10 20 30 40 50 60 70 80 2IN9 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 06-OCT-06 2IN9
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: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PX
KEYWDS HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR P.VAN ROEY
REVDAT 2 24-FEB-09 2IN9 1 VERSN REVDAT 1 01-MAY-07 2IN9 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1016164.800 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 11288 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) : 0.236 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1105 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) (%) : 6.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 109 REMARK 3 BIN R VALUE (WORKING SET) : 0.4040 REMARK 3 BIN FREE R VALUE : 0.4370 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 16.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 22 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.093 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1087 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 95 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.43000 REMARK 3 B22 (A**2) : 14.91000 REMARK 3 B33 (A**2) : -8.48000 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) : 0.43 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) : 0.53 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) : 24.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.68 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) : 1.340 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.010 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.930 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.760 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 45.13 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 2IN9 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-06. REMARK 100 THE RCSB ID CODE IS RCSB039777.
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) : 1.5418 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 : 11342 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.100 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 (%): 34.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 65% AMMMONIUM SULFATE 100 MM REMARK 280 TRIS.HCL, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 18.36500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.12500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.71000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.12500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.36500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.71000 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 ASP A 37 34.18 -88.15 REMARK 500 GLU A 99 -75.42 -91.35 REMARK 500 GLU A 427 -57.61 65.33 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 300
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: 2IN8 RELATED DB: PDB
DBREF 2IN9 A 1 102 UNP P0A5U4 RECA_MYCTU 252 353 DBREF 2IN9 A 404 440 UNP P0A5U4 RECA_MYCTU 655 691
SEQADV 2IN9 VAL A 95 UNP P0A5U4 GLN 346 ENGINEERED SEQADV 2IN9 ARG A 96 UNP P0A5U4 PRO 347 ENGINEERED SEQADV 2IN9 ASP A 97 UNP P0A5U4 ARG 348 ENGINEERED SEQADV 2IN9 VAL A 98 UNP P0A5U4 ARG 349 ENGINEERED SEQADV 2IN9 GLU A 99 UNP P0A5U4 PHE 350 ENGINEERED SEQADV 2IN9 THR A 100 UNP P0A5U4 ASP 351 ENGINEERED SEQADV 2IN9 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 VAL 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
HET SO4 A 300 5
HETNAM SO4 SULFATE ION
FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *95(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 THR A 420 N GLN A 51 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 436 N ALA A 433
SITE 1 AC1 8 ALA A 62 GLY A 63 ARG A 410 HIS A 429 SITE 2 AC1 8 HIS A 439 ASN A 440 HOH A 448 HOH A 495
CRYST1 36.730 49.420 64.250 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 0.027226 0.000000 0.000000 0.00000
SCALE2 0.000000 0.020235 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015564 0.00000