10 20 30 40 50 60 70 80 2IN0 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 05-OCT-06 2IN0
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: SPLCING 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: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PX
KEYWDS HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR P.VAN ROEY
REVDAT 2 24-FEB-09 2IN0 1 VERSN REVDAT 1 01-MAY-07 2IN0 0
JRNL AUTH P.VAN ROEY,B.PEREIRA,Z.LI,K.HIRAGA,M.BELFORT, JRNL AUTH 2 V.DERBYSHIRE JRNL TITL CRYSTALLOGRAPHIC AND MUTATIONAL STUDIES OF JRNL TITL 2 MYCOBACTERIUM TUBERCULOSIS RECA MINI-INTEINS JRNL TITL 3 SUGGEST A PIVOTAL ROLE FOR A HIGHLY CONSERVED JRNL TITL 4 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 1
REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 870647.450 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 15439 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) : 0.245 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1554 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2236 REMARK 3 BIN R VALUE (WORKING SET) : 0.4630 REMARK 3 BIN FREE R VALUE : 0.4850 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 243 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1088 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 112 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.54000 REMARK 3 B22 (A**2) : 9.34000 REMARK 3 B33 (A**2) : -5.80000 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) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.54 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) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.60 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.69 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) : 1.290 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.990 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.930 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.850 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 47.90 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 2IN0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-06. REMARK 100 THE RCSB ID CODE IS RCSB039768.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : NULL 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 : 15495 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 29.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.48900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2IMZ REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6-8% PEG8000, 0.1M TRIS.HCL PH 8.5, REMARK 280 5% PEG400
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 18.42000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.31500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.73000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.31500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.42000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.73000 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 GLU A 427 -55.11 65.51 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IMZ RELATED DB: PDB REMARK 900 RELATED ID: 2IN8 RELATED DB: PDB REMARK 900 RELATED ID: 2IN9 RELATED DB: PDB
DBREF 2IN0 A 1 102 UNP P0A5U4 RECA_MYCTU 252 353 DBREF 2IN0 A 404 440 UNP P0A5U4 RECA_MYCTU 655 691
SEQADV 2IN0 LEU A 67 UNP P0A5U4 VAL 318 ENGINEERED SEQADV 2IN0 VAL A 95 UNP P0A5U4 GLN 346 ENGINEERED SEQADV 2IN0 ARG A 96 UNP P0A5U4 PRO 347 ENGINEERED SEQADV 2IN0 ASP A 97 UNP P0A5U4 ARG 348 ENGINEERED SEQADV 2IN0 VAL A 98 UNP P0A5U4 ARG 349 ENGINEERED SEQADV 2IN0 GLU A 99 UNP P0A5U4 PHE 350 ENGINEERED SEQADV 2IN0 THR A 100 UNP P0A5U4 ASP 351 ENGINEERED SEQADV 2IN0 GLU A 102 UNP P0A5U4 PHE 353 ENGINEERED
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 ASP 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 ASP LEU GLU VAL GLU GLU LEU HIS THR LEU SEQRES 11 A 139 VAL ALA GLU GLY VAL VAL VAL HIS ASN
FORMUL 2 HOH *112(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 95 O ARG A 405 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 95 O ARG A 405 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 436 N ALA A 433
CRYST1 36.840 47.460 64.630 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 0.027144 0.000000 0.000000 0.00000
SCALE2 0.000000 0.021070 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015473 0.00000