HEADER HYDROLASE 06-OCT-06 2IN8 TITLE CRYSTAL STRUCTURE OF MTU RECA INTEIN, SPLICING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE PI-MTUI; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SPLICING DOMAIN; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: RECA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JM101; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PX KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.VAN ROEY REVDAT 5 30-AUG-23 2IN8 1 REMARK REVDAT 4 20-OCT-21 2IN8 1 REMARK SEQADV REVDAT 3 16-AUG-17 2IN8 1 SOURCE REVDAT 2 24-FEB-09 2IN8 1 VERSN REVDAT 1 01-MAY-07 2IN8 0 JRNL AUTH P.VAN ROEY,B.PEREIRA,Z.LI,K.HIRAGA,M.BELFORT,V.DERBYSHIRE JRNL TITL CRYSTALLOGRAPHIC AND MUTATIONAL STUDIES OF MYCOBACTERIUM JRNL TITL 2 TUBERCULOSIS RECA MINI-INTEINS SUGGEST A PIVOTAL ROLE FOR A JRNL TITL 3 HIGHLY CONSERVED ASPARTATE RESIDUE. JRNL REF J.MOL.BIOL. V. 367 162 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17254599 JRNL DOI 10.1016/J.JMB.2006.12.050 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 945804.880 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 13338 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.252 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1322 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1928 REMARK 3 BIN R VALUE (WORKING SET) : 0.5190 REMARK 3 BIN FREE R VALUE : 0.4990 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 223 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.033 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1080 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 114 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.82000 REMARK 3 B22 (A**2) : 17.76000 REMARK 3 B33 (A**2) : -9.94000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.57 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.64 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.660 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.370 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.120 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.020 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.880 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 48.68 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2IN8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000039776. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13488 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.35400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY: 2IMZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 65% AMMONIUM SULFATE 100 MM TRIS.HCL, REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K 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 18.43500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.23500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.63500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.23500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.43500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.63500 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 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: 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 35 -158.09 -84.14 REMARK 500 ASP A 37 19.79 -62.80 REMARK 500 GLU A 427 -58.16 67.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IMZ RELATED DB: PDB REMARK 900 RELATED ID: 2IN0 RELATED DB: PDB REMARK 900 RELATED ID: 2IN9 RELATED DB: PDB DBREF 2IN8 A 1 102 UNP P0A5U4 RECA_MYCTU 252 353 DBREF 2IN8 A 404 440 UNP P0A5U4 RECA_MYCTU 655 691 SEQADV 2IN8 GLY A 24 UNP P0A5U4 ASP 275 ENGINEERED MUTATION SEQADV 2IN8 LEU A 67 UNP P0A5U4 VAL 318 ENGINEERED MUTATION SEQADV 2IN8 VAL A 95 UNP P0A5U4 GLN 346 ENGINEERED MUTATION SEQADV 2IN8 ARG A 96 UNP P0A5U4 PRO 347 ENGINEERED MUTATION SEQADV 2IN8 ASP A 97 UNP P0A5U4 ARG 348 ENGINEERED MUTATION SEQADV 2IN8 VAL A 98 UNP P0A5U4 ARG 349 ENGINEERED MUTATION SEQADV 2IN8 GLU A 99 UNP P0A5U4 PHE 350 ENGINEERED MUTATION SEQADV 2IN8 THR A 100 UNP P0A5U4 ASP 351 ENGINEERED MUTATION SEQADV 2IN8 GLU A 102 UNP P0A5U4 PHE 353 ENGINEERED MUTATION SEQADV 2IN8 GLY A 422 UNP P0A5U4 ASP 673 ENGINEERED MUTATION SEQRES 1 A 139 CYS LEU ALA GLU GLY THR ARG ILE PHE ASP PRO VAL THR SEQRES 2 A 139 GLY THR THR HIS ARG ILE GLU ASP VAL VAL GLY GLY ARG SEQRES 3 A 139 LYS PRO ILE HIS VAL VAL ALA ALA ALA LYS ASP GLY THR SEQRES 4 A 139 LEU HIS ALA ARG PRO VAL VAL SER TRP PHE ASP GLN GLY SEQRES 5 A 139 THR ARG ASP VAL ILE GLY LEU ARG ILE ALA GLY GLY ALA SEQRES 6 A 139 ILE LEU TRP ALA THR PRO ASP HIS LYS VAL LEU THR GLU SEQRES 7 A 139 TYR GLY TRP ARG ALA ALA GLY GLU LEU ARG LYS GLY ASP SEQRES 8 A 139 ARG VAL ALA VAL ARG ASP VAL GLU THR GLY GLU LEU ARG SEQRES 9 A 139 TYR SER VAL ILE ARG GLU VAL LEU PRO THR ARG ARG ALA SEQRES 10 A 139 ARG THR PHE GLY LEU GLU VAL GLU GLU LEU HIS THR LEU SEQRES 11 A 139 VAL ALA GLU GLY VAL VAL VAL HIS ASN HET SO4 A 400 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *114(H2 O) HELIX 1 1 ILE A 19 GLY A 25 1 7 HELIX 2 2 GLY A 85 LEU A 87 5 3 SHEET 1 A 6 HIS A 30 ALA A 34 0 SHEET 2 A 6 LEU A 40 ILE A 61 -1 O HIS A 41 N ALA A 33 SHEET 3 A 6 ILE A 66 ALA A 69 -1 O ALA A 69 N ILE A 57 SHEET 4 A 6 LEU A 2 ALA A 3 -1 N ALA A 3 O TRP A 68 SHEET 5 A 6 LEU A 404 VAL A 425 -1 O PHE A 421 N LEU A 2 SHEET 6 A 6 ARG A 92 ARG A 96 -1 N VAL A 93 O SER A 407 SHEET 1 B 4 HIS A 30 ALA A 34 0 SHEET 2 B 4 LEU A 40 ILE A 61 -1 O HIS A 41 N ALA A 33 SHEET 3 B 4 LEU A 404 VAL A 425 -1 O LEU A 413 N GLY A 58 SHEET 4 B 4 ARG A 92 ARG A 96 -1 N VAL A 93 O SER A 407 SHEET 1 C 2 ARG A 7 PHE A 9 0 SHEET 2 C 2 THR A 16 ARG A 18 -1 O HIS A 17 N ILE A 8 SHEET 1 D 2 LYS A 74 THR A 77 0 SHEET 2 D 2 GLY A 80 ALA A 83 -1 O ARG A 82 N VAL A 75 SHEET 1 E 2 THR A 430 ALA A 433 0 SHEET 2 E 2 VAL A 436 HIS A 439 -1 O VAL A 438 N LEU A 431 SITE 1 AC1 7 ALA A 62 GLY A 63 ARG A 410 HIS A 429 SITE 2 AC1 7 HIS A 439 ASN A 440 HOH A 446 CRYST1 36.870 49.270 64.470 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 0.027122 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020296 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015511 0.00000