HEADER RNA BINDING PROTEIN 02-SEP-21 7PMM TITLE DEAD-BOX HELICASE DBPA IN THE ACTIVE CONFORMATION BOUND TO A SS/DSRNA TITLE 2 JUNCTION AND ADP/BEF3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT RNA HELICASE DBPA; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.6.4.13; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (45MER) CONTAINING HP92 OF THE 23S RRNA; COMPND 8 CHAIN: C, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: DBPA, B1343, JW1337; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS DEAD-BOX HELICASE, RNA, RIBOSOME BIOGENESIS, ATPASE, RNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.P.WURM REVDAT 3 01-MAY-24 7PMM 1 REMARK REVDAT 2 20-SEP-23 7PMM 1 JRNL REVDAT 1 14-SEP-22 7PMM 0 JRNL AUTH J.P.WURM JRNL TITL STRUCTURAL BASIS FOR RNA-DUPLEX UNWINDING BY THE DEAD-BOX JRNL TITL 2 HELICASE DBPA. JRNL REF RNA V. 29 1339 2023 JRNL REFN ESSN 1469-9001 JRNL PMID 37221012 JRNL DOI 10.1261/RNA.079582.123 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874+SVN 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 33285 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1664 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 48.3900 - 6.8600 1.00 2827 148 0.1723 0.1996 REMARK 3 2 6.8600 - 5.4500 1.00 2699 143 0.2248 0.2265 REMARK 3 3 5.4500 - 4.7600 1.00 2653 139 0.1828 0.2020 REMARK 3 4 4.7600 - 4.3300 1.00 2629 139 0.1617 0.1994 REMARK 3 5 4.3300 - 4.0200 1.00 2627 138 0.1858 0.1871 REMARK 3 6 4.0200 - 3.7800 1.00 2622 138 0.2004 0.2519 REMARK 3 7 3.7800 - 3.5900 1.00 2604 137 0.2142 0.2713 REMARK 3 8 3.5900 - 3.4300 1.00 2602 137 0.2277 0.2853 REMARK 3 9 3.4300 - 3.3000 1.00 2587 136 0.2349 0.2785 REMARK 3 10 3.3000 - 3.1900 1.00 2585 136 0.2490 0.2673 REMARK 3 11 3.1900 - 3.0900 1.00 2587 136 0.2731 0.3273 REMARK 3 12 3.0900 - 3.0000 1.00 2599 137 0.2953 0.3335 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) : 0.403 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.583 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 95.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 116.8 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 8992 REMARK 3 ANGLE : 0.767 12612 REMARK 3 CHIRALITY : 0.053 1546 REMARK 3 PLANARITY : 0.004 1306 REMARK 3 DIHEDRAL : 17.098 3581 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 0 THROUGH 44) REMARK 3 ORIGIN FOR THE GROUP (A): 43.7918 -63.6899 25.6395 REMARK 3 T TENSOR REMARK 3 T11: 1.8966 T22: 1.4978 REMARK 3 T33: 1.2654 T12: 0.2527 REMARK 3 T13: 0.0638 T23: 0.0550 REMARK 3 L TENSOR REMARK 3 L11: 4.0346 L22: 2.2869 REMARK 3 L33: -0.7913 L12: -4.4773 REMARK 3 L13: 0.9590 L23: 0.2855 REMARK 