HEADER TRANSFERASE 16-JUL-10 3NZM TITLE CRYSTAL STRUCTURE OF DNAE INTEIN WITH N-EXTEIN IN REDOX TRAP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE III SUBUNIT ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNAE INTEIN (UNP RESIDUES 771-933); COMPND 5 SYNONYM: SSP DNAE INTEIN; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCYSTIS SP. PCC 6803; SOURCE 3 ORGANISM_TAXID: 1148; SOURCE 4 STRAIN: PCC6803; SOURCE 5 GENE: DNAE-N, SLR0603, DNAE-C, SLL1572; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ORIGAMI DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET47 KEYWDS DISULFIDE BOND, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.VAN ROEY,M.BELFORT,B.P.CALLAHAN REVDAT 4 15-NOV-23 3NZM 1 LINK ATOM REVDAT 3 06-SEP-23 3NZM 1 REMARK SEQADV LINK REVDAT 2 15-JUN-11 3NZM 1 CONECT LINK REMARK REVDAT 1 01-JUN-11 3NZM 0 JRNL AUTH B.P.CALLAHAN,N.I.TOPILINA,M.J.STANGER,P.VAN ROEY,M.BELFORT JRNL TITL STRUCTURE OF CATALYTICALLY COMPETENT INTEIN CAUGHT IN A JRNL TITL 2 REDOX TRAP WITH FUNCTIONAL AND EVOLUTIONARY IMPLICATIONS. JRNL REF NAT.STRUCT.MOL.BIOL. V. 18 630 2011 JRNL REFN ISSN 1545-9993 JRNL PMID 21460844 JRNL DOI 10.1038/NSMB.2041 REMARK 2 REMARK 2 RESOLUTION. 1.55 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 815584.060 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 21960 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) : 0.220 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2221 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.62 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2394 REMARK 3 BIN R VALUE (WORKING SET) : 0.7130 REMARK 3 BIN FREE R VALUE : 0.7780 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 273 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.047 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1293 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 209 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.86000 REMARK 3 B22 (A**2) : -0.64000 REMARK 3 B33 (A**2) : -0.22000 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) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.30 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) : 0.20 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.34 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) : 24.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 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) : 1.060 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.530 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.880 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.780 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 53.25 REMARK 3 REMARK 3 NCS MODEL : NONE 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 3NZM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000060478. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRROR 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 REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21996 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.730 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.39 REMARK 200 R MERGE FOR SHELL (I) : 0.44500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 1ZD7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 54% AMMONIUM SULFATE, 2% PEG400, 0.1M REMARK 280 HEPES, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 