1 A 395 GLY ALA MET ALA LYS SER PHE ASP GLU LEU GLY LEU ALA SEQRES 2 A 395 PRO GLU LEU LEU LYS GLY ILE TYR ALA MET LYS PHE GLN SEQRES 3 A 395 LYS PRO SER LYS ILE GLN GLU ARG ALA LEU PRO LEU LEU SEQRES 4 A 395 LEU HIS ASN PRO PRO ARG ASN MET ILE ALA GLN SER GLN SEQRES 5 A 395 SER GLY THR GLY LYS THR ALA ALA PHE SER LEU THR MET SEQRES 6 A 395 LEU THR ARG VAL ASN PRO GLU ASP ALA SER PRO GLN ALA SEQRES 7 A 395 ILE CYS LEU ALA PRO SER ARG GLU LEU ALA ARG GLN THR SEQRES 8 A 395 LEU GLU VAL VAL GLN GLU MET GLY LYS PHE THR LYS ILE SEQRES 9 A 395 THR SER GLN LEU ILE VAL PRO ASP SER PHE GLU LYS ASN SEQRES 10 A 395 LYS GLN ILE ASN ALA GLN VAL ILE VAL GLY THR PRO GLY SEQRES 11 A 395 THR VAL LEU ASP LEU MET ARG ARG LYS LEU MET GLN LEU SEQRES 12 A 395 GLN LYS ILE LYS ILE PHE VAL LEU ASP GLU ALA ASP ASN SEQRES 13 A 395 MET LEU ASP GLN GLN GLY LEU GLY ASP GLN CYS ILE ARG SEQRES 14 A 395 VAL LYS ARG PHE LEU PRO LYS ASP THR GLN LEU VAL LEU SEQRES 15 A 395 PHE SER ALA THR PHE ALA ASP ALA VAL ARG GLN TYR ALA SEQRES 16 A 395 LYS LYS ILE VAL PRO ASN ALA ASN THR LEU GLU LEU GLN SEQRES 17 A 395 THR ASN GLU VAL ASN VAL ASP ALA ILE LYS GLN LEU TYR SEQRES 18 A 395 MET ASP CYS LYS ASN GLU ALA ASP LYS PHE ASP VAL LEU SEQRES 19 A 395 THR GLU LEU TYR GLY LEU MET THR ILE GLY SER SER ILE SEQRES 20 A 395 ILE PHE VAL ALA THR LYS LYS THR ALA ASN VAL LEU TYR SEQRES 21 A 395 GLY LYS LEU LYS SER GLU GLY HIS GLU VAL SER ILE LEU SEQRES 22 A 395 HIS GLY ASP LEU GLN THR GLN GLU ARG ASP ARG LEU ILE SEQRES 23 A 395 ASP ASP PHE ARG GLU GLY ARG SER LYS VAL LEU ILE THR SEQRES 24 A 395 THR ASN VAL LEU ALA ARG GLY ILE ASP ILE PRO THR VAL SEQRES 25 A 395 SER MET VAL VAL ASN TYR ASP LEU PRO THR LEU ALA ASN SEQRES 26 A 395 GLY GLN ALA ASP PRO ALA THR TYR ILE HIS ARG ILE GLY SEQRES 27 A 395 ARG THR GLY ARG PHE GLY ARG LYS GLY VAL ALA ILE SER SEQRES 28 A 395 PHE VAL HIS ASP LYS ASN SER PHE ASN ILE LEU SER ALA SEQRES 29 A 395 ILE GLN LYS TYR PHE GLY ASP ILE GLU MET THR ARG VAL SEQRES 30 A 395 PRO THR ASP ASP TRP ASP GLU VAL GLU LYS ILE VAL LYS SEQRES 31 A 395 LYS VAL LEU LYS ASP SEQRES 1 B 6 U U U U U U HET ADP A1000 27 HET MG A1001 1 HET BEF A1002 4 HET MG A1003 2 HET MG A1004 1 HET NO3 A1005 4 HET NO3 A1006 4 HET NO3 A1007 4 HET GOL A1008 6 HET NO3 B1009 4 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM BEF BERYLLIUM TRIFLUORIDE ION HETNAM NO3 NITRATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 MG 3(MG 2+) FORMUL 5 BEF BE F3 1- FORMUL 8 NO3 4(N O3 1-) FORMUL 11 GOL C3 H8 O3 FORMUL 13 HOH *493(H2 O) HELIX 1 1 ALA A 100 MET A 110 1 11 HELIX 2 2 SER A 116 HIS A 128 1 13 HELIX 3 3 GLY A 143 VAL A 156 1 14 HELIX 4 4 SER A 171 GLY A 186 1 16 HELIX 5 5 THR A 215 ARG A 225 1 11 HELIX 6 6 GLU A 240 GLN A 247 1 8 HELIX 7 7 GLY A 249 PHE A 260 1 12 HELIX 8 8 ALA A 275 VAL A 286 1 12 HELIX 9 9 GLN A 295 VAL A 299 5 5 HELIX 10 10 ASN A 313 GLY A 326 1 14 HELIX 11 11 THR A 339 GLU A 353 1 15 HELIX 12 12 GLN A 365 GLU A 378 1 14 HELIX 13 13 ASN A 388 ALA A 391 5 4 HELIX 14 14 ASP A 416 GLY A 425 1 10 HELIX 15 15 ASP A 442 PHE A 456 1 15 HELIX 16 16 ASP A 468 LYS A 481 1 14 SHEET 1 A 7 SER A 193 ILE A 196 0 SHEET 2 A 7 VAL A 211 GLY A 214 1 O VAL A 213 N ILE A 196 SHEET 3 A 7 ALA A 165 LEU A 