HEADER UNKNOWN FUNCTION 09-MAR-12 4E2U TITLE CRYSTAL STRUCTURES OF RADAMIN INTEIN FROM PYROCOCCUS HORIKOSHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHO RADA INTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DNA REPAIR AND RECOMBINATION PROTEIN RADA; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 STRAIN: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3; SOURCE 5 GENE: RADA, PH0263; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ER2566; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCARSF15 KEYWDS HINT-FOLD, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR J.S.OEEMIG,D.ZHOU,T.KAJANDER,A.WLODAWER,H.IWAI REVDAT 3 13-SEP-23 4E2U 1 SEQADV REVDAT 2 25-JUL-12 4E2U 1 JRNL REVDAT 1 16-MAY-12 4E2U 0 JRNL AUTH J.S.OEEMIG,D.ZHOU,T.KAJANDER,A.WLODAWER,H.IWAI JRNL TITL NMR AND CRYSTAL STRUCTURES OF THE PYROCOCCUS HORIKOSHII RADA JRNL TITL 2 INTEIN GUIDE A STRATEGY FOR ENGINEERING A HIGHLY EFFICIENT JRNL TITL 3 AND PROMISCUOUS INTEIN. JRNL REF J.MOL.BIOL. V. 421 85 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22560994 JRNL DOI 10.1016/J.JMB.2012.04.029 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 27680 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.200 REMARK 3 FREE R VALUE TEST SET COUNT : 887 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 46.0181 - 2.8747 1.00 4685 162 0.1668 0.1922 REMARK 3 2 2.8747 - 2.2818 1.00 4531 142 0.1672 0.1945 REMARK 3 3 2.2818 - 1.9933 1.00 4464 145 0.1515 0.1713 REMARK 3 4 1.9933 - 1.8111 1.00 4439 151 0.1497 0.1864 REMARK 3 5 1.8111 - 1.6813 1.00 4435 140 0.1822 0.2072 REMARK 3 6 1.6813 - 1.5821 0.96 4239 147 0.2325 0.2824 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 51.08 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.260 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) : 2.97080 REMARK 3 B22 (A**2) : -6.02830 REMARK 3 B33 (A**2) : 3.05740 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 : 0.011 1401 REMARK 3 ANGLE : 1.399 1908 REMARK 3 CHIRALITY : 0.100 211 REMARK 3 PLANARITY : 0.008 246 REMARK 3 DIHEDRAL : 12.185 515 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID -3:174) REMARK 3 ORIGIN FOR THE GROUP (A): 3.1164 9.2798 6.8406 REMARK 3 T TENSOR REMARK 3 T11: 0.0644 T22: 0.0861 REMARK 3 T33: 0.0850 T12: -0.0019 REMARK 3 T13: 0.0098 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 0.3570 L22: 0.9417 REMARK 3 L33: 0.7385 L12: -0.0959 REMARK 3 L13: -0.0256 L23: 0.0630 REMARK 3 S TENSOR REMARK 3 S11: 0.0086 S12: -0.0006 S13: -0.0019 REMARK 3 S21: -0.0335 S22: 0.0194 S23: 0.0475 REMARK 3 S31: -0.0050 S32: 0.0089 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 4E2U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000071098. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93340 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27745 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 46.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.08600 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) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.45400 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: PHASES REMARK 200 STARTING MODEL: 4E2T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M TRI-SODIUM CITRATE, PH 4.7, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 23.46500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.27600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.82450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.27600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.46500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.82450 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 241 O HOH A 347 2.00 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 ALA A 1 -35.37 -140.37 REMARK 500 ASP A 13 -105.98 57.23 REMARK 500 ASP A 38 -126.93 57.66 REMARK 500 ARG A 99 -96.31 -123.