HEADER IMMUNE SYSTEM/RNA 30-JAN-11 3QJP TITLE AN RAMP PROTEIN BINDING DIFFERENT RNA SUBSTRATES COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(P*UP*AP*GP*UP*UP*UP*AP*A)-3'); COMPND 3 CHAIN: R; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CRISPR; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN PH0350; COMPND 8 CHAIN: A; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 5 ORGANISM_TAXID: 53953; SOURCE 6 GENE: PH0350 KEYWDS FERRIDOXIN-FOLD, WORK IN IMMUNE SYSTEM IN PROKARYOTES, IMMUNE SYSTEM- KEYWDS 2 RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.WANG,H.ZHENG,G.PREAMPLUME,H.LI REVDAT 2 21-FEB-24 3QJP 1 DBREF SEQADV REVDAT 1 08-FEB-12 3QJP 0 JRNL AUTH R.WANG,H.ZHENG,G.PREAMPLUME,H.LI JRNL TITL COOPERATIVE AND SPECIFIC BINDING OF A RAMP PROTEIN TO JRNL TITL 2 SINGLE-STRANDED CRISPR REPEAT RNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_589) 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) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 8928 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.231 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 896 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 30.2966 - 5.9811 1.00 1502 167 0.2286 0.2562 REMARK 3 2 5.9811 - 4.7533 0.99 1394 152 0.2113 0.2478 REMARK 3 3 4.7533 - 4.1542 0.99 1374 152 0.1689 0.2187 REMARK 3 4 4.1542 - 3.7751 0.97 1316 151 0.2359 0.3050 REMARK 3 5 3.7751 - 3.5050 0.96 1279 146 0.2906 0.3686 REMARK 3 6 3.5050 - 3.2986 0.86 1167 128 0.3446 0.4038 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 : 0.30 REMARK 3 B_SOL : 58.24 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.910 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) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 : 0.008 2176 REMARK 3 ANGLE : 1.359 2965 REMARK 3 CHIRALITY : 0.086 337 REMARK 3 PLANARITY : 0.005 344 REMARK 3 DIHEDRAL : 21.398 858 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 3QJP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000063730. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5621 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9254 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.299 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M MGSO4, 0.05 M NA CACODYLATE REMARK 280 (PH6.0), AND 1.8 M LITHIUM SULFATE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 96.53900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.39050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.39050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 48.26950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.39050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.39050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 144.80850 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.39050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.39050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 48.26950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.39050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.39050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 144.80850 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 96.53900 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: 2270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: R, A 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 HIS A -2 REMARK 465 HIS A -1 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 A R 9 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 PRO A 64 C - N - CA ANGL. DEV. = 10.8 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 LYS A 11 -74.52 -95.59 REMARK 500 PRO A 98 49.26 -78.38 REMARK 500 SER A 130 133.64 -175.29 REMARK 500 VAL A 171 -58.49 -127.69 REMARK 500 PHE A 188 145.86 -178.