HEADER 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 5 30-AUG-23 2IN9 1 REMARK
REVDAT 4 20-OCT-21 2IN9 1 REMARK SEQADV
REVDAT 3 16-AUG-17 2IN9 1 SOURCE
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,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. 1.80 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) : 1.300
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.90
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.680
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. 3.30, 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_1000039777.
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 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 18.36500
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 MUTATION
SEQADV 2IN9 ARG A 96 UNP P0A5U4 PRO 347 ENGINEERED MUTATION
SEQADV 2IN9 ASP A 97 UNP P0A5U4 ARG 348 ENGINEERED MUTATION
SEQADV 2IN9 VAL A 98 UNP P0A5U4 ARG 349 ENGINEERED MUTATION
SEQADV 2IN9 GLU A 99 UNP P0A5U4 PHE 350 ENGINEERED MUTATION
SEQADV 2IN9 THR A 100 UNP P0A5U4 ASP 351 ENGINEERED MUTATION
SEQADV 2IN9 GLU A 102 UNP P0A5U4 PHE 353 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 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
(ATOM LINES ARE NOT SHOWN.)
END
