HEADER HYDROLASE 17-MAY-16 5K08 TITLE RECA MINI INTEIN-ZEISE'S SALT COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECA MINI INTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CISPLATIN, ZEISE'S SALT, INHIBITOR, INTEIN, COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.LI,H.M.LI REVDAT 4 27-SEP-23 5K08 1 REMARK REVDAT 3 04-DEC-19 5K08 1 REMARK REVDAT 2 20-SEP-17 5K08 1 REMARK REVDAT 1 21-SEP-16 5K08 0 JRNL AUTH H.CHAN,S.PEARSON,C.M.GREEN,Z.LI,J.ZHANG,S.LIPPARD,G.BELFORT, JRNL AUTH 2 A.SHEKHTMAN,H.M.LI,M.BELFORT JRNL TITL STRUCTURAL INSIGHTS INTO PROTEIN SPLICING INHIBITION BY JRNL TITL 2 PLATINUM THERAPEUTICS AS POTENTIAL ANTI-MICROBIALS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 51783 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.240 REMARK 3 FREE R VALUE TEST SET COUNT : 3748 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1103 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 127 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.140 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5K08 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221525. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07136 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27687 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.40 REMARK 200 R MERGE FOR SHELL (I) : 0.91300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5I0A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 54%-59% (W/V) AMMONIUM SULFATE, 0.1 M REMARK 280 TRIS, PH 8.5, 2 MM ZEISE'S SALT, 2 MM TCEP, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 28.84350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.96500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.84350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.96500 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 648 O HOH A 722 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 -53.95 73.94 REMARK 500 CYS A 441 -149.57 -105.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 727 DISTANCE = 5.85 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 TCE A 504 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZPT A 502 PT REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 1 N REMARK 620 2 CYS A 1 SG 82.2 REMARK 620 3 HOH A 603 O 109.6 136.8 REMARK 620 4 HOH A 697 O 163.1 109.7 70.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZPT A 501 PT REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 439 NE2 REMARK 620 2 CYS A 441 SG 92.8 REMARK 620 3 HOH A 716 O 173.1 84.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZPT A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZPT A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TCE A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5I0A RELATED DB: PDB DBREF 5K08 A 1 443 PDB 5K08 5K08 1 443 SEQRES 1 A 142 CYS LEU ALA GLU GLY THR ARG ILE PHE ASP PRO VAL THR SEQRES 2 A 142 GLY THR THR HIS ARG ILE GLU ASP VAL VAL ASP GLY ARG SEQRES 3 A 142 LYS PRO ILE HIS VAL VAL ALA ALA ALA LYS ASP GLY THR SEQRES 4 A 142 LEU HIS ALA ARG PRO VAL VAL SER TRP PHE ASP GLN GLY SEQRES 5 A 142 THR ARG ASP VAL ILE GLY LEU ARG ILE ALA GLY GLY ALA SEQRES 6 A 142 ILE LEU TRP ALA THR PRO ASP HIS LYS VAL LEU THR GLU SEQRES 7 A 142 TYR GLY TRP ARG ALA ALA GLY GLU LEU ARG LYS GLY ASP SEQRES 8 A 142 ARG VAL ALA VAL ARG ASP VAL GLU THR GLY GLU LEU ARG SEQRES 9 A 142 TYR SER VAL ILE ARG GLU VAL LEU PRO THR ARG ARG ALA SEQRES 10 A 142 ARG THR PHE ASP LEU GLU VAL GLU GLU LEU HIS THR LEU SEQRES 11 A 142 VAL ALA GLU GLY VAL VAL VAL HIS ALA CYS SER PRO HET ZPT A 501 1 HET ZPT A 502 1 HET SO4 A 503 5 HET TCE A 504 11 HETNAM ZPT TRICHLORO(ETHENE)PLATINATE(II) HETNAM SO4 SULFATE ION HETNAM TCE 3,3',3''-PHOSPHANETRIYLTRIPROPANOIC ACID HETSYN ZPT ZEISE'S SALT HETSYN TCE 3-[BIS(2-CARBOXYETHYL)PHOSPHANYL]PROPANOIC ACID FORMUL 2 ZPT 2(C2 H4 CL3 PT 1-) FORMUL 4 SO4 O4 S 2- FORMUL 5 TCE C9 H15 O6 P FORMUL 6 HOH *127(H2 O) HELIX 1 AA1 ILE A 19 GLY A 25 1 7 HELIX 2 AA2 GLY A 85 LEU A 87 5 3 SHEET 1 AA1 6 HIS A 30 ALA A 34 0 SHEET 2 AA1 6 LEU A 40 ILE A 61 -1 O HIS A 41 N ALA A 33 SHEET 3 AA1 6 ILE A 66 ALA A 69 -1 O ALA A 69 N ILE A 57 SHEET 4 AA1 6 LEU A 2 ALA A 3 -1 N ALA A 3 O TRP A 68 SHEET 5 AA1 6 LEU A 404 VAL A 425 -1 O PHE A 421 N LEU A 2 SHEET 6 AA1 6 ARG A 92 ARG A 96 -1 N VAL A 95 O ARG A 405 SHEET 1 AA2 4 HIS A 30 ALA A 34 0 SHEET 2 AA2 4 LEU A 40 ILE A 61 -1 O HIS A 41 N ALA A 33 SHEET 3 AA2 4 LEU A 404 VAL A 425 -1 O LEU A 413 N GLY A 58 SHEET 4 AA2 4 ARG A 92 ARG A 96 -1 N VAL A 95 O ARG A 405 SHEET 1 AA3 2 ARG A 7 PHE A 9 0 SHEET 2 AA3 2 THR A 16 ARG A 18 -1 O HIS A 17 N ILE A 8 SHEET 1 AA4 2 LYS A 74 THR A 77 0 SHEET 2 AA4 2 GLY A 80 ALA A 83 -1 O ARG A 82 N VAL A 75 SHEET 1 AA5 2 THR A 430 ALA A 433 0 SHEET 2 AA5 2 VAL A 436 HIS A 439 -1 O VAL A 438 N LEU A 431 LINK N CYS A 1 PT ZPT A 502 1555 1555 2.24 LINK SG CYS A 1 PT ZPT A 502 1555 1555 2.15 LINK NE2 HIS A 439 PT ZPT A 501 1555 1555 2.21 LINK SG CYS A 441 PT ZPT A 501 1555 1555 2.24 LINK PT ZPT A 501 O HOH A 716 1555 1555 2.16 LINK PT ZPT A 502 O HOH A 603 1555 1555 2.24 LINK PT ZPT A 502 O HOH A 697 1555 1555 2.23 SITE 1 AC1 4 HIS A 439 CYS A 441 TCE A 504 HOH A 716 SITE 1 AC2 4 CYS A 1 ASP A 72 HOH A 603 HOH A 697 SITE 1 AC3 7 ARG A 7 ARG A 18 ALA A 62 GLY A 63 SITE 2 AC3 7 ARG A 410 HOH A 649 HOH A 675 SITE 1 AC4 8 LYS A 36 LYS A 74 TRP A 81 LEU A 428 SITE 2 AC4 8 THR A 430 HIS A 439 ZPT A 501 HOH A 645 CRYST1 57.687 63.930 37.307 90.00 90.00 90.00 P 21 21 2 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 0.017335 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015642 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026805 0.00000