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4E2T RELATED DB: PDB REMARK 900 RELATED ID: 2LQM RELATED DB: PDB DBREF 4E2U A -4 174 UNP O58001 RADA_PYRHO 150 326 SEQADV 4E2U SER A -4 UNP O58001 EXPRESSION TAG SEQADV 4E2U GLN A -3 UNP O58001 SER 150 ENGINEERED MUTATION SEQADV 4E2U HIS A -2 UNP O58001 GLY 151 ENGINEERED MUTATION SEQADV 4E2U MET A -1 UNP O58001 LYS 152 ENGINEERED MUTATION SEQADV 4E2U ALA A 1 UNP O58001 CYS 153 ENGINEERED MUTATION SEQADV 4E2U A UNP O58001 GLU 273 DELETION SEQADV 4E2U A UNP O58001 GLU 274 DELETION SEQADV 4E2U A UNP O58001 VAL 275 DELETION SEQADV 4E2U A UNP O58001 LEU 276 DELETION SEQADV 4E2U A UNP O58001 ARG 277 DELETION SEQADV 4E2U A UNP O58001 ARG 278 DELETION SEQADV 4E2U A UNP O58001 ARG 279 DELETION SEQADV 4E2U A UNP O58001 ILE 280 DELETION SEQADV 4E2U A UNP O58001 ILE 281 DELETION SEQADV 4E2U A UNP O58001 SER 282 DELETION SEQADV 4E2U ASN A 131 UNP O58001 LYS 283 ENGINEERED MUTATION SEQADV 4E2U ALA A 173 UNP O58001 THR 325 ENGINEERED MUTATION SEQRES 1 A 168 SER GLN HIS MET ALA PHE ALA ARG ASP THR GLU VAL TYR SEQRES 2 A 168 TYR GLU ASN ASP THR VAL PRO HIS MET GLU SER ILE GLU SEQRES 3 A 168 GLU MET TYR SER LYS TYR ALA SER MET ASN GLY GLU LEU SEQRES 4 A 168 PRO PHE ASP ASN GLY TYR ALA VAL PRO LEU ASP ASN VAL SEQRES 5 A 168 PHE VAL TYR THR LEU ASP ILE ALA SER GLY GLU ILE LYS SEQRES 6 A 168 LYS THR ARG ALA SER TYR ILE TYR ARG GLU LYS VAL GLU SEQRES 7 A 168 LYS LEU ILE GLU ILE LYS LEU SER SER GLY TYR SER LEU SEQRES 8 A 168 LYS VAL THR PRO SER HIS PRO VAL LEU LEU PHE ARG ASP SEQRES 9 A 168 GLY LEU GLN TRP VAL PRO ALA ALA GLU VAL LYS PRO GLY SEQRES 10 A 168 ASP VAL VAL VAL GLY VAL ARG ASN GLY GLU LEU GLU PHE SEQRES 11 A 168 HIS GLU VAL SER SER VAL ARG ILE ILE ASP TYR ASN ASN SEQRES 12 A 168 TRP VAL TYR ASP LEU VAL ILE PRO GLU THR HIS ASN PHE SEQRES 13 A 168 ILE ALA PRO ASN GLY LEU VAL LEU HIS ASN ALA GLN FORMUL 2 HOH *251(H2 O) HELIX 1 1 ILE A 21 GLY A 33 1 13 HELIX 2 2 ALA A 108 VAL A 110 5 3 SHEET 1 A 7 LEU A 35 PHE A 37 0 SHEET 2 A 7 GLY A 40 PRO A 44 -1 O ALA A 42 N LEU A 35 SHEET 3 A 7 TYR A 67 LEU A 81 -1 O ILE A 68 N VAL A 43 SHEET 4 A 7 SER A 86 VAL A 89 -1 O VAL A 89 N ILE A 77 SHEET 5 A 7 PHE A 2 ALA A 3 -1 N ALA A 3 O LYS A 88 SHEET 6 A 7 GLU A 133 VAL A 155 -1 O TYR A 152 N PHE A 2 SHEET 7 A 7 VAL A 115 ARG A 120 -1 N GLY A 118 O GLU A 135 SHEET 1 B 5 LEU A 35 PHE A 37 0 SHEET 2 B 5 GLY A 40 PRO A 44 -1 O ALA A 42 N LEU A 35 SHEET 3 B 5 TYR A 67 LEU A 81 -1 O ILE A 68 N VAL A 43 SHEET 4 B 5 GLU A 133 VAL A 155 -1 O ARG A 143 N GLU A 78 SHEET 5 B 5 VAL A 115 ARG A 120 -1 N GLY A 118 O GLU A 135 SHEET 1 C 4 VAL A 15 SER A 20 0 SHEET 2 C 4 GLU A 7 ASN A 12 -1 N VAL A 8 O GLU A 19 SHEET 3 C 4 VAL A 48 LEU A 53 -1 O PHE A 49 N GLU A 11 SHEET 4 C 4 ILE A 60 ARG A 64 -1 O THR A 63 N VAL A 50 SHEET 1 D 2 PRO A 94 PHE A 98 0 SHEET 2 D 2 LEU A 102 PRO A 106 -1 O GLN A 103 N LEU A 97 SHEET 1 E 2 ASN A 161 ILE A 163 0 SHEET 2 E 2 VAL A 169 HIS A 171 -1 O LEU A 170 N PHE A 162 CRYST1 46.930 63.649 66.552 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 0.021308 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015711 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015026 0.00000