3 S TENSOR REMARK 3 S11: 0.0494 S12: 1.6403 S13: 0.6891 REMARK 3 S21: -0.1923 S22: -0.6568 S23: -0.3698 REMARK 3 S31: -1.1076 S32: -0.0300 S33: 0.6744 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 0 THROUGH 44) REMARK 3 ORIGIN FOR THE GROUP (A): 26.9499 -73.4533 55.2488 REMARK 3 T TENSOR REMARK 3 T11: 1.4861 T22: 1.3518 REMARK 3 T33: 1.3753 T12: 0.3819 REMARK 3 T13: 0.1517 T23: 0.2049 REMARK 3 L TENSOR REMARK 3 L11: 0.9140 L22: 4.1103 REMARK 3 L33: -0.4206 L12: -2.1862 REMARK 3 L13: -1.2036 L23: 0.7274 REMARK 3 S TENSOR REMARK 3 S11: -0.4877 S12: 0.1025 S13: -0.0995 REMARK 3 S21: 1.5116 S22: 0.2383 S23: 0.1342 REMARK 3 S31: -0.0125 S32: -0.3508 S33: 0.3572 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 1 THROUGH 457) REMARK 3 ORIGIN FOR THE GROUP (A): 59.2989 -89.8031 37.0687 REMARK 3 T TENSOR REMARK 3 T11: 0.7027 T22: 0.5338 REMARK 3 T33: 0.6883 T12: -0.0993 REMARK 3 T13: -0.1037 T23: 0.0254 REMARK 3 L TENSOR REMARK 3 L11: 1.1059 L22: 1.3110 REMARK 3 L33: 2.8012 L12: -0.1887 REMARK 3 L13: -0.3895 L23: -0.0069 REMARK 3 S TENSOR REMARK 3 S11: -0.1321 S12: 0.0910 S13: 0.0322 REMARK 3 S21: -0.0693 S22: 0.0676 S23: 0.1389 REMARK 3 S31: -0.5565 S32: -0.2447 S33: 0.0570 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 0 THROUGH 456) REMARK 3 ORIGIN FOR THE GROUP (A): 10.9023 -47.2066 45.9287 REMARK 3 T TENSOR REMARK 3 T11: 1.0576 T22: 0.7038 REMARK 3 T33: 0.8754 T12: 0.2197 REMARK 3 T13: -0.0233 T23: 0.0299 REMARK 3 L TENSOR REMARK 3 L11: 2.1629 L22: 1.6903 REMARK 3 L33: 1.7998 L12: 0.3588 REMARK 3 L13: -0.3344 L23: 0.1862 REMARK 3 S TENSOR REMARK 3 S11: 0.0634 S12: 0.1675 S13: -0.4651 REMARK 3 S21: -0.2692 S22: -0.0707 S23: 0.1911 REMARK 3 S31: 0.5461 S32: -0.1253 S33: -0.0247 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 7PMM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1292117019. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33298 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 48.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 36.15 REMARK 200 R MERGE (I) : 0.12080 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.3400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.04300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.110 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.18.2_3874+SVN REMARK 200 STARTING MODEL: PDB DEPOSITION D_1292103740 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M DI-SODIUM TARTATE, 20 %(W/V) PEG REMARK 280 3350, PH 7.