168 1 N ALA A 165 O ILE A 212 SHEET 4 A 7 ILE A 235 ASP A 239 1 O VAL A 237 N ILE A 166 SHEET 5 A 7 GLN A 266 SER A 271 1 O GLN A 266 N PHE A 236 SHEET 6 A 7 MET A 134 GLN A 137 1 N ALA A 136 O LEU A 269 SHEET 7 A 7 ASN A 290 LEU A 292 1 O ASN A 290 N ILE A 135 SHEET 1 B 7 SER A 358 LEU A 360 0 SHEET 2 B 7 VAL A 383 THR A 386 1 O ILE A 385 N SER A 358 SHEET 3 B 7 SER A 332 PHE A 336 1 N ILE A 335 O LEU A 384 SHEET 4 B 7 VAL A 399 ASN A 404 1 O VAL A 403 N PHE A 336 SHEET 5 B 7 GLY A 434 VAL A 440 1 O ILE A 437 N ASN A 404 SHEET 6 B 7 ILE A 304 ASP A 310 1 N LYS A 305 O GLY A 434 SHEET 7 B 7 THR A 462 ARG A 463 1 O THR A 462 N GLN A 306 LINK OD1 ASP A 264 MG B MG A1003 1555 1555 1.95 LINK OD1 ASP A 264 MG A MG A1003 1555 1555 2.40 LINK O2B ADP A1000 MG MG A1001 1555 1555 2.03 LINK O1B ADP A1000 BE BEF A1002 1555 1555 1.84 LINK MG MG A1001 O HOH A1010 1555 1555 2.15 LINK MG MG A1001 O HOH A1095 1555 1555 2.08 LINK MG MG A1001 O HOH A1096 1555 1555 2.08 LINK MG MG A1001 O HOH A1481 1555 1555 2.09 LINK MG A MG A1003 O HOH A1117 1555 1555 1.93 LINK MG B MG A1003 O HOH A1117 1555 1555 2.05 LINK MG A MG A1003 O HOH A1125 1555 1555 1.80 LINK MG B MG A1003 O HOH A1125 1555 1555 2.81 LINK MG A MG A1003 O AHOH A1147 1555 1555 1.95 LINK MG B MG A1003 O BHOH A1148 1555 1555 2.10 LINK MG A MG A1003 O HOH A1228 1555 1555 2.01 LINK MG A MG A1003 O HOH A1234 1555 1555 2.12 LINK MG B MG A1003 O HOH A1320 1555 1555 2.33 LINK MG B MG A1003 O HOH A1356 1555 1555 2.15 LINK MG MG A1004 O HOH A1200 1555 1555 1.95 LINK MG MG A1004 O HOH A1215 1555 1555 1.98 LINK MG MG A1004 O HOH A1349 1555 1555 2.00 LINK MG MG A1004 O HOH A1403 1555 1555 1.91 LINK MG MG A1004 O HOH A1477 1555 1555 2.27 LINK MG MG A1004 O HOH A1483 1555 1555 2.15 CISPEP 1 ASN A 129 PRO A 130 0 -0.36 SITE 1 AC1 22 PHE A 112 LYS A 114 GLN A 119 GLY A 141 SITE 2 AC1 22 THR A 142 GLY A 143 LYS A 144 THR A 145 SITE 3 AC1 22 ASP A 395 ARG A 429 PHE A 430 MG A1001 SITE 4 AC1 22 BEF A1002 HOH A1025 HOH A1035 HOH A1058 SITE 5 AC1 22 HOH A1085 HOH A1094 HOH A1095 HOH A1119 SITE 6 AC1 22 HOH A1216 HOH A1481 SITE 1 AC2 6 ADP A1000 BEF A1002 HOH A1010 HOH A1095 SITE 2 AC2 6 HOH A1096 HOH A1481 SITE 1 AC3 13 SER A 140 LYS A 144 GLU A 240 GLY A 393 SITE 2 AC3 13 ARG A 426 ARG A 429 ADP A1000 MG A1001 SITE 3 AC3 13 HOH A1010 HOH A1012 HOH A1096 HOH A1168 SITE 4 AC3 13 HOH A1481 SITE 1 AC4 9 ASP A 264 HOH A1117 HOH A1125 HOH A1147 SITE 2 AC4 9 HOH A1148 HOH A1228 HOH A1234 HOH A1320 SITE 3 AC4 9 HOH A1356 SITE 1 AC5 6 HOH A1200 HOH A1215 HOH A1349 HOH A1403 SITE 2 AC5 6 HOH A1477 HOH A1483 SITE 1 AC6 6 LYS A 105 PHE A 188 ILE A 255 LYS A 258 SITE 2 AC6 6 ARG A 259 ILE A 285 SITE 1 AC7 6 ARG A 132 ASN A 288 ARG A 463 PRO A 465 SITE 2 AC7 6 HOH A1044 HOH A1334 SITE 1 AC8 6 LYS A 205 ASN A 208 ARG A 224 ARG A 256 SITE 2 AC8 6 HOH A1176 HOH A1278 SITE 1 AC9 9 THR A 189 LYS A 190 ILE A 191 ARG A 225 SITE 2 AC9 9 LYS A 226 HOH A1091 HOH A1143 HOH A1338 SITE 3 AC9 9 HOH A1392 SITE 1 BC1 3 GLN A 253 U B 4 U B 5 CRYST1 42.136 92.206 104.524 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.023733 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010845 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009567 0.00000