20.11000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.98000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.87000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.98000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.11000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.87000 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS A -9 REMARK 465 SER A -8 REMARK 465 PRO A -7 REMARK 465 ASP A -6 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 GLN A 102 57.88 -91.59 REMARK 500 GLN A 145 -84.52 -113.22 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZDE RELATED DB: PDB REMARK 900 MUTATED PRECURSOR REMARK 900 RELATED ID: 1ZD7 RELATED DB: PDB REMARK 900 CLEAVED PRODUCT DBREF 3NZM A -4 159 UNP P74750 DPO3A_SYNY3 771 933 SEQADV 3NZM LYS A -9 UNP P74750 ENGINEERED MUTATION SEQADV 3NZM SER A -8 UNP P74750 ENGINEERED MUTATION SEQADV 3NZM PRO A -7 UNP P74750 ENGINEERED MUTATION SEQADV 3NZM ASP A -6 UNP P74750 ENGINEERED MUTATION SEQADV 3NZM PRO A -5 UNP P74750 ENGINEERED MUTATION SEQADV 3NZM CYS A -3 UNP P74750 ALA 772 ENGINEERED MUTATION SEQADV 3NZM PRO A -2 UNP P74750 GLU 773 ENGINEERED MUTATION SEQADV 3NZM GLY A -1 UNP P74750 TYR 774 ENGINEERED MUTATION SEQRES 1 A 168 LYS SER PRO ASP PRO PHE CYS PRO GLY CYS LEU SER PHE SEQRES 2 A 168 GLY THR GLU ILE LEU THR VAL GLU TYR GLY PRO LEU PRO SEQRES 3 A 168 ILE GLY LYS ILE VAL SER GLU GLU ILE ASN CYS SER VAL SEQRES 4 A 168 TYR SER VAL ASP PRO GLU GLY ARG VAL TYR THR GLN ALA SEQRES 5 A 168 ILE ALA GLN TRP HIS ASP ARG GLY GLU GLN GLU VAL LEU SEQRES 6 A 168 GLU TYR GLU LEU GLU ASP GLY SER VAL ILE ARG ALA THR SEQRES 7 A 168 SER ASP HIS ARG PHE LEU THR THR ASP TYR GLN LEU LEU SEQRES 8 A 168 ALA ILE GLU GLU ILE PHE ALA ARG GLN LEU ASP LEU LEU SEQRES 9 A 168 THR LEU GLU ASN ILE LYS GLN THR GLU GLU ALA LEU ASP SEQRES 10 A 168 ASN HIS ARG LEU PRO PHE PRO LEU LEU ASP ALA GLY THR SEQRES 11 A 168 ILE LYS MET VAL LYS VAL ILE GLY ARG ARG SER LEU GLY SEQRES 12 A 168 VAL GLN ARG ILE PHE ASP ILE GLY LEU PRO GLN ASP HIS SEQRES 13 A 168 ASN PHE LEU LEU ALA ASN GLY ALA ILE ALA ALA SNN MODRES 3NZM SNN A 159 ASN L-3-AMINOSUCCINIMIDE HET SNN A 159 8 HET SO4 A 301 5 HET SO4 A 302 5 HETNAM SNN L-3-AMINOSUCCINIMIDE HETNAM SO4 SULFATE ION FORMUL 1 SNN C4 H6 N2 O2 FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *209(H2 O) HELIX 1 1 ILE A 18 GLU A 24 1 7 HELIX 2 2 ILE A 84 GLN A 91 1 8 HELIX 3 3 LEU A 116 GLY A 120 1 5 SHEET 1 A 5 LEU A 2 SER A 3 0 SHEET 2 A 5 VAL A 65 ALA A 68 -1 O ARG A 67 N SER A 3 SHEET 3 A 5 GLN A 46 LEU A 60 -1 N TYR A 58 O ILE A 66 SHEET 4 A 5 VAL A 127 GLY A 142 -1 O ARG A 131 N GLU A 57 SHEET 5 A 5 LEU A 2 SER A 3 -1 N LEU A 2 O PHE A 139 SHEET 1 B 2 GLU A 7 THR A 10 0 SHEET 2 B 2 GLY A 14 PRO A 17 -1 O LEU A 16 N ILE A 8 SHEET 1 C 3 SER A 29 VAL A 33 0 SHEET 2 C 3 ARG A 38 ALA A 43 -1 O TYR A 40 N SER A 32 SHEET 3 C 3 PHE A 114 PRO A 115 -1 O PHE A 114 N VAL A 39 SHEET 1 D 2 ARG A 73 LEU A 75 0 SHEET 2 D 2 LEU A 81 ALA A 83 -1 O LEU A 82 N PHE A 74 SHEET 1 E 2 LEU A 94 LEU A 97 0 SHEET 2 E 2 ILE A 122 VAL A 125 -1 O LYS A 123 N THR A 96 SHEET 1 F 2 PHE A 149 LEU A 150 0 SHEET 2 F 2 ILE A 156 ALA A 157 -1 O ALA A 157 N PHE A 149 SSBOND 1 CYS A -3 CYS A 1 1555 1555 2.03 LINK C ALA A 158 N SNN A 159 1555 1555 1.33 CISPEP 1 LEU A 112 PRO A 113 0 0.06 SITE 1 AC1 8 SER A 3 PHE A 4 GLY A 5 ARG A 67 SITE 2 AC1 8 HOH A 194 HOH A 204 HOH A 315 HOH A 324 SITE 1 AC2 3 ARG A 67 ARG A 131 HOH A 321 CRYST1 40.220 53.740 67.960 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 0.024863 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018608 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014715 0.00000