HEADER RNA BINDING PROTEIN/RNA 26-NOV-18 6N6D TITLE VIBRIO CHOLERAE OLIGORIBONUCLEASE BOUND TO PAG COMPND MOL_ID: 1; COMPND 2 MOLECULE: OLIGORIBONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.-.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(P*AP*G)-3'); COMPND 8 CHAIN: D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 GENE: ORN; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS 3'-5' EXORIBONUCLEASE, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.D.LORMAND,H.SONDERMANN REVDAT 4 11-OCT-23 6N6D 1 LINK REVDAT 3 01-JAN-20 6N6D 1 REMARK REVDAT 2 16-OCT-19 6N6D 1 JRNL REVDAT 1 12-JUN-19 6N6D 0 JRNL AUTH S.K.KIM,J.D.LORMAND,C.A.WEISS,K.A.EGER,H.TURDIEV,A.TURDIEV, JRNL AUTH 2 W.C.WINKLER,H.SONDERMANN,V.T.LEE JRNL TITL A DEDICATED DIRIBONUCLEOTIDASE RESOLVES A KEY BOTTLENECK FOR JRNL TITL 2 THE TERMINAL STEP OF RNA DEGRADATION. JRNL REF ELIFE V. 8 2019 JRNL REFN ESSN 2050-084X JRNL PMID 31225796 JRNL DOI 10.7554/ELIFE.46313 REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 41592 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.158 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2081 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 44.8862 - 3.7825 1.00 2774 148 0.1349 0.1535 REMARK 3 2 3.7825 - 3.0025 1.00 2678 144 0.1328 0.1465 REMARK 3 3 3.0025 - 2.6230 1.00 2658 140 0.1417 0.1408 REMARK 3 4 2.6230 - 2.3832 1.00 2647 138 0.1469 0.1497 REMARK 3 5 2.3832 - 2.2124 1.00 2651 139 0.1428 0.1455 REMARK 3 6 2.2124 - 2.0820 1.00 2625 141 0.1425 0.1633 REMARK 3 7 2.0820 - 1.9777 1.00 2623 138 0.1444 0.1784 REMARK 3 8 1.9777 - 1.8916 1.00 2620 138 0.1481 0.1493 REMARK 3 9 1.8916 - 1.8188 1.00 2621 136 0.1510 0.1523 REMARK 3 10 1.8188 - 1.7560 1.00 2620 135 0.1627 0.1771 REMARK 3 11 1.7560 - 1.7011 1.00 2613 138 0.1638 0.1843 REMARK 3 12 1.7011 - 1.6525 1.00 2594 135 0.1669 0.1818 REMARK 3 13 1.6525 - 1.6090 1.00 2618 140 0.1813 0.2390 REMARK 3 14 1.6090 - 1.5697 1.00 2606 137 0.1897 0.1988 REMARK 3 15 1.5697 - 1.5340 0.97 2563 134 0.2260 0.2366 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.43 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 1:24) REMARK 3 ORIGIN FOR THE GROUP (A): -44.2248 6.6454 1.0769 REMARK 3 T TENSOR REMARK 3 T11: 0.1582 T22: 0.0873 REMARK 3 T33: 0.0852 T12: -0.0066 REMARK 3 T13: -0.0145 T23: 0.0052 REMARK 3 L TENSOR REMARK 3 L11: 4.5638 L22: 3.5558 REMARK 3 L33: 2.1060 L12: -1.8592 REMARK 3 L13: -1.7503 L23: 1.2081 REMARK 3 S TENSOR REMARK 3 S11: -0.0060 S12: 0.1008 S13: -0.0715 REMARK 3 S21: -0.2059 S22: -0.0162 S23: -0.0665 REMARK 3 S31: 0.0308 S32: -0.0205 S33: 0.0730 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 25:99) REMARK 3 ORIGIN FOR THE GROUP (A): -47.3122 14.0414 -2.0992 REMARK 3 T TENSOR REMARK 3 T11: 0.1767 T22: 0.1353 REMARK 3 T33: 0.1260 T12: -0.0050 REMARK 3 T13: -0.0070 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 1.7297 L22: 1.5552 REMARK 3 L33: 1.8168 L12: -0.9676 REMARK 3 L13: -1.4743 L23: 0.7622 REMARK 3 S TENSOR REMARK 3 S11: 0.0492 S12: 0.1431 S13: 0.0002 REMARK 3 S21: -0.1901 S22: -0.0564 S23: 0.0210 REMARK 3 S31: -0.0715 S32: -0.1853 S33: 0.0143 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 100:181) REMARK 3 ORIGIN FOR THE GROUP (A): -35.1196 6.2462 6.6883 REMARK 3 T TENSOR REMARK 3 T11: 0.1685 T22: 0.1411 REMARK 3 T33: 0.1643 T12: -0.0129 REMARK 3 T13: 0.0156 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 1.3655 L22: 1.4854 REMARK 3 L33: 1.1307 L12: -0.2776 REMARK 3 L13: 0.3745 L23: -0.6420 REMARK 3 S TENSOR REMARK 3 S11: -0.0493 S12: -0.0317 S13: 0.0030 REMARK 3 S21: 0.0287 S22: -0.0490 S23: -0.2277 REMARK 3 S31: -0.1073 S32: 0.1016 S33: 0.1047 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 6N6D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1000238259. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 REMARK 200 MONOCHROMATOR : SI(111) CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41621 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.534 REMARK 200 RESOLUTION RANGE LOW (A) : 47.235 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 19.