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 3QJP R 3 10 PDB 3QJP 3QJP 3 10 DBREF 3QJP A 1 239 UNP O58088 O58088_PYRHO 1 239 SEQADV 3QJP HIS A -2 UNP O58088 EXPRESSION TAG SEQADV 3QJP HIS A -1 UNP O58088 EXPRESSION TAG SEQADV 3QJP HIS A 0 UNP O58088 EXPRESSION TAG SEQRES 1 R 8 U A G U U U A A SEQRES 1 A 242 HIS HIS HIS MET ARG ILE GLU VAL LYS LEU LEU PRO LEU SEQRES 2 A 242 LYS ASP ASN PRO ILE LEU PRO PHE ASN TYR ASN TYR GLU SEQRES 3 A 242 VAL TYR SER GLN ILE LEU GLU LYS VAL ASN SER ILE GLU SEQRES 4 A 242 PRO THR ILE ALA LYS LEU LEU SER SER PRO HIS GLY PHE SEQRES 5 A 242 TRP THR PHE SER ARG ILE ILE VAL ARG LYS ARG LYS ILE SEQRES 6 A 242 LEU PRO ASP LYS GLY ILE GLU ILE LEU SER ASP ASP VAL SEQRES 7 A 242 SER LEU TYR ILE SER SER SER ASN GLU ASP ILE ILE ARG SEQRES 8 A 242 ALA ILE ALA GLU ALA VAL GLU LYS SER PRO GLU PHE LYS SEQRES 9 A 242 ILE GLY GLU LEU SER PHE LEU VAL GLY ASP ILE LYS ALA SEQRES 10 A 242 ILE LYS VAL LYS GLU LEU GLY LYS GLU ASN VAL PHE SER SEQRES 11 A 242 THR LEU SER PRO ILE VAL VAL ARG THR VAL LYS PHE GLU SEQRES 12 A 242 GLY ASN LYS LEU ARG HIS TRP ASP LEU TYR PRO HIS ASP SEQRES 13 A 242 GLU LEU PHE MET ASP ARG LEU ARG LYS VAL MET ILE LEU SEQRES 14 A 242 ARG TYR SER GLU VAL MET GLY GLU THR PRO LYS ASP ARG SEQRES 15 A 242 ASP PHE THR ILE GLU VAL LEU LYS PHE LYS PRO THR ARG SEQRES 16 A 242 LEU MET VAL GLY SER SER TYR ILE ARG GLY SER LEU MET SEQRES 17 A 242 VAL PHE ARG TYR ALA GLY SER GLU GLU ILE ALA ARG PHE SEQRES 18 A 242 GLY TYR GLU ASN GLY PHE GLY GLU LYS THR GLY LEU GLY SEQRES 19 A 242 PHE GLY MET VAL LYS LEU ILE GLU HELIX 1 1 TYR A 20 GLU A 36 1 17 HELIX 2 2 ILE A 39 SER A 44 1 6 HELIX 3 3 ASN A 83 SER A 97 1 15 HELIX 4 4 ASP A 153 GLU A 170 1 18 HELIX 5 5 SER A 212 GLY A 223 1 12 HELIX 6 6 LYS A 227 GLY A 231 5 5 SHEET 1 A 5 THR A 51 PHE A 52 0 SHEET 2 A 5 VAL A 75 SER A 81 -1 O SER A 80 N THR A 51 SHEET 3 A 5 MET A 1 LEU A 10 -1 N LEU A 7 O VAL A 75 SHEET 4 A 5 LEU A 105 ILE A 115 -1 O LEU A 108 N LEU A 8 SHEET 5 A 5 GLU A 99 ILE A 102 -1 N PHE A 100 O PHE A 107 SHEET 1 B 3 ILE A 15 LEU A 16 0 SHEET 2 B 3 GLY A 67 ILE A 70 -1 O ILE A 68 N LEU A 16 SHEET 3 B 3 ARG A 60 LEU A 63 -1 N LYS A 61 O GLU A 69 SHEET 1 C 4 THR A 182 VAL A 185 0 SHEET 2 C 4 VAL A 206 ALA A 210 -1 O ARG A 208 N GLU A 184 SHEET 3 C 4 ASN A 124 THR A 128 -1 N PHE A 126 O PHE A 207 SHEET 4 C 4 VAL A 235 LEU A 237 -1 O LYS A 236 N SER A 127 SHEET 1 D 2 ARG A 135 GLU A 140 0 SHEET 2 D 2 LYS A 143 ASP A 148 -1 O TRP A 147 N THR A 136 SHEET 1 E 2 LYS A 189 VAL A 195 0 SHEET 2 E 2 SER A 198 LEU A 204 -1 O ILE A 200 N LEU A 193 CISPEP 1 LEU A 10 LYS A 11 0 8.05 CRYST1 76.781 76.781 193.078 90.00 90.00 90.00 P 41 21 2 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 0.013024 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013024 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005179 0.00000