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 84.84500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 84.84500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.99500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 84.84500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 84.84500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.99500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 84.84500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 84.84500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 55.99500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 84.84500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 84.84500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 55.99500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 47600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -117.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 -1 REMARK 465 GLY A 0 REMARK 465 GLY B -1 REMARK 465 GLY B 402 REMARK 465 ALA B 403 REMARK 465 LEU B 404 REMARK 465 THR B 405 REMARK 465 GLY B 406 REMARK 465 ASP B 407 REMARK 465 ILE B 408 REMARK 465 GLY B 409 REMARK 465 LEU B 410 REMARK 465 ASP B 411 REMARK 465 ALA B 432 REMARK 465 VAL B 433 REMARK 465 ALA B 434 REMARK 465 HIS B 435 REMARK 465 LYS B 436 REMARK 465 GLY B 443 REMARK 465 GLY B 444 REMARK 465 LYS B 445 REMARK 465 LYS B 457 REMARK 465 U C 16 REMARK 465 C C 34 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 C 22 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U C 22 C6 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 G D 1 OP1 - P - OP2 ANGL. DEV. = -12.0 DEGREES REMARK 500 G D 1 O5' - P - OP1 ANGL. DEV. = -7.1 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 ASP A 201 76.54 50.83 REMARK 500 GLU A 206 79.00 -107.09 REMARK 500 PRO A 215 76.52 -65.79 REMARK 500 VAL B 9 -38.38 -131.81 REMARK 500 PHE B 70 57.56 -92.47 REMARK 500 ALA B 146 33.74 -98.88 REMARK 500 TRP B 187 82.38 -153.33 REMARK 500 PRO B 215 83.67 -65.57 REMARK 500 PRO B 370 -70.19 -68.70 REMARK 500 ASN B 372 49.51 -146.17 REMARK 500 SER B 374 87.52 57.14 REMARK 500 ALA B 413 -3.79 67.29 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 BEF A 501 BE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A 500 O1B REMARK 620 2 BEF A 501 F1 104.3 REMARK 620 3 BEF A 501 F2 104.2 115.8 REMARK 620 4 BEF A 501 F3 104.5 114.0 112.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A 500 O3B REMARK 620 2 HOH A 601 O 90.0 REMARK 620 3 HOH A 602 O 89.0 90.1 REMARK 620 4 HOH A 603 O 177.9 90.0 88.9 REMARK 620 5 HOH A 604 O 90.0 179.9 90.0 90.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BEF B 501 BE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP B 500 O2B REMARK 620 2 BEF B 501 F1 104.5 REMARK 620 3 BEF B 501 F2 104.8 117.0 REMARK 620 4 BEF B 501 F3 104.3 113.9 110.