HEADER RNA 29-MAY-13 4KZ2 TITLE CRYSTAL STRUCTURE OF PHI29 PRNA 3WJ CORE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHI29 PRNA 3WJ CORE RNA 18 MER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PHI29 PRNA 3WJ CORE RNA 20 MER; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PHI29 PRNA 3WJ CORE RNA 16 MER; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 7 MOL_ID: 3; SOURCE 8 SYNTHETIC: YES; SOURCE 9 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS PHI29 DNA PACKAGING MOTOR PRNA CORE ELEMENT, RNA EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,J.A.ENDRIZZI,Y.SHU,F.HAQUE,C.SAUTER,P.GUO,Y.-I.CHI REVDAT 1 16-OCT-13 4KZ2 0 JRNL AUTH H.ZHANG,J.A.ENDRIZZI,Y.SHU,F.HAQUE,C.SAUTER, JRNL AUTH 2 L.S.SHLYAKHTENKO,Y.LYUBCHENKO,P.GUO,Y.I.CHI JRNL TITL CRYSTAL STRUCTURE OF 3WJ CORE REVEALING DIVALENT JRNL TITL 2 ION-PROMOTED THERMOSTABILITY AND ASSEMBLY OF THE PHI29 JRNL TITL 3 HEXAMERIC MOTOR PRNA. JRNL REF RNA V. 19 1226 2013 JRNL REFN ISSN 1355-8382 JRNL PMID 23884902 JRNL DOI 10.1261/RNA.037077.112 REMARK 2 REMARK 2 RESOLUTION. 3.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 4201 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 215 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 75.20 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 : 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 : NULL 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 4KZ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUL-13. REMARK 100 THE RCSB ID CODE IS RCSB079974. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98789 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK MONOCHROMATOR REMARK 200 HIGH-RESOLUTION DOUBLE-CRYSTAL SI REMARK 200 (111) SAGITTAL FOCUSING. REMARK 200 ROSENBAUM-ROCK VERTICAL FOCUSING REMARK 200 MIRROR. REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4203 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.050 REMARK 200 RESOLUTION RANGE LOW (A) : 88.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.000 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : 0.08800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 30.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHENIX REMARK 200 STARTING MODEL: 7 BASE-PAIR A-FORM HELIX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM ACETATE, 24-26% MPD, 20MM REMARK 280 CACL2, 10MM MNCL2, PH 4.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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,X,Z REMARK 290 4555 Y,-X,Z 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+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 62.50600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 62.50600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 13.49450 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 62.50600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 62.50600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 13.49450 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 62.50600 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 62.50600 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 13.49450 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 62.50600 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 62.50600 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 13.49450 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: 3400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 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 MN B 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C B 20 O3' REMARK 620 2 C B 20 O2' 71.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN C 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A C 6 OP1 REMARK 620 2 C A 4 OP1 159.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A C 7 OP1 REMARK 620 2 G A 3 OP1 164.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN C 101 DBREF 4KZ2 A 1 18 PDB 4KZ2 4KZ2 1 18 DBREF 4KZ2 B 1 20 PDB 4KZ2 4KZ2 1 20 DBREF 4KZ2 C 1 16 PDB 4KZ2 4KZ2 1 16 SEQRES 1 A 18 U U G C C A U G U G U A U SEQRES 2 A 18 G U G G G SEQRES 1 B 20 C C C A C A U A C U U U G SEQRES 2 B 20 U U G A U C C SEQRES 1 C 16 G G A U C A A U C A U G G SEQRES 2 C 16 C A A HET MN A 101 1 HET MN B 101 1 HET MN C 101 1 HETNAM MN MANGANESE (II) ION FORMUL 4 MN 3(MN 2+) FORMUL 7 HOH *2(H2 O) LINK O3' C B 20 MN MN B 101 1555 1555 2.04 LINK OP1 A C 6 MN MN C 101 1555 1555 2.17 LINK OP1 C A 4 MN MN C 101 1555 1555 2.33 LINK OP1 A C 7 MN MN A 101 1555 1555 2.34 LINK OP1 G A 3 MN MN A 101 1555 1555 2.35 LINK O2' C B 20 MN MN B 101 1555 1555 2.66 SITE 1 AC1 3 G A 3 C B 19 A C 7 SITE 1 AC2 1 C B 20 SITE 1 AC3 4 C A 4 G A 18 C B 20 A C 6 CRYST1 125.012 125.012 26.989 90.00 90.00 90.00 I 4 8 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 0.007999 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007999 0.000000 0.00000 SCALE3 0.000000 0.000000 0.037052 0.00000 MASTER 251 0 3 0 0 0 3 6 0 0 0 6 END