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 11.20 REMARK 200 R MERGE FOR SHELL (I) : 0.89400 REMARK 200 R SYM FOR SHELL (I) : 0.89400 REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6N6A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BISTRIS (PH 5.5), 17% REMARK 280 POLYETHYLENE GLYCOL 3350, AND 20% XYLITOL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.65667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.82833 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 19.82833 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 39.65667 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: 1120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 HOH A 482 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 483 LIES ON A SPECIAL POSITION. 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 MET A 1 CG SD CE 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 A D 603 P A D 603 OP3 -0.127 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 SER A 2 33.34 -83.99 REMARK 500 MET A 120 55.29 -141.50 REMARK 500 GLN A 145 75.12 -157.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 486 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A 487 DISTANCE = 5.94 ANGSTROMS 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 NA D 701 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 12 OD1 REMARK 620 2 HOH A 217 O 93.7 REMARK 620 3 HOH A 249 O 85.5 86.1 REMARK 620 4 A D 603 O3' 155.3 108.1 84.7 REMARK 620 5 G D 604 OP1 101.9 164.3 95.7 56.7 REMARK 620 6 HOH D 812 O 86.9 96.0 172.2 101.7 84.3 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 NA D 701 DBREF1 6N6D A 1 181 UNP A0A0H6V4D7_VIBCL DBREF2 6N6D A A0A0H6V4D7 1 181 DBREF 6N6D D 603 604 PDB 6N6D 6N6D 603 604 SEQRES 1 A 181 MET SER PHE SER ASP GLN ASN LEU ILE TRP ILE ASP LEU SEQRES 2 A 181 GLU MET THR GLY LEU ASP PRO GLU MET HIS LYS ILE ILE SEQRES 3 A 181 GLU MET ALA THR ILE VAL THR ASP SER GLU LEU ASN ILE SEQRES 4 A 181 LEU ALA GLU GLY PRO VAL ILE ALA ILE HIS GLN PRO GLU SEQRES 5 A 181 SER GLU LEU ALA LYS MET ASP GLU TRP CYS THR THR THR SEQRES 6 A 181 HIS THR ALA SER GLY LEU VAL ALA ARG VAL ARG GLN SER SEQRES 7 A 181 GLN VAL SER GLU GLU GLU ALA ILE ASP GLN THR LEU ALA SEQRES 8 A 181 PHE LEU LYS GLN TRP VAL PRO GLU GLY LYS SER PRO ILE SEQRES 9 A 181 CYS GLY ASN SER ILE GLY GLN ASP ARG ARG PHE LEU TYR SEQRES 10 A 181 LYS HIS MET PRO ARG LEU GLU ALA TYR PHE HIS TYR ARG SEQRES 11 A 181 TYR ILE ASP VAL SER THR ILE LYS GLU LEU THR ARG ARG SEQRES 12 A 181 TRP GLN PRO GLU VAL LEU LYS GLU PHE SER LYS THR GLY SEQRES 13 A 181 SER HIS LEU ALA LEU ASP ASP ILE ARG GLU SER ILE ALA SEQRES 14 A 181 GLU LEU GLN PHE TYR ARG LYS ALA VAL PHE LYS ILE SEQRES 1 D 2 A G HET NA D 701 1 HETNAM NA SODIUM ION FORMUL 3 NA NA 1+ FORMUL 4 HOH *304(H2 O) HELIX 1 AA1 PRO A 51 ALA A 56 1 6 HELIX 2 AA2 ASP A 59 SER A 69 1 11 HELIX 3 AA3 GLY A 70 SER A 78 1 9 HELIX 4 AA4 SER A 81 LYS A 94 1 14 HELIX 5 AA5 SER A 108 MET A 120 1 13 HELIX 6 AA6 MET A 120 ALA A 125 1 6 HELIX 7 AA7 VAL A 134 GLN A 145 1 12 HELIX 8 AA8 PRO A 146 PHE A 152 5 7 HELIX 9 AA9 LEU A 159 VAL A 178 1 20 SHEET 1 AA1 5 ILE A 39 ALA A 47 0 SHEET 2 AA1 5 ILE A 25 THR A 33 -1 N THR A 30 O GLY A 43 SHEET 3 AA1 5 LEU A 8 MET A 15 -1 N TRP A 10 O ILE A 31 SHEET 4 AA1 5 ILE A 104 GLY A 106 1 O CYS A 105 N ILE A 11 SHEET 5 AA1 5 TYR A 131 ASP A 133 1 O ILE A 132 N ILE A 104 LINK OD1 ASP A 12 NA NA D 701 1555 1555 2.35 LINK O HOH A 217 NA NA D 701 1555 1555 2.36 LINK O HOH A 249 NA NA D 701 1555 1555 2.40 LINK O3' A D 603 NA NA D 701 1555 1555 2.64 LINK OP1 G D 604 NA NA D 701 1555 1555 2.46 LINK NA NA D 701 O HOH D 812 1555 1555 2.33 SITE 1 AC1 6 ASP A 12 HOH A 217 HOH A 249 A D 603 SITE 2 AC1 6 G D 604 HOH D 812 CRYST1 89.734 89.734 59.485 90.00 90.00 120.00 P 32 2 1 6 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 0.011144 0.006434 0.000000 0.00000 SCALE2 0.000000 0.012868 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016811 0.00000