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP B 500 O3B REMARK 620 2 HOH B 601 O 89.7 REMARK 620 3 HOH B 602 O 179.3 89.6 REMARK 620 4 HOH B 603 O 90.0 90.0 89.9 REMARK 620 5 HOH B 604 O 90.1 90.0 90.0 179.9 REMARK 620 N 1 2 3 4 DBREF 7PMM A 1 457 UNP P21693 DBPA_ECOLI 1 457 DBREF 7PMM B 1 457 UNP P21693 DBPA_ECOLI 1 457 DBREF 7PMM C 1 44 PDB 7PMM 7PMM 1 44 DBREF 7PMM D 1 44 PDB 7PMM 7PMM 1 44 SEQADV 7PMM GLY A -1 UNP P21693 EXPRESSION TAG SEQADV 7PMM GLY A 0 UNP P21693 EXPRESSION TAG SEQADV 7PMM GLY B -1 UNP P21693 EXPRESSION TAG SEQADV 7PMM GLY B 0 UNP P21693 EXPRESSION TAG SEQRES 1 A 459 GLY GLY MET THR ALA PHE SER THR LEU ASN VAL LEU PRO SEQRES 2 A 459 PRO ALA GLN LEU THR ASN LEU ASN GLU LEU GLY TYR LEU SEQRES 3 A 459 THR MET THR PRO VAL GLN ALA ALA ALA LEU PRO ALA ILE SEQRES 4 A 459 LEU ALA GLY LYS ASP VAL ARG VAL GLN ALA LYS THR GLY SEQRES 5 A 459 SER GLY LYS THR ALA ALA PHE GLY LEU GLY LEU LEU GLN SEQRES 6 A 459 GLN ILE ASP ALA SER LEU PHE GLN THR GLN ALA LEU VAL SEQRES 7 A 459 LEU CYS PRO THR ARG GLU LEU ALA ASP GLN VAL ALA GLY SEQRES 8 A 459 GLU LEU ARG ARG LEU ALA ARG PHE LEU PRO ASN THR LYS SEQRES 9 A 459 ILE LEU THR LEU CYS GLY GLY GLN PRO PHE GLY MET GLN SEQRES 10 A 459 ARG ASP SER LEU GLN HIS ALA PRO HIS ILE ILE VAL ALA SEQRES 11 A 459 THR PRO GLY ARG LEU LEU ASP HIS LEU GLN LYS GLY THR SEQRES 12 A 459 VAL SER LEU ASP ALA LEU ASN THR LEU VAL MET ASP GLU SEQRES 13 A 459 ALA ASP ARG MET LEU ASP MET GLY PHE SER ASP ALA ILE SEQRES 14 A 459 ASP ASP VAL ILE ARG PHE ALA PRO ALA SER ARG GLN THR SEQRES 15 A 459 LEU LEU PHE SER ALA THR TRP PRO GLU ALA ILE ALA ALA SEQRES 16 A 459 ILE SER GLY ARG VAL GLN ARG ASP PRO LEU ALA ILE GLU SEQRES 17 A 459 ILE ASP SER THR ASP ALA LEU PRO PRO ILE GLU GLN GLN SEQRES 18 A 459 PHE TYR GLU THR SER SER LYS GLY LYS ILE PRO LEU LEU SEQRES 19 A 459 GLN ARG LEU LEU SER LEU HIS GLN PRO SER SER CYS VAL SEQRES 20 A 459 VAL PHE CYS ASN THR LYS LYS ASP CYS GLN ALA VAL CYS SEQRES 21 A 459 ASP ALA LEU ASN GLU VAL GLY GLN SER ALA LEU SER LEU SEQRES 22 A 459 HIS GLY ASP LEU GLU GLN ARG ASP ARG ASP GLN THR LEU SEQRES 23 A 459 VAL ARG PHE ALA ASN GLY SER ALA ARG VAL LEU VAL ALA SEQRES 24 A 459 THR ASP VAL ALA ALA ARG GLY LEU ASP ILE LYS SER LEU SEQRES 25 A 459 GLU LEU VAL VAL ASN PHE GLU LEU ALA TRP ASP PRO GLU SEQRES 26 A 459 VAL HIS VAL HIS ARG ILE GLY ARG THR ALA ARG ALA GLY SEQRES 27 A 459 ASN SER GLY LEU ALA ILE SER PHE CYS ALA PRO GLU GLU SEQRES 28 A 459 ALA GLN ARG ALA ASN ILE ILE SER ASP MET LEU GLN ILE SEQRES 29 A 459 LYS LEU ASN TRP GLN THR PRO PRO ALA ASN SER SER ILE SEQRES 30 A 459 ALA THR LEU GLU ALA GLU MET ALA THR LEU CYS ILE ASP SEQRES 31 A 459 GLY GLY LYS LYS ALA LYS MET ARG PRO GLY ASP VAL LEU SEQRES 32 A 459 GLY ALA LEU THR GLY ASP ILE GLY LEU ASP GLY ALA ASP SEQRES 33 A 459 ILE GLY LYS ILE ALA VAL HIS PRO ALA HIS VAL TYR VAL SEQRES 34 A 459 ALA VAL ARG GLN ALA VAL ALA HIS LYS ALA TRP LYS GLN SEQRES 35 A 459 LEU GLN GLY GLY LYS ILE LYS GLY LYS THR CYS ARG VAL SEQRES 36 A 459 ARG LEU LEU LYS SEQRES 1 B 459 GLY GLY MET THR ALA PHE SER THR LEU ASN VAL LEU PRO SEQRES 2 B 459 PRO ALA GLN LEU THR ASN LEU ASN GLU LEU GLY TYR LEU SEQRES 3 B 459 THR MET THR PRO VAL GLN ALA ALA ALA LEU PRO ALA ILE SEQRES 4 B 459 LEU ALA GLY LYS ASP VAL ARG VAL GLN ALA LYS THR GLY SEQRES 5 B 459 SER GLY LYS THR ALA ALA PHE GLY LEU GLY LEU LEU GLN SEQRES 6 B 459 GLN ILE ASP ALA SER LEU PHE GLN THR GLN ALA LEU VAL SEQRES 7 B 459 LEU CYS PRO THR ARG GLU LEU ALA ASP GLN VAL ALA GLY SEQRES 8 B 459 GLU LEU ARG ARG LEU ALA ARG PHE LEU PRO ASN THR LYS SEQRES 9 B 459 ILE LEU THR LEU CYS GLY GLY GLN PRO PHE GLY MET GLN SEQRES 10 B 459 ARG ASP SER LEU GLN HIS ALA PRO HIS ILE ILE VAL ALA SEQRES 11 B 459 THR PRO GLY ARG LEU LEU ASP HIS LEU GLN LYS GLY THR SEQRES 12 B 459 VAL SER LEU ASP ALA LEU ASN THR LEU VAL MET ASP GLU SEQRES 13 B 459 ALA ASP ARG MET LEU ASP MET GLY PHE SER ASP ALA ILE SEQRES 14 B 459 ASP ASP VAL ILE ARG PHE ALA PRO ALA SER ARG GLN THR SEQRES 15 B 459 LEU LEU PHE SER ALA THR TRP PRO GLU ALA ILE ALA ALA SEQRES 16 B 459 ILE SER GLY ARG VAL GLN ARG ASP PRO LEU ALA ILE GLU SEQRES 17 B 459 ILE ASP SER THR ASP ALA LEU PRO PRO ILE GLU GLN GLN SEQRES 18 B 459 PHE TYR GLU THR SER SER LYS GLY LYS ILE PRO LEU LEU SEQRES 19 B 459 GLN ARG LEU LEU SER LEU HIS GLN PRO SER SER CYS VAL SEQRES 20 B 459 VAL PHE CYS ASN THR LYS LYS ASP CYS GLN ALA VAL CYS SEQRES 21 B 459 ASP ALA LEU ASN GLU VAL GLY GLN SER ALA LEU SER LEU SEQRES 22 B 459 HIS GLY ASP LEU GLU GLN ARG ASP ARG ASP GLN THR LEU SEQRES 23 B 459 VAL ARG PHE ALA ASN GLY SER ALA ARG VAL LEU VAL ALA SEQRES 24 B 459 THR ASP VAL ALA ALA ARG GLY LEU ASP ILE LYS SER LEU SEQRES 25 B 459 GLU LEU VAL VAL ASN PHE GLU LEU ALA TRP ASP PRO GLU SEQRES 26 B 459 VAL HIS VAL HIS ARG ILE GLY ARG THR ALA ARG ALA GLY SEQRES 27 B 459 ASN SER GLY LEU ALA ILE SER PHE CYS ALA PRO GLU GLU SEQRES 28 B 459 ALA GLN ARG ALA ASN ILE ILE SER ASP MET LEU GLN ILE SEQRES 29 B 459 LYS LEU ASN TRP GLN THR PRO PRO ALA ASN SER SER ILE SEQRES 30 B 459 ALA THR LEU GLU ALA GLU MET ALA THR LEU CYS ILE ASP SEQRES 31 B 459 GLY GLY LYS LYS ALA LYS MET ARG PRO GLY ASP VAL LEU SEQRES 32 B 459 GLY ALA LEU THR GLY ASP ILE GLY LEU ASP GLY ALA ASP SEQRES 33 B 459 ILE GLY LYS ILE ALA VAL HIS PRO ALA HIS VAL TYR VAL SEQRES 34 B 459 ALA VAL ARG GLN ALA VAL ALA HIS LYS ALA TRP LYS GLN SEQRES 35 B 459 LEU GLN GLY GLY LYS ILE LYS GLY LYS THR CYS ARG VAL SEQRES 36 B 459 ARG LEU LEU LYS SEQRES 1 C 44 G G G A A C C C U U C C C SEQRES 2 C 44 A A U A U G G C U G U U C SEQRES 3 C 44 G C C A U U U C G G G A A SEQRES 4 C 44 G G G U U SEQRES 1 D 44 G G G A A C C C U U C C C SEQRES 2 D 44 A A U A U G G C U G U U C SEQRES 3 D 44 G C C A U U U C G G G A A SEQRES 4 D 44 G G G U U HET ADP A 500 27 HET BEF A 501 4 HET MG A 502 1 HET ADP B 500 27 HET BEF B 501 4 HET MG B 502 1 HET POP C 101 9 HET PO4 D 101 5 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM BEF BERYLLIUM TRIFLUORIDE ION HETNAM MG MAGNESIUM ION HETNAM POP PYROPHOSPHATE 2- HETNAM PO4 PHOSPHATE ION FORMUL 5 ADP 2(C10 H15 N5 O10 P2) FORMUL 6 BEF 2(BE F3 1-) FORMUL 7 MG 2(MG 2+) FORMUL 11 POP H2 O7 P2 2- FORMUL 12 PO4 O4 P 3- FORMUL 13 HOH *8(H2 O) HELIX 1 AA1 THR A 2 ASN A 8 5 7 HELIX 2 AA2 PRO A 11 GLY A 22 1 12 HELIX 3 AA3 THR A 27 ALA A 39 1 13 HELIX 4 AA4 GLY A 52 GLN A 64 1 13 HELIX 5 AA5 THR A 80 ALA A 95 1 16 HELIX 6 AA6 PRO A 111 LEU A 119 1 9 HELIX 7 AA7 THR A 129 LYS A 139 1 11 HELIX 8 AA8 GLU A 154 LEU A 159 1 6 HELIX 9 AA9 PHE A 163 ALA A 174 1 12 HELIX 10 AB1 PRO A 188 SER A 195 1 8 HELIX 11 AB2 GLY A 196 GLN A 199 5 4 HELIX 12 AB3 GLY A 227 GLN A 240 1 14 HELIX 13 AB4 THR A 250 VAL A 264 1 15 HELIX 14 AB5 GLU A 276 GLY A 290 1 15 HELIX 15 AB6 ASP A 299 ALA A 302 5 4 HELIX 16 AB7 ASP A 321 GLY A 330 1 10 HELIX 17 AB8 ALA A 346 GLU A 348 5 3 HELIX 18 AB9 GLU A 349 GLN A 361 1 13 HELIX 19 AC1 GLY A 390 LYS A 394 5 5 HELIX 20 AC2 ARG A 396 GLY A 406 1 11 HELIX 21 AC3 ASP A 411 ALA A 413 5 3 HELIX 22 AC4 VAL A 433 GLY A 444 1 12 HELIX 23 AC5 ALA B 3 ASN B 8 5 6 HELIX 24 AC6 PRO B 11 LEU B 21 1 11 HELIX 25 AC7 THR B 27 ALA B 39 1 13 HELIX 26 AC8 GLY B 52 GLN B 63 1 12 HELIX 27 AC9 THR B 80 ALA B 95 1 16 HELIX 28 AD1 ARG B 96 LEU B 98 5 3 HELIX 29 AD2 PRO B 111 LEU B 119 1 9 HELIX 30 AD3 THR B 129 LYS B 139 1 11 HELIX 31 AD4 GLU B 154 LEU B 159 1 6 HELIX 32 AD5 ASP B 160 ARG B 172 1 13 HELIX 33 AD6 PRO B 188 SER B 195 1 8 HELIX 34 AD7 GLY B 196 VAL B 198 5 3 HELIX 35 AD8 GLY B 227 GLN B 240 1 14 HELIX 36 AD9 THR B 250 VAL B 264 1 15 HELIX 37 AE1 GLU B 276 ASN B 289 1 14 HELIX 38 AE2 ASP B 299 ALA B 302 5 4 HELIX 39 AE3 ASP B 321 GLY B 330 1 10 HELIX 40 AE4 ALA B 346 GLU B 348 5 3 HELIX 41 AE5 GLU B 349 GLN B 361 1 13 HELIX 42 AE6 GLY B 390 LYS B 394 5 5 HELIX 43 AE7 ARG B 396 LEU B 401 1 6 HELIX 44 AE8 TRP B 438 GLN B 442 1 5 SHEET 1 AA1 7 ILE A 103 LEU A 106 0 SHEET 2 AA1 7 ILE A 125 ALA A 128 1 O ILE A 125 N LEU A 104 SHEET 3 AA1 7 ALA A 74 LEU A 77 1 N VAL A 76 O ILE A 126 SHEET 4 AA1 7 THR A 149 ASP A 153 1 O VAL A 151 N LEU A 75 SHEET 5 AA1 7 GLN A 179 SER A 184 1 O GLN A 179 N LEU A 150 SHEET 6 AA1 7 VAL A 43 GLN A 46 1 N VAL A 45 O LEU A 182 SHEET 7 AA1 7 LEU A 203 GLU A 206 1 O ILE A 205 N ARG A 44 SHEET 1 AA2 6 ILE A 216 GLU A 222 0 SHEET 2 AA2 6 GLY A 339 CYS A 345 1 O ALA A 341 N GLU A 217 SHEET 3 AA2 6 LEU A 312 ASN A 315 1 N ASN A 315 O PHE A 344 SHEET 4 AA2 6 CYS A 244 PHE A 247 1 N VAL A 245 O VAL A 314 SHEET 5 AA2 6 VAL A 294 ALA A 297 1 O ALA A 297 N VAL A 246 SHEET 6 AA2 6 ALA A 268 LEU A 271 1 N LEU A 269 O VAL A 296 SHEET 1 AA3 4 ILE A 415 VAL A 420 0 SHEET 2 AA3 4 HIS A 424 ARG A 430 -1 O ALA A 428 N GLY A 416 SHEET 3 AA3 4 MET A 382 ASP A 388 -1 N ILE A 387 O VAL A 425 SHEET 4 AA3 4 VAL A 453 LEU A 455 -1 O ARG A 454 N CYS A 386 SHEET 1 AA4 7 ILE B 103 LEU B 106 0 SHEET 2 AA4 7 ILE B 125 ALA B 128 1 O ILE B 125 N LEU B 104 SHEET 3 AA4 7 ALA B 74 LEU B 77 1 N VAL B 76 O ALA B 128 SHEET 4 AA4 7 THR B 149 ASP B 153 1 O THR B 149 N LEU B 75 SHEET 5 AA4 7 GLN B 179 SER B 184 1 O GLN B 179 N LEU B 150 SHEET 6 AA4 7 VAL B 43 GLN B 46 1 N VAL B 45 O LEU B 182 SHEET 7 AA4 7 LEU B 203 GLU B 206 1 O ILE B 205 N ARG B 44 SHEET 1 AA5 6 ILE B 216 GLU B 222 0 SHEET 2 AA5 6 GLY B 339 CYS B 345 1 O ALA B 341 N GLU B 217 SHEET 3 AA5 6 LEU B 312 ASN B 315 1 N ASN B 315 O PHE B 344 SHEET 4 AA5 6 CYS B 244 PHE B 247 1 N PHE B 247 O VAL B 314 SHEET 5 AA5 6 VAL B 294 ALA B 297 1 O LEU B 295 N VAL B 246 SHEET 6 AA5 6 ALA B 268 LEU B 271 1 N LEU B 269 O VAL B 296 SHEET 1 AA6 4 ILE B 415 VAL B 420 0 SHEET 2 AA6 4 HIS B 424 ARG B 430 -1 O TYR B 426 N ALA B 419 SHEET 3 AA6 4 MET B 382 ASP B 388 -1 N ILE B 387 O VAL B 425 SHEET 4 AA6 4 VAL B 453 LEU B 455 -1 O ARG B 454 N CYS B 386 LINK P G C 1 O2 POP C 101 1555 1555 1.63 LINK P G D 1 O4 PO4 D 101 1555 1555 1.62 LINK O1B ADP A 500 BE BEF A 501 1555 1555 1.84 LINK O3B ADP A 500 MG MG A 502 1555 1555 2.03 LINK MG MG A 502 O HOH A 601 1555 1555 2.02 LINK MG MG A 502 O HOH A 602 1555 1555 2.04 LINK MG MG A 502 O HOH A 603 1555 1555 2.03 LINK MG MG A 502 O HOH A 604 1555 1555 2.01 LINK O2B ADP B 500 BE BEF B 501 1555 1555 1.85 LINK O3B ADP B 500 MG MG B 502 1555 1555 2.03 LINK MG MG B 502 O HOH B 601 1555 1555 2.03 LINK MG MG B 502 O HOH B 602 1555 1555 2.03 LINK MG MG B 502 O HOH B 603 1555 1555 2.02 LINK MG MG B 502 O HOH B 604 1555 1555 2.02 CRYST1 169.690 169.690 111.990 90.00 90.00 90.00 P 42 21 2 16 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 0.005893 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005893 